INCORPORATION OF HEALTH MEASUREMENTS IN ANALYSIS AND INTERPRETATION OF FUNCTIONAL BIOLOGICAL RESPONSE DATA

Cross reference

[001] This application claims priority to U.S. Patent Provisional Application Nos.

61/436,534, filed January 26, 2011, and 61/374,613, filed August 18, 2010, each of which are hereby incorporated by reference in their entireties.

Background

[002] Some cell assays may be inaccurate due to the presence of unhealthy cells.

Methods to increase the sensitivity of cell based assays are advantageous and are described herein.

Summary

[003] An embodiment is based on the finding that cell signaling potential (e.g.,

activation of an activable element) can be a function of cell health. In one embodiment, a method is provided for creating improved classifiers for diagnosis, prognosis, drug development and research applications, and to adjust classifers by measures of sample quality. For example, in one embodiment, a method is provided for obtaining cells, determining the health of those cells, determining a biological characteristic of the cells, such as the activation state or activation level of one or more intracellular activatable elements in single cells, excluding (or conversely, not including) cells from an analysis that are unhealthy, and analyzing cell signaling (iein cells that are healthy.

[004] Indicators of cell health include, but are not limited to measures of an unhealthy cell, such as apoptosis (e.g., measures of apoptosis include levels of cleaved PARP (cPARP) or MCL-1), necrosis, autophagy and the like.

[005] In another embodiment, a method is provided to analyze cells comprising

obtaining cells, determining if the cell is undergoing apoptosis and then excluding cells from a final analysis that are undergoing apoptosis. One way to determine if a cell is undergoing apoptosis is by measuring the intracellular level of one or more activatable elements related to cell health such as cleaved PARP, MCL-1, or other compounds whose activation state or activation level correlate to a level of apoptosis within single cells.

[006] Another embodiment comprises obtaining cells, determining which cells are

healthy by measuring the levels of an activatable element related to cell health within the cell, analyzing intracellular activatable elements related to cell signaling in single cells Atty Dkt o. 33118-747601

using flow cytometry, contacting cells with a modulator, contacting cells with a binding element specific for an intracellular activatable element related to signaling or any other cellular process, contacting cells with a binding element specific for activatable elements related to a cell health marker, measuring the level of activatable elements related to signaling and cell health within the cells, analyzing only those cells that lack a cell health marker , and analyzing activatable elements related to signaling in cells thatlack a cell health marker, where the presence of the cell health marker indicates poor cell health i.e. apoptosis. There are multiple embodiments of the methods described herein. One method may be a direct analysis of viable cells in one aliquot and its application to other aliquots that have undergone other analysis as a measure of sample health. For example, cells may be analyzed for percent healthy cells in the sample, and then the results of tests involving cells in another sample can be adjusted using a factor determined from the percent healthy cell analysis. In another embodiment, healthy cells can be measured directly for each assay or aliquot, and only cells that lack a cell health marker can be included into the cell signaling analysis (e.g., measurement of activation level of an activatable element), for example.

[007] Indicators for cell health can include molecules and activatable elements within molecules associated with apoptosis, necrosis, and/or autophagy, including but not limited to caspases, caspase cleavage products such as dye substrates, cleaved PARP, cleaved cytokeratin 18, cleaved caspase, cleaved caspase 3, cytochrome C, apoptosis inducing factor (AIF), Inhibitor of Apoptosis (IAP) family members, as well as other molecules such as Bcl-2 family members including anti-apoptotic proteins (MCL-1, BCL-2, BCL-XL), BH3-only apoptotic sensitizers (PUMA, NOXA, Bim, Bad), and pro- apoptotic proteins (Bad, Bax) (see below), p53, c-myc proto-oncogene, APO- 1/Fas/CD95, growth stimulating genes, or tumor suppressor genes, mitochondrial membrane dyes, Annexin-V, 7-AAD, Amine Aqua, trypan blue, propidium iodide or other viability dyes.

[008] In one embodiment flow cytometry or mass spectrometry is used to analyze cells.

One embodiment further comprises calculating the number of healthy cells versus the total cells and disregarding the entire sample if the ratio is less than a set threshold.

Another embodiment further comprises calculating the number of healthy cells versus the total cells and using this measurement to adjust or normalize measurements of the activation status or activation level of other activatable elements, such as signaling or other cellular processes, within the cells, or within the healthy cells. Atty Dkt o. 33118-747601

[009] In one aspect, a method is provided comprising assaying for one or more cell health markers in a first sample of cells, wherein the one or more cell health markers comprise one or more earlier markers of apoptosis, necrosis, or autophagy that preceed loss of cellular membrane integrity; measuring an activation level of one or more activatable elements in a second sample of cells; and adjusting the activation level of the one or more activatable elements in the second sample of cells based on the one or more cell health markers in the first sample of cells. In one embodiment, the one or more cell health markers comprise one or more intracellular cell health markers. In another embodiment, the one or more cell health markers measures cell membrane integrity. In another embodiment, the method further comprises determining the percentage of cells in the first sample of cells that lack the one or more cell health markers. In another embodiment, the method further comprises determining the percentage of healthy cells in the first sample of cells. In another embodiment, the adjusting comprises adjusting by residuals. In another embodiment, the adjusting comprises adjusting by population modeling.

[0010] In another embodiment, the one or more cell health markers comprise one or more of a caspase, protein caspase substrate, cytochrome C, apoptosis inducing factor (AIF), Inhibitor of Apoptosis (IAP) family member, Annexin-V, Bcl-2 family, BH3-only apoptotic sensitizer, pro-apoptotic protein, APO-l/Fas/CD95, growth stimulating gene, tumor suppressor gene, or a dye. In another embodiment, the protein caspase substrate is PARP or cytokeratin 18. In another embodiment, the one or more cell health markers is cleaved PARP or cleaved cytokeratin 18. In another embodiment, the one or more cell health markers is cleaved PARP. In another embodiment, the dye is a fluorescent dye or fluorogenic caspase substrate dye. In another embodiment, the tumor suppressor gene is p53. In another embodiment, the growth stimulating gene is c-myc proto -oncogene. In another embodiment, the Bcl-2 family member is MCL-1, BCL-2, or BCL-XL. In another embodiment, the BH3-only apoptosis sensitizer is PUMA, NOXA, Bim, or Bad. In another embodiment, the protein caspase substrate is caspase 3. In another embodiment, the pro-apoptotic proteins comprise Bad, Bak or Bax.

[0011] In another embodiment, the one or more activatable elements comprise one or more proteins. In another embodiment, the one or more activatable elements comprise one or more phosphorylation sites. In another embodiment, the measuring the activation level of the one or more phosphorylation sites comprises measuring the level of Atty Dkt o. 33118-747601

phosphorylation at the one or more phosphorylation sites amongst a plurality of cells in the second sample.

[0012] In another embodiment, the measuring the activation level of the one or more activatable elements in the second sample of cells comprises flow cytometry. In another embodiment, the assaying for one or more cell health markers in the first sample of cells comprises flow cytometry.

[0013] In another embodiment, the method further comprises contacting cells in a third sample of cells with a modulator. In another embodiment, the modulator is a chemotherapy drug, growth factor, or mitogen. In another embodiment, the modulator is a phosphatase inhibitor. In another embodiment, the method further comprises measuring the activation level of the one or more activatable elements in cells in the third samples of cells. In another embodiment, the method further comprises adjusting the activation level measurement of the one or more activatable elements in the third sample of cells based on the cell health markers in the first sample of cells. In another embodiment, the method further comprises comparing the adjusted activation level measurement of the one or more activatable elements in the second sample of cells to the adjusted activation level measurement of the one or more activatable elements in the third sample of cells. In another embodiment, the method further comprises factoring into the adjusted activation level measurement of the one or more activatable elements in the second sample of cells the activation level of the one or more activation elements in a fourth sample of cells if the percentage of healthy cells in the fourth sample of cells is above a threshold.

[0014] In another embodiment, the threshold is about 50%, 55%, 60%, 65%, 70%, 75%, 80%), or 85%) percent healthy cells.

[0015] In another embodiment, the adjusting takes into account the apoptosis stage of cells in the first sample of cells.

[0016] In another embodiment, the assaying one or more cell health markers comprises determining the level of one or more cell health markers. In another embodiment, the measuring the activation level of the phosphorylation site comprises measuring the number of cells in the second sample in which the phosphorylation site is

phosphorylated. In another embodiment, the one or more cell health markers comprise one or more activatable elements. In another embodiment, the adjusting the activation level measurement of the one or more activatable elements in the second sample of cells comprises use of a computer. In another embodiment, the method further comprises Atty Dkt o. 33118-747601 making a diagnosis or prognosis based on the adjusted activation level of the one or more activatable elements in the second sample. In another embodiment, the measuring the activation level of the one or more activatable elements in cells in a second sample of cells comprises contacting the cells with one or more binding elements. In another embodiment, the one or more binding elements comprise phospho-specific antibodies.

[0017] In another aspect, a method is provided comprising assaying for one or more cell health markers in a first sample of cells, wherein the one or more cell health markers comprise one or more earlier markers of apoptosis, necrosis, or autophagy that preceed loss of cellular membrane integrity; assaying for an activation state of one or more activatable elements in the first sample of cells; and determining an activation level of the one or more activatable elements for a subset of cells in the first sample of cells, wherein the subset of cells is selected based on the assaying for one or more cell health markers in the first sample of cells. In one embodiment, the one or more cell health markers comprise one or more intracellular cell health markers. In another embodiment, the one or more cell health markers do not comprise viability markers. In another embodiment, the subset of cells selected do not comprise the one or more cell health markers. In another embodiment, the subset of cells is selected by physically isolating the subset of cells in the first sample. In another embodiment, the subset of cells is selected by analyzing data on the one or more cell health markers in the first sample of cells. In another embodiment, the subset of cells is selected by determining a level of one or more cell health markers in individual cells, comparing the level of the one or more cell health markers in the individual cells to a threshold, and selecting the individual cells that have a level of the one or more cell health markers above or below the threshold.

[0018] In another embodiment, the one or more cell health markers comprise one or more of a caspase, protein caspase substrate, cytochrome C, apoptosis inducing factor (AIF), Inhibitor of Apoptosis (IAP) family member, Annexin-V, Bcl-2 family, BH3-only apoptotic sensitizer, pro-apoptotic protein, APO-l/Fas/CD95, growth stimulating gene, tumor suppressor gene, or a dye. In another embodiment, the protein caspase substrate is PARP or cytokeratin 18. In another embodiment, the one or more cell health markers comprise cleaved PARP or cleaved cytokeratin 18. In another embodiment, the one or more intracellular cell health markers is cleaved PARP. In another embodiment, the dye is a fluorescent dye or fluorogenic caspase substrate dye. In another embodiment, the tumor suppressor gene is p53. In another embodiment, the growth stimulating gene is c- myc proto -oncogene. In another embodiment, the Bcl-2 family member is MCL-1, BCL- Atty Dkt o. 33118-747601

2, or BCL-XL. In another embodiment, the BH3-only apoptosis sensitizer is PUMA, NOXA, Bim, or Bad. In another embodiment, the protein caspase substrate is caspase 3. In another embodiment, the pro-apoptotic proteins comprise Bad, Bak or Bax.

[0019] In another embodiment, the method further comprises contacting the first sample of cells with one or more modulators. In another embodiment the modulator is a chemotherapy drug, growth factor, or mitogen. In another embodiment, the modulator is a phosphatase inhibitor. In another embodiment, the one or more activatable elements comprises one or more proteins. In another embodiment, the one or more activatable elements comprises one or more one or more phosphorylation sites. In another embodiment, the activation level of the one or more activatable elements comprises the phosphorylation level of the one or more activatable elements. In another embodiment, the assaying for the activation state of one or more activatable elements in the first sample of cells comprises flow cytometry. In another embodiment, the assaying for one or more cell health markers in the first sample of cells comprises flow cytometry. In another embodiment, the method further comprises contacting cells in a second sample of cells with a modulator.

[0020] In another embodiment, the method further comprises assaying for one or more cell health markers in the second sample of cells; assaying for an activation state of the one or more activatable elements in the second sample of cells; and determining an activation level of the one or more activatable elements for a subset of cells in the second sample of cells, wherein the subset of cells is selected based on the assaying for one or more cell health markers in the second sample of cells. In another embodiment, the method further comprises comparing the activation level of the one or more activatable elements for the subset of cells in the first sample of cells to the activation level of the one or more activatable elements for the subset of cells in the second sample of cells.

[0021] In another embodiment, the assaying the activation state of the one or more

activatable elements in the first sample of cells comprises contacting the cells with one or more binding elements. In another embodiment, wherein the one or more binding elements comprise phospho-specific antibodies. In another embodiment, wherein the determining the activation level of the one or more activatable elements for a subset of cells in the first sample of cells comprises using a computer. In another embodiment, the method further comprises making a diagnosis or prognosis based on the activation level of the one or more activatable elements in the subset of cells in the first sample of cells. Atty Dkt o. 33118-747601

[0022] In another aspect, a method is provided comprising assaying for one or more cell health markers in an individual cell in a first sample of cells, wherein the one or more cell health markers comprise one or more earlier markers of apoptosis, necrosis, or autophagy that preceed loss of cellular membrane integrity; measuring an activation level of one or more activatable elements in the individual cell in the first sample of cells; and adjusting the activation level of the one or more activatable elements in the individual cell in the first sample of cells based on the assaying for one or more cell health markers in the individual cell in the first sample of cells.

[0023] In one embodiment, the adjusting comprises increasing or decreasing the

measured activation level. In another embodiment, the adjusting comprises increasing the measured activation level if the individual cell comprises one or more cell health markers. In another embodiment, the adjusting comprises decreasing the measured activation level if the individual cell lacks one or more cell health markers. In another embodiment, the individual cell is undergoing apoptosis, and the adjusting comprises adjusting based on the apoptotic stage of the individual cell. In another embodiment, the one or more cell health markers comprise one or more apoptosis, necrosis, and/or autophagy markers.

[0024] In another embodiment, the one or more cell health markers comprise a viability marker. In another embodiment, the one or more cell health markers comprise one or more of a caspase, protein caspase substrate, cytochrome C, apoptosis inducing factor (AIF), Inhibitor of Apoptosis (IAP) family member, Annexin-V, Bcl-2 family, BH3-only apoptotic sensitizer, pro-apoptotic protein, APO-l/Fas/CD95, growth stimulating gene, tumor suppressor gene, or a dye. In another embodiment, the protein caspase substrate is PARP or cytokeratin 18. In another embodiment, the one or more cell health markers comprise cleaved PARP or cleaved cytokeratin 18. In another embodiment, the one or more intracellular cell health markers is cleaved PARP. In another embodiment, the dye is a fluorescent dye or fluorogenic caspase substrate dye. In another embodiment, the tumor suppressor gene is p53. In another embodiment, the growth stimulating gene is c- myc proto -oncogene. In another embodiment, the Bcl-2 family member is MCL-1, BCL- 2, or BCL-XL. In another embodiment, the BH3-only apoptosis sensitizer is PUMA, NOXA, Bim, or Bad. In another embodiment, the protein caspase substrate is caspase 3. In another embodiment, the pro-apoptotic proteins comprise Bad, Bak or Bax. In another embodiment, the one or more activatable elements comprises one or more proteins. In another embodiment, the one or more activatable elements comprises one or more one or Atty Dkt o. 33118-747601

more phosphorylation sites. In another embodiment, the activation level of the one or more activatable elements comprises the phosphorylation level of the one or more activatable elements. In another embodiment, the measuring the activation level of one or more activatable elements in the first sample of cells comprises flow cytometry. In another embodiment, the assaying for one or more cell health markers in the first sample of cells comprises flow cytometry. In another embodiment, the assaying the activation state of the one or more activatable elements in the first sample of cells comprises contacting the cells with one or more binding elements. In another embodiment, the one or more binding elements comprise phospho-specific antibodies.

Brief Description of the Figures

[0025] Figure 1 shows a flow diagram of an embodiment of a method for removing samples of cells with low viability from an analysis, adjusting signaling for a sample, or individually gating for healthy cells.

[0026] Figure 2 shows that high cleaved PARP positive (c-PARP+) samples display low induced signaling. An overall comparison of mean SCF, FLT3L, IL-27, G-CSF signaling and basal 6h c-PARP levels is provided.

[0027] Figure 3 shows the difference between two samples in which low basal apoptosis correlates to high induced signaling and high basal apoptosis correlates to low induced signaling.

[0028] Figure 4 shows C-PARP+ cells are refractory to signaling, and removal (via

gating) improves assay robustness.

[0029] Figure 5 shows alternate metrics to measure total or induced apoptosis starting at time zero. Percent healthy are normalized by the first available time point (i.e., 6 firs unstim. percent healthy). That is, 80% Healthy _unst i _m and 40% Healthy _st i _m converts to 100%) Healthy _uns tim and 50%> Healthy _st i _m (Normalized). New metrics are designed to measure proportion of cells that were healthy at the first time point (i.e., 6 hours) undergoing apoptosis with time and modulation.

Incorporation By Reference

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. Atty Dkt o. 33118-747601

Detailed Description

[0030] The present methods incorporate information disclosed in other applications and texts. The following patent and other publications are hereby incorporated by reference in their entireties: Haskell et al, Cancer Treatment, 5 ^th Ed., W.B. Saunders and Co., 2001; Alberts et al, The Cell, 4 ^th Ed., Garland Science, 2002; Vogelstein and Kinzler, The Genetic Basis of Human Cancer, 2d Ed., McGraw Hill, 2002; Michael, Biochemical Pathways, John Wiley and Sons, 1999; Weinberg, The Biology of Cancer, 2007;

Immunobiology, Janeway et al. 7 ^th Ed., Garland, and Leroith and Bondy, Growth Factors and Cytokines in Health and Disease, A Multi Volume Treatise, Volumes 1 A and IB, Growth Factors, 1996. Other conventional techniques and descriptions can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press), Stryer, L. (1995) Biochemistry (4th Ed.)

Freeman, New York, Gait, "Oligonucleotide Synthesis: A Practical Approach" 1984, IRL Press, London, Nelson and Cox (2000), Lehninger, Principles of Biochemistry 3rd Ed., W. H. Freeman Pub., New York, N.Y. and Berg et al. (2002) Biochemistry, 5th Ed., W. H. Freeman Pub., New York, N.Y.; and Sambrook, Fritsche and Maniatis. "Molecular Cloning A laboratory Manual" 3rd Ed. Cold Spring Harbor Press (2001), all of which are herein incorporated in their entirety by reference for all purposes.

[0031] Patents and applications that are also incorporated by reference in their entirety include U.S. Patent Nos. 7,381,535, 7,393,656, 7,695,924 and 7,695,926 and U.S. Patent Application Nos. 10/193,462; 11/655,785; 11/655,789; 11/655,821; 11/338,957,

12/877,998; 12/784,478; 12/730,170; 12/703,741; 12/687,873; 12/617,438; 12/606,869; 12/713,165; 12/293,081; 12/581,536; 12/776,349; 12/538,643; 12/501,274; 61/079,537 ; 12/501,295; 12/688,851; 12/471,158 ; 12/910,769; 12/460,029 ; 12/432,239; 12/432,720; 12/229,476, 12/877,998, 13/083,156, 61/469812, 61/436,534, 61/317,187, and 61/353,155; and PCT No. PCT/US2011/029845.

[0032] Some commercial reagents, protocols, software and instruments that are useful in some embodiments of the present invention are available at the Becton Dickinson Website http://www.bdbiosciences.com/features/products/, and the Beckman Coulter website, http://www.beckmancoulter.com/Default. asp ?bhfv=7. Relevant articles include High-content single-cell drug screening with phosphospecific flow cytometry, Krutzik et al, Nature Chemical Biology, 23 December 2007; Irish et al, FLt3 ligand Y591 Atty Dkt o. 33118-747601

duplication and Bcl-2 over expression are detected in acute myeloid leukemia cells with high levels of phosphorylated wild-type p53, Neoplasia, 2007; Irish et al. Mapping normal and cancer cell signaling networks: towards single-cell proteomics, Nature, Vol. 6 146-155, 2006; Irish et al, Single cell profiling of potentiated phospho -protein networks in cancer cells, Cell, Vol. 118, 1-20 July 23, 2004; Schulz, K. R., et al, Single-cell phospho -protein analysis by flow cytometry, Curr Protoc Immunol, 2007, 78:8 8.17.1-20; Krutzik, P.O., et al, Coordinate analysis of murine immune cell surface markers and intracellular phosphoproteins by flow cytometry, J Immunol. 2005 Aug 15;175(4):2357-65; Krutzik, P.O., et al, Characterization of the murine immunological signaling network with phosphospecific flow cytometry, J Immunol. 2005 Aug 15;175(4):2366-73; Shulz et al, Current Protocols in Immunology 2007, 78:8.17.1-20; Stelzer et al, Use of Multiparameter Flow Cytometry and Immunophenotyping for the Diagnosis and Classification of Acute Myeloid Leukemia, Immunophenotyping, Wiley, 2000; and Krutzik, P.O. and Nolan, G. P., Intracellular phospho-protein staining techniques for flow cytometry: monitoring single cell signaling events, Cytometry A. 2003 Oct;55(2):61-70; Hanahan D. ,Weinberg, The Hallmarks of Cancer, Cell, 2000 Jan 7; 100(1) 57-70; and Krutzik et al, High content single cell drug screening with phophosphospecific flow cytometry, Nat Chem Biol. 2008 Feb;4(2): 132-42. Experimental and process protocols and other helpful information can be found at http:/proteomics. stanford.edu. The articles and other references cited below are also incorporated by reference in their entireties for all purposes. More specific procedures can be found in the following manuscripts: Rosen DB, Putta S, Covey T et al. Distinct Patterns of DNA Damage Response and Apoptosis Correlate with Jak/Stat and PBKinase Response Profiles in Human Acute Myelogenous Leukemia. 2010. PLoS ONE. 5 (8): el2405; Kornblau SM, Minden MD, Rosen DB, Putta S, Cohen A, Covey T, et al, Dynamic Single-Cell Network Profiles in Acute Myelogenous Leukemia Are Associated with Patient Response to Standard Induction Therapy. 2010. Clinical Cancer Research. 16 (14): 3721-33 Jan 31 ; Rosen DB et al, Functional Characterization of FLT3 Receptor Signaling Deregulation in AML by Single Cell Network Profiling (SCNP). 2010. PLoS ONE. 5 (10): el3543. Covey TM, Putta S, Cesano A. Single cell network profiling (SCNP): mapping drug and target interactions. Assay Drug Dev Technol. 2010;8:321-43.

Overview

[0033] In general, methods are provided for adjusting a cell signaling analysis based on the quality of cells in the sample. Unhealthy cells can reduce the quality of a cell sample. Atty Dkt o. 33118-747601

An unhealthy cell may not have the capacity to signal, or signal in response to a modulator, e.g., an external stimulus, at the same level as a healthy cell. For example, an unhealthy cell may not have the ability to activate an activatable element to the same level as a healthy cell. In one embodiment, a method is provided herein for reducing the signal to noise ratio in a single cell analysis.

[0034] In some embodiments, an analysis of cell health in a first sample of cells is used to adjust a measurement of the activation level of an activable element in a second, different sample of cells. This type of assay can be considered an indirect assay.

[0035] In some embodiments, cell health and an activation status or level of one or more activatable elements are determined in the same sample of cells. This type of assay can be considered a direct assay. In some embodiments, an activation level of an activatable element is determined in a subset of cells of the sample. For example, the cells can be gated. The subset of cells can be the healthy cells. In some embodiments, healthy cells and unhealthy cells can be physically separated. In some embodiments, the activation status of activatable elements in healthy and unhealthy cells is determined, healthy cells are identified, and the activation level of the activatable elements among the healthy cells is determined. In some embodiments, the activation level of an activatable element in an individual cell is adjusted based on whether the individual cell has one or more cell health markers or whether the cell is unhealthy.

[0036] In one aspect, a method is provided comprising assaying for one or more cell health markers in a first sample of cells; measuring the activation level of one or more activatable elements in a second sample of cells; and adjusting the activation level measurement of the one or more activatable elements in the second sample of cells based on the one or more cell health markers in the first sample of cells.

[0037] In one embodiment, the one or more cell health markers comprise one or more apoptosis, necrosis, and/or autophagy markers. In another embodiment, the one or more apoptosis, necrosis, and autophagy markers comprise cleaved PARP or MCL-1. In another embodiment, the one or more cell health markers do not comprise cell viability.

[0038] In one embodiment, the method further comprises determining the percentage of cells in the first sample of cells that lack the one or more cell health markers. In one embodiment, the method further comprises determining the percentage of healthy cells in the first sample. In one embodiment, healthy cells are cells that do not have a cell health marker and have an intact cell membrane. In one embodiment, a healthy cell is a viable, nonapoptotic cell. Atty Dkt o. 33118-747601

[0039] In another embodiment, the method further comprises determining the percentage of cells in the first sample of cells that both i) lack the one or more cell health markers and ii) have an intact cell membrane. In another embodiment, the method further comprises determining the percentage of cells in the first sample of cells that either i) comprise one or more cell health markers and/or ii) are nonviable.

[0040] In one embodiment, the one or more activatable elements comprise one or more proteins. In another embodiment, the one or more activatable elements comprise one or more phosphorylation sites.

[0041] In another aspect, a method is provided comprising assaying for one or more cell health markers in a first sample of cells; assaying for an activation state of one or more activatable elements in the first sample of cells; and determining an activation level of the one or more activatable elements for a subset of cells in the first sample of cells, wherein the subset of cells is selected based on the assaying for one or more cell health markers in the first sample of cells.

[0042] In one embodiment, the subset of cells is selected by determining a level of one or more cell health markers in individual cells, comparing the level of the one or more cell health markers in the individual cells to a threshold, and selecting the individual cells that have a level of the one or more cell health markers above or below the threshold.

[0043] In another aspect, a method is provided comprising assaying for one or more cell health markers in an individual cell in a first sample of cells; measuring an activation level of one or more activatable elements in the individual cell in the first sample of cells; and adjusting the measured activation level of the one or more activatable elements in the individual cell in the first sample of cells based on the assaying for one or more cell health markers in the individual cell in the first sample of cells.

[0044] In one embodiment, the adjusting comprises increasing or decreasing the

measured activation level. In another embodiment, the adjusting comprises increasing the measured activation level if the individual cell comprises one or more cell health markers. In another embodiment, the adjusting comprises decreasing the measured activation level if the individual cell lacks one or more cell health markers. In another embodiment, the individual cell is undergoing apoptosis, and the adjusting comprises adjusting based on the apoptotic stage of the individual cell. In one embodiment, gating does not occur before cell health analysis.

[0045] In some embodiments, a method further comprises determining the percentage of viable cells in a sample. In another embodiment, the method further comprises including Atty Dkt o. 33118-747601 a sample of cells in an assay if the percentage of viable cells in the sample is above a threshold, e.g., at least 80% viable cells in a sample. In another embodiment, the method further comprises excluding a sample of cells from an assay if the percentage of viable cells in the sample is below a threshold, e.g., at least 80% viable cells in a sample.

[0046] Figure 1 illustrates an embodiment of a method for analyzing cells.

Cell health

[0047] "Cell health" can be measured by assaying for cell viability (e.g., by measuring cell membrane integrity) and/or assaying one or more earlier markers of apoptosis, necrosis, and/or autophagy.

[0048] A cell health marker can be an apoptosis, necrosis, and/or autophagy marker. A cell health marker can be cell viability. In one embodiment, cell viability is not a cell health marker. A cell health marker can be an intracellular cell health marker. A cell health marker can preceed the loss of cellular membrane integrity in the process of cell death in the cell.

[0049] A healthy cell can be a cell that lacks a cell health marker. A healthy cell can be cell that is viable and lacks an apoptosis, necrosis, and/or autophagy marker. A healthy cell can be a cell that comprises an intact cell membrane and lacks an apoptosis, necrosis, and/or autophagy marker. A healthy cell can be a viable, nonapoptic cell.

[0050] An unhealthy cell can be a cell that comprises a cell health marker. An unhealthy cell can be a cell that comprises one or more apoptosis, necrosis, and/or autophagy markers. An unhealthy cell can be a nonviable cell. An unhealthy cell can be a viable cell that comprises one or more apoptosis, necrosis, and/or autophagy markers. An unhealthy cell can be a cell that comprises an intact cell membrane and comprises one or more cell health markers. An unhealthy cell can be a cell that comprises an intact cell membrane and comprises one or more apoptosis, necrosis, and/or autophagy markers. In one embodiment, an unhealthy cell is a cell undergoing apoptosis. In one embodiment, the cell undergoing apoptosis can have an intact cell membrane. In one embodiment, the cell undergoing apoptosis is a viable cell.

[0051] In one embodiment, a method is provided to detect and exclude unhealthy (e.g., apoptotic cells) from an analysis, e.g., a cell signaling profile analysis, e.g., measurement of the activation level of an activatable element. In one embodiment, a method is provided to differentiate between healthy, non apoptotic leukemia cells and unhealthy, apoptotic leukemia cells. Use of the method does not require that the cells be diseased, Atty Dkt o. 33118-747601 such as a leukemia cell. Rather, the method can be used to examine whether cells are unhealthy (e.g., apoptotic) or healthy (e.g., nonapoptotic).

[0052] Apoptosis is a complex pathway in which cells undergo cell death. See DNA Damage and Apoptosis section below. There are methods, indicators and reagents to detect cells that are undergoing apoptosis. Examples of apoptosis markers include, e.g., caspases, caspase cleavage products such as fluorogenic dye caspase substrates, cleaved PARP, cleaved cytokeratin 18, cleaved caspases, cleaved caspase 3, cytochrome C, apoptosis inducing factor (AIF), Inhibitor of Apoptosis (IAP) family members, Bcl-2 family members (e.g., anti-apoptotic proteins (e.g., MCL-1 , BCL-2, BCL-X _L )), BH3-only apoptotic sensitizers (e.g., PUMA, NOXA, Bim, Bad), pro-apoptotic proteins (e.g., Bad, Bax), p53, c-myc proto-oncogene, APO-l/Fas/CD95, growth stimulating genes, or tumor suppressor genes. In one embodiment, the presence a molecule (e.g., cleaved PARP) in a cell is an apoptotic and/or necrosis marker. In another embodiment, the absence of a molecule in a cell is an apoptotic and/or necrosis marker. In another embodiment, an apoptosis and/or necrosis marker is an intracellular apoptosis and/or necrosis cell marker.

[0053] In one embodiment, a cell health marker is a necrosis marker. In one

embodiment, the necrosis marker includes, e.g., beta-glucuronidase, BV2, cardiac troponin, cardiac troponin I , C-reactive protein, creatine kinase MB (CPK-MB), Factor VIII procoagulant, H-FAMP (heart-type fatty acid-binding protein), FINK1-, isocitrate dehydrogenase (ICDH), IL-6, IL-18, lactate dehydrogenase, myoglobin, myosin, pro calcitonin, serum immunoreactive prolyl 4-hydroxylase (S-IRPH), tenascin-C, TNF- alpha, TNF-R1 , troponin I, and troponin T.

[0054] In one embodiment, a cell health marker is an autophagy marker. The autophagy can be macro-autophagy, micro-autophagy, and chaperone-mediated autophagy. In one embodiment, the autophagy marker includes, e.g. AMPK, mTOR, ULK1 , ULK2 and other Atg family members (e.g., ATG16L), PIK3C3, BECN1 , Vps34, Beclin-1 , MAP1LC3A,B,C, GABARAP, GABARAPL1 , GABARAPL2, UVRAG, IRGM, CLN3, Parkin, p62, and LAMP2 and other autophagy proteins as described in Behrends, Harper et al. Network organization of the human autophagy system. Nature. 2010 Jul l ;466(7302):68-76 and Glick, Macleod et al. Autophagy: cellular and molecular mechanisms. J Pathol. 2010 May;221(l):3-12.

[0055] In one embodiment, the one or more cell health markers, e.g., one or more

intracellular cell health markers, can be one or more activatable elements. In some embodiments, the one or more cell health markers can comprise 1 , 2, 3, 4, 5, 6, 7, 8, 9, or Atty Dkt o. 33118-747601

more cell health markers, e.g., intracellular cell health markers. In another embodiment, the one or more cell health markers, e.g., intracellular cell health markers, can comprise 1-10, 1-5, 2-10, 2-7, or 2-5 cell health markers. In another embodiment, the cell health marker is an extracellular marker.

[0056] Reagents that can be used to determine whether a cell is undergoing apoptosis include, e.g, mitochondrial membrane dyes, Annexin-V, 7-AAD (7-aminoactinomycin), Amine Aqua, trypan blue, propidium iodide or other viability dyes and other compounds that are recited below or are in the cell apoptosis pathway.

[0057] Cells can become unhealthy (e.g., have one or more cell health markers, e.g., one or more apoptosis, necrosis, and/or autophagy markers) over time due to sample treatment, removal from the body, storage, etc. For example, cells in a sample can display one or more cell health markers, e.g., one or more intracellular cell health markers, over time due to the means by which the cells are handled. For example, sample treatment, removal of the cells from the body, storage of the cells, etc., can cause a cell to display one or more cell health markers. The one or more cell health markers can be one or more intracellular cell health markers.

[0058] The percentage of healthy cells in a sample can decrease over time due to sample treatment, removal from the body, storage, etc. Due to the practicalities of sample collection, cells may be frozen for transport and/or storage prior to assaying by a functional assay, e.g., single cell network profiling (SCNP), as described below. In one embodiment, a sample of frozen cells is thawed, the cells are stimulated with a modulator, fixed, permeabilized, stained with fluorophore-conjugated antibodies that bind a phosphorylated protein, and then analyzed by flow cytometry. After thawing, the percentage of unhealthy cells (e.g., cells with a cell health marker) in a sample may increase. Some cells may become unhealthy (e.g., display one or more apoptosis, necrosis, and/or autophagy markers) that may affect the results of an assay, e.g., a measurement of the activation level of an activatable element. In one embodiment, a method is provided that accounts for the affect on the activation level of the activatable element of the unhealthy cells.

[0059] In one embodiment, an unhealthy cell is a nonviable cell. Cell viability can be determined by analyzing cells by dye exclusion, by profiling DNA content, and by assaying for morphological changes. In one embodiment, a DNA stain can be used to analyze cells by dye exclusion, by profiling DNA content, or by assaying for morphological changes. Atty Dkt o. 33118-747601

[0060] In one embodiment, cell viability is determined by determining the integrity of the membrane of a cell. A cell can be considered dead (nonviable) when the plasma membrane of the cell has lost its integrity. When a cell plasma membrane is intact, an exclusion dye cannot cross the intact cell plasma membrane. When a cell plasma membrane is not intact, an exclusion dye can cross the plasma membrane. In one embodiment, cell membrane integrity can be determined with a cell exclusion dye. In one embodiment, a cell that does not stain with a cell exclusion dye is a viable cell. In another embodiment, a cell that is stained with a cell exclusion dye is a nonviable cell. In one embodiment, the cell exclusion dye is trypan blue, Eosin, 7-AAD, Amine Aqua, an amine-reactive fluorescent dye, erythrosine, or propidium iodide.

[0061] In another embodiment, cell membrane integrity can be assayed by assaying for DNA content of a cell. If a cell is permeabilized, low molecular weight DNA can leak out. In one embodiment, measuring the DNA content of a cell with a DNA stain can be used to determine if a cell is nonviable. Since a non-viable cell, (which can be a fixed or permeabilized cell) can have less DNA than a viable cell, a non- viable cell can contain less DNA staining when DNA of the cell is stained using, e.g., a fluorochrome. A cell with lower DNA staining than that of a cell in the Gl phase of the cell cycle (cells in so called "sub-Gl peaks" or "GO" cells of a flow cytometry analysis) can be considered apoptotic or non viable. The distinction between apoptotic and non- viable could be further determined in combination with a fixation insensitive viability dye such as Amine Aqua or equivalent amine reactive dye which survives the fixation process. The reduction in staining/DNA content of these cells can be measured by flow cytometry or by analyzing fixed cells.

[0062] A G2 -phase cell can exhibit a reduced DNA content, but such a cell can be

indistinguishable from a Gl -phase cell that has similar DNA content of a Gl-cell in a flow cytometry analysis. Therefore, an apoptotic G2 -phase cell may not be detected as apoptotic, e.g., in a flow cytometry analysis. The inability to distinguish an apoptotic G2 -phase cell from a Gl-cell in a sample of cells can result in an underestimation of the apoptotic population of cells in the sample of cells.

[0063] Assays that examine chromatin morphology can be used to distinguish between viable and nonviable cells. Hoechst 33342 is a nucleic acid stain. Acridine orange (Hoechst 33342) plus DRAQ5 can penetrate the plasma membrane of a cell and stain DNA in the cell without permeablization of the membrane of the cell. In contrast to the nuclei of normal cells, the nuclei of apoptotic cells have highly condensed chromatin that Atty Dkt o. 33118-747601

can be uniformly stained by Hoechst 33342. DRAQ5 can also measure DNA content of live cells and be used to identify and potentially exclude unhealthy cells with lower "sub- Gl peaks" from a live cell assay.

[0064] The percent of viable cells in a sample can decrease over time due to sample treatment, removal from the body, storage, etc. Due to the practicalities of sample collection, cells may be frozen for transport and/or storage prior to assaying by a functional assay, e.g., single cell network profiling (SCNP), as described below. In one embodiment, a sample of frozen cells is thawed, the cells are stimulated with a modulator, fixed and permeabilized, the cells are stained with fluorophore-conjugated antibodies that bind a phosphorylated protein, and the cells are then analyzed with flow cytometry. After thawing, the percentage of viable cells (cells without an intact cell membrane) in a sample may decrease.

Single cell network profiling (SCNP)

[0065] Single cell network profiling (SCNP) is a method that can be used analyze

activatable elements such as phosphorylation sites of proteins in signaling pathways in single cells in response to modulation by signaling agonists or inhibitors (e.g., kinase inhibitors). Other examples of activatable elements include an acetylation site, a ubiquitination site, a methylation site, a hydroxylation site, a SUMOylation site, or a cleavage site. Activation of an activatable element can involve a change in cellular localization or conformation state of individual proteins, or change in ion levels, oxidation state, pH etc. It is useful to classify cells and to provide diagnosis or prognosis as well as other activities, such as drug screening or research, based on the cell classifications. SCNP is one method that can be used in conjunction with an analysis of cell health, but there are other methods that may benefit from this analysis. Embodiments of SCNP are shown in references cited herein. See for example, U.S. Patent No. 7,695,924.

[0066] In one embodiment, SCNP can be used to generate a cell signaling profile. In another embodiment, SCNP can be used to measure apoptosis in cells stained with an antibody with specific affinity to cleaved PARP (cPARP), for example, after the cells have been exposed to one or more modulators, such as chemotherapy drugs or other treatments. Other cell health markers may be quantified as well. In one embodiment, the one or more cell health markers can be MCL-1 and/or cPARP.

[0067] A significant fraction of cells with high cleaved PARP levels or low MCL-1 levels, before or without treatment with, e.g., a modulator, can indicate that some cells Atty Dkt o. 33118-747601 are undergoing apoptosis before treatment with a modulator. For some experiments, the activation state or activation level of an activatable element in an untreated sample of cells may be attributable to cells undergoing apoptosis due to one or more reasons related to sample processing (e.g., shipment conditions, cryogenic storage, thawing of cryogenically stored cells, etc.). If the apoptotic cells are not physically removed from the analysis, or data from apoptotic cells is not removed from an analysis of cell signaling data, apoptotic cells (which can be cleaved PARP positive or MCL-1 negative) can negatively impact the measurement of treatment (e.g., with a modulator) induced activation of an activatable element, e.g., phosphorylation of a phosphorylation site, and cause a misleading view of the signaling potential for the specific cell population being studied.

[0068] The level of apoptosis (and correlated background activation of an activatable element, e.g., phosphorylation noise) in thawed cell populations can be attributable to sample handling, including a freeze-thaw process. Therefore, in one embodiment, the use of an antibody directed to a cell health marker, e.g., an activatable element, e.g., cleaved PARP or MCL-1, in combination with phospho-specific and cell lineage specific antibodies allows subsequent analysis and exclusion (or non inclusion) from an analysis of a cell signaling profile (e.g., activation level of an activatable element) of cells that are unhealthy. Incorporating an apoptosis analysis using an MCL-1 or anti-cleaved PARP antibody, for example, into an assay, e.g., an assay for the activation state or activation level of an activatable element, can improve the quality and consistency of data, e.g., cell signaling data, within and across cell populations in, e.g., a SCNP assay and other assays. More generally, an apoptosis assay with an anti-cleaved PARP or MCL-1 antibody, for example, can be used to measure freeze-thaw quality as a quality-control test. In one embodiment apoptosis can be measured and quantified in samples that have been frozen and thawed and cells undergoing apoptosis after thawing can be excluded from an experiment before the cells are stimulated with a modulator. Other markers of apoptosis, e.g., Annexin V, can be employed to direct which cells can be physically excluded.

Annexin V is an extracellular apoptosis marker.

[0069] In one embodiment, a method is provided comprising a) thawing a sample of cells; b) contacting said sample of cells with Aqua reagent (or other amino reactive dye) to distinguish dead (nonviable cells) from live cells in said sample of cells ; c) contacting said sample of cells with an an experimental treatment (e.g., a modulator) to modulate phospho -proteins (e.g., signaling agonist or inhibitor can be used as a modulator); d) Atty Dkt o. 33118-747601 fixing and permeabilizing cells in said sample of cells; e) staining said sample of cells with a fluorophore conjugated antibody cocktail comprisingan antibody (e.g., and antibody directed to cleaved PARP or MCL-1) + a phospho-specific antibody + a cell lineage specific antibody; f) analyzing said sample of cells with SCNP technology; g) using anti-cleaved PARP antibody (for example) parameter to gate cells that are not undergoing apoptosis; and h) analyzing signaling pathway protein phosphorylation levels in cleaved PARP "negative" cells that appear "healthy."

[0070] In one embodiment Annexin V is also used in combination with a cell health antibody (an antibody that recognizes a cell health marker). (See e.g., Koopman G, Reutelingsperger CP, Kuijten GAM et al. (1994). "Annexin V for flow cytometric detection of phosphatidylserine expression on B cells undergoing apoptosis". Blood 84 (5): 1415-20 for information on Annexin V) Annexin V stain (available, e.g., from Sigma- Aldrich and eBioscience, San Diego, CA) can be used for early apoptosis detection for intact cells. Live cells can be stained with Annexin V which can bind phosphatidylserine, which is normally intracellular but is shifted to the cell surface when cells are undergoing apoptosis or other forms of cell death. PARP cleavage can be a late apoptosis readout, and fixed and permabilized cells can be used to analyze PARP cleavage. PARP cleavage can result from caspase activation because PARP is a caspase target. To assay for cleaved PARP, cells can befixed and permeabilized and then stained for cleaved PARP. In one embodiment, a method is provided comprising staining for Annexin V on live cells using a PFA/methanol insensitive dye; washing away excess Annexin V stain; fixing and permeabilizing cells (with PFA/ methanol); and using intracellular staining for one or more intracellular cell health markers of interest, including cleaved PARP or MCL-1, an earlier apoptosis marker.

[0071] In one embodiment, a method is provided to use Annexin V conjugated beads or columns or other device to isolate and physically bind and remove apoptotic cells. This embodiment involves incubating a sample with Annexin-V coated purifying element (such as magnetic beads) and running the sample through a magnetic column to select for healthy Annexin-V negative cells (negative selection). Cells could then be used in SCNP assays or used as desired for other readouts.

Cell health markers (e.g., markers of apoptosis, necrosis, and/or autophagy)

[0072] In one embodiment, an unhealthy cell is a cell undergoing apoptosis or cell

mediated cytotoxicity. A cell undergoing apoptosis or cell mediated cytotoxicity can be characterized by cleavage of genomic DNA into discrete fragments prior to membrane Atty Dkt o. 33118-747601

disintegration of the cell. Genomic DNA can be assayed in at least the following ways: by assaying for apoptotic DNA "ladders" (with 180 bp multiples as "rungs" of the ladder) derived from a population of cells, or by quantification of histone complexed DNA fragments with an ELISA, or by quantifying total cellular DNA Content.

[0073] In one embodiment, a cell health marker is a caspase. Caspases can be indicators of cell health. Proteases can be involved in the early stages of apoptosis. The appearance of caspases can set off a cascade of events that can disable a multitude of cell functions. Caspase activation can be analyzed in different ways, such as by an in vitro enzyme assay, e.g., active Caspase 3 in cellular lysates. They may also be analyzed by detection of an in vivo caspase substrate. For instance, caspase 3 can be activated during early stages of apoptosis. A caspase 3 substrate is PARP (Poly-ADP-Ribose-Polymerase), and cleaved PARP can be detected with an anti-PARP antibody. Caspases can also be analyzed by M30 CytoDeath (available from Hoffman La Roche), which measures caspase-cleaved cytokeratin 18 (not detectable in native CK18 of normal cells) with M30 antibody. Some caspase cleavage dyes fluoresce when cleaved. Such dyes can be added to a cell, be cleaved in vivo, and fluorescence can be detected. An example of a caspase cleavage dye is CellEvent Caspase-3/7 Green Detection Reagent from Invitrogen, which is an intrinsically non- fluorescent as a four amino acid peptide (DEVD) conjugated to a nucleic acid binding dye. The DEVD sequence can be a cleavage site for caspase-3/7 and the conjugated dye can be non- fluorescent until it is cleaved from the peptide and bound to DNA.

[0074] In another embodiment, a cell health marker is the release of cytochrome C and AIF (apoptosis inducing factor) into the cytoplasm by mitochondria. During apoptosis, mitochondrial permeability can be altered and apoptosis specific protease activators can be released from mitochondria. Specifically, the discontinuity of the outer mitochondrial membrane results in the redistribution of cytochrome C to the cytosol followed by subsequent depolarization of the inner mitochondrial membrane. Cytochrome C (Apaf-2) release further promotes caspase activation by binding Apaf-1 and therefore activating Apaf-3 (caspase 9). AIF released in the cytoplasm can have proteolytic activity and can by itself be sufficient to induce apoptosis.

[0075] In another embodiment, a cell health marker, e.g., an early indicator of apoptosis in mammalian cells, is the loss of the phospholipid membrane asymmetry of the cell. This results in exposure of phosphatidylserine on the outer surface of the plasma membrane. The change in membrane asymmetry can be analyzed using Annexin V Atty Dkt o. 33118-747601

antibody binding followed by quantification with flow cytometry. An assay using Annexin V can be an extracellular assay.

[0076] In another embodiment, a cell health marker is an apoptosis related protein. Cell health may be determined by the detection of apoptosis related proteins. These proteins include: the Bcl-2 protein family (increased apoptosis with high Bax levels or low Bcl-2 levels); p53; c-myc proto-oncogene; cell surface receptors (such as APO-l/Fas/CD95 for example); growth stimulating genes (such as Ras for example); and tumor suppressor genes (such as Rb for example). Another embodiment includes measuring changes in surface or lineage markers such as CD45, CD34, and CD1 lb. Further proteins are listed under the heading "DNA damage and Apoptosis".

[0077] One embodiment measures sample viability or cell health and calculates the

sample's "percent healthy" (percentage of healthy viable, non-apoptotic cells) to exclude samples of low sample viability or cell health from further analysis. In one embodiment, a threshold of percent healthy is used, such as about 5%, 10%, 20%>, 25%, or 30%, as a cut off for the percentage of healthy cells in a cell sample required for that sample to be further analyzed for signaling biology and other cellular readouts. For example, if less than about 5%, 10%, 20%>, 25%, or 30% of the cells in a sample are healthy, the sample can be excluded from an analysis, e.g., an analysis of signaling biology and other cellular readouts. If more than about 5%, 10%, 20%, 25%, or 30% of the cells in a sample are healthy, the sample can be included in an analysis e.g., an analysis of signaling biology and other cellular readouts. In one embodiment, a threshold is used of about 35%, 40%, 45%), 50%), 55%) or 60% as the cutoff prior to measuring signaling biology and other cellular readouts as shown below. For example, if less than about 35%, 40%, 45%, 50%, 55% or 60% of the cells in a sample are healthy, the sample can be excluded from an analysis, e.g., an analysis of signaling biology and other cellular readouts. If more than about 35%, 40%, 45%, 50%, 55% or 60% of the cells in a sample are healthy, the sample can be included in an analysis, e.g., an analysis of signaling biology and other cellular readouts. In another embodiment, the threshold is about 65%, 70%, 75%, 80%, 85%, 90%, or 95%. For example, if less than about 65%, 70%, 75%, 80%, 85%, 90%, or 95% of the cells in a sample are healthy, the sample can be excluded from an analysis, e.g., an analysis of signaling biology and other cellular readouts. If more than about 65%, 70%, 75%), 80%), 85%), 90%), or 95% of the cells in a sample are healthy, the sample can be included in an analysis e.g., an analysis of signaling biology and other cellular readouts. Atty Dkt o. 33118-747601

[0078] In one embodiment, a sample of cells is excluded (or not included) in an analysis if the percentage of nonviable cells in the sample is above a threshold. In one embodiment, the threshold is about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% nonviable cells. In one embodiment, a sample of cells is included in an analysis if the percentage of viable cells in the sample is below a threshold. In one embodiment, the threshold is about 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% viable cells in a sample.

[0079] In another embodiment, a cell in a sample can be individually gated from an

analysis based on the viability and/or health of the cell. In another embodiment, a cell in a sample can be gated from an analysis if the cell is viable and/or healthy. In another embodiment, a cell can be included in an analysis if the cell is viable and/or healthy. In another embodiment, a cell can be excluded from an analysis if the cell is not viable and/or not healthy.

[0080] A measurement of sample viability or cell health may occur at the beginning of an experiment, which can be after a ficoll separation and rest step. This time period may be called time 0 in an experiment with no modulator is applied to a sample of cells or time 15 minutes in an experiment where a modulator is applied to a sample of cells. Sample viability or cell health may also be measured at later timepoints in an experiment, such as after about 5 min, 10 min, 15 min, 20 min, 25 min, 30 min, 35 min, 40 min, 45 min, 50 min, 55 min, lh, 2h, 3h, 4h, 5h, 6h, 7h, 8h, 9h, lOh, l lh, 12h, 13h, 14h, 15h, 16h, 17h, 18h, 19h, 20h, 21h, 22h, 23h, 24hr, 30h, 36h, 40h, 48h, 72, or more or with incubation with a modulator. Sample viability or cell health may be measured after about 5 min to 48 h, 15 min to 48 h, 30 min to 48h, 1 h to 48h, 1 h to 36 h, lh to 24 h, or 12h to 24h, or with incubation with a modulator.

Calculation of percent healthy cells

[0081] One embodiment focuses on a cell population of interest. In one embodiment, the cells are gated for leukemic blasts (PI) and healthy cells in the blast population (Healthy PI). In one embodiment intact cells are identified using light scattering properties (Forward and Side Scatter), live cells are identified using Amine Aqua, leukemic blasts are identified using Side Scatter and CD45, and non apoptotic leukemic blasts (Healthy PI) are identified by assaying for cleaved PARP. A higher range of induced signaling (e.g., of an activatable element) can occur when cleaved PARP+ cells are removed to make a healthy PI population. G-CSF can be used as a modulator and p-STAT3 can be Atty Dkt o. 33118-747601 the activatable element. Percent healthy analysis can be performed by looking at PBK/Ras signaling S6 as modulated by SCF or Flt3 Ligand.

[0082] Figure 4 shows that cPARP+ cells can be refractory to signaling, and removal (via gating) can improve assay robustness. Figure 4A shows SCNP flow cytometry contour plots from one leukapheresis mononuclear cell AML patient sample that is representative of the entire set. Cells were gated to remove non- viable cells (Amine Aqua+), and to remove debris. cPARP+ (apoptotic) percentage is based on the viable, non-debris fraction. Figure 4B shows contour plots of G-CSF induced p-STAT3 and p- STAT5 signaling from cPARP+ cells (top row) or cPARP ^neg cells (bottom row). Figure 4C shows the same two gating schemes for Pt.2 showing the basal and SCF stimulated median fluorescent intensity data for p-ER . High statistical significant was only achieved by excluding cPARP+ cells. Figure 4D shows percent healthy cells versus Jak/Stat signaling.

[0083] In another embodiment, the method gates on a Healthy PI sample, applies the appropriate preset value or threshold to remove unhealthy cells from the analysis, and then adjusts the signaling for the remaining cells, including the Healthy PI cells, by the percent healthy. This method first removes the cells that are actually apoptosing

("unhealthy" cells) and then adjusts for the effects of those apoptosing cells on otherwise healthy cells. Otherwise healthy cells can have low signaling values because of an effect of an apoptosing cell on the otherwise healthy cells. Without wishing to be bound by theory, an apoptosing cell could affect the extracellular conditions of the healthy cells, which could affect the signaling of healthy cells. In some embodiments, samples with low percent healthy (for example, less than a preset value as recited herein, such as 25%) may be removed from the analysis even after gating for healthy cells. In another embodiment, gating does not occur before cell health analysis.

[0084] Multiple methods may be used to incorporate the cell health into the cell signaling data to improve the accuracy of predictive accuracy (measured by performance characteristic like AUC _ROC , Sensitivity, Specificity, Negative Predictive Value, Positive predictive value) of test classifiers. In one embodiment, cell health is determined directly for each cell. Then the cell may be excluded if the health is within or outside of a preset range, or above/below a certain threshold, or if the cell has a cell health marker, e.g., an intracellular cell health marker. Direct measurements may be made by measuring an apoptotic marker in each cell. One example of a cell health marker is the amount of cleaved PARP, but one or more other markers may be used. In one embodiment samples Atty Dkt o. 33118-747601 can be gated on cleaved PARP (cPARP), allowing one to focus on the populations of cPARP - and cPARP + cells. Since cPARP + cells (higher apoptosis) have reduced sensitivity to modulators, cells that are not gated and excluded may "dampen" a SCNP profile.

[0085] In another embodiment, MCL-1 can be used. Absence of MCL-1 is a measure (marker) of apoptosis and measurements above/below a certain threshold, or outside/within a certain range, can indicate cell health.

[0086] In another embodiment, cell health may be calculated for one cell population and applied to others in an indirect measurement. In one embodiment, the percentage of healthy cells in one sample of cells is used to adjust the measurement of an activation level of an activatable element for another sample of cells. The percent healthy calculation for AML samples, for example, can be obtained various ways, such as:

# PARP ^" myeloid cells or # PARP ^" myeloid cells

Total Events # Intact cells or # PARP ^" myeloid cells

# Intact myeloid cells where "Intact" is defined by a cell size and granularity gate (Forward and Side Scatter parameters), where Myeloid is defined by markers of myeloid cells (e.g., CD45 and Side Scatter, or other myeloid markers e.g., CD13, CD33), where PARP- cells are defined by cleaved PARP measurements within myeloid cells.

[0087] In one embodiment, the percentage of unhealthy cells in a sample is the

percentage of cells in the sample with one or more cell health markers out the total number of cells in the sample. In another embodiment, the percentage of unhealthy cells in a sample is the percentage of cells in the sample with one or more intracellular cell health markers out the total number of cells in the sample. In another embodiment, the percentage of unhealthy cells in a sample is the percentage of cells in the sample with both one or more cell health markers and an intact cell membrane, out of the total number of cells with an intact cell membrane in the sample.

[0088] These measures can be highly correlated.

[0089] A percent healthy calculation can be used to adjust one or more SCNP profiles for a patient, resulting in improvements in the predictive accuracy of the test classifiers Atty Dkt o. 33118-747601

(measured by performance characteristic like AUCROC , Sensitivity, Specificity, Negative

Predictive Value, Positive predictive value). The adjustments to the SCNP profiles can be performed in two ways: by adjusting by residual or adjusting the population modeling.

In one embodiment, adjusting by residuals comprises looking at a plot of induced signaling vs. percent healthy for a node (e.g., a modulator/activatable element pair).

Generally, a plot might show that the induced signaling increases as the percent healthy increases. The data average can be fit with some linear trend. The residual can be found by measuring how far above or below the linear trend a single node data point lays. In another embodiment adjusting is by adjusting by population modeling. With regard to adjusting by population modeling, within a sample, since dead or apoptosing cells do not signal in response to certain modulators, dead or apoptosing cells (e.g., 40% of the sample) can have the same phospho-flow cytometry profile in multiple wells (e.g., multiple samples) even when treated with one or more modulators as compared to the cells that have not been treated. However, the remaining 60% healthy cells can have a different profile in different wells when treated with one or more modulators, depending on the modulator, as compared to the cells that have not been treated. Population modeling can be used to estimate the signal of the healthy cells within each examined node. The term "node" can describe a specific modulator/activatable element pair. Nodes can be represented using the notation modulator->activatable element. For example, IL-

6->pStat5 represents the modulator IL-6 and the activatable element pStat5. Examples of activatable elements are described below.

[0090] The measurement of the percent healthy cells in a population of cells that do not change signaling profiles can be used to indirectly calculate the signaling profiles of cells that do change signaling profiles based upon varying stimulation conditions. Details of a calculation:

Pol _d = ^Me s _tim

Mean _uns ti _m

[0091] Since Mean _stim can be described by

(funhealthy * ^ ^{e an} Onhealthy + fhealthy * ^ ^{e an} healthy) where M eCM-unhealthy I ^{S ME} mean for the cells that are undergoing apoptosis, Mean _healthy is the mean for the cells that are healthy, f 'unhealthy ^an d f healthy ^are the fraction of apoptosing and healthy cells. Since apoptosing cells are unlikely to change in level of signaling due to modulation Mean _Unhealthy = Mean _unstim which can be known from a well with no modulation. Atty Dkt o. 33118-747601

The fold formula above can be written instead as: Mean _stim = f unhealthy * Mean _unstim + f Wealthy * Mean _hea i _th y

[0092] The values of f healthy ^an d f unhealthy, ^me fraction of unhealthy and healthy cells, can be obtained from the percent healthy calculation within a population, leaving only Mean eait _h y unknown and able to be calculated. The above formula can be applied within viable cells, within a specific cell population such as PI .

[0093] An apoptosis readout like cPARP, when tested in combination with other SCNP readouts (e.g., p-Akt) in the same well, can be used to apply an adjustment for cell health at an individual cell level. For example, p-Akt readout for each cell can be weighted by the cPARP signal for that cell, so that modulated levels of p-Akt from dying cells can be either increased or decreased when computing normalized metrics like 'Fold' change.

[0094] An adjustment for cell health at an individual cell level can be applied to an

individual cell based on where the individual cell is on an apoptosis timeline (stage of a cell in apoptosis). An apoptosis timeline is described, for example, at

http://www.in vitrogen.com/site/u^

and-Tissue- Analysis/Flo w-Cytometry/FC-Misc/ Apoptosis.html. After induction of apoptosis, cell function changes can occur generally in the following order: decrease in mitochondrial membrane potential, mitochondrial transition pore opening,

phosphatidylserine translocation to outer membrane, increase in caspase activity, decrease in metabolic activity, increase in DNA condensation, decrease in plasma membrane integrity, and increase in DNA fragmentation. Markers can be used to detect events along a linear apoptosis continuum to determine how close a cell is to death. The activation status or activation level of an activatable element may be affected based on the position of the cell in the apoptosis timeline. For example, the activation level of an activatable element may decrease the closer the cell is to the end of the apoptosis timeline. Various factors can be employed to adjust the signaling level. For example, the presence of an early apoptosis marker, or even a pre-apoptosis marker (cell cycle arrest, DNA damage, presence of viral infection etc.), can indicate a small correction of cell signaling data (e.g., measurement of the activation level of an activatable element) is appropriate whereas the presence of a later apoptosis marker can indicate a larger correction of cell signaling data is appropriate, up to and including elimination of the cell from the signaling analysis. In one embodiment, an entire population of cells can be adjusted by a factor instead of individual adjustments to individual cells. In one Atty Dkt o. 33118-747601

embodiment, the activation level of an activatable element for an entire population of cells can be adjusted by a factor instead of individual adjustments to activation levels of activatable elements in individual cells.

[0095] An alternative metric can be used to measure induced apoptosis at various time points, including experiment time zero. This alternative metric minimizes the effects of pre-existing sample viability, which can be affected by sample preparation, handling, cryopreservation and/or thawing before the experiment. This inherent variation in preexisting sample viability can confound classification of samples. For example, the variability between samples may be due to sample handling and not true disease differences. The alternative metric normalizes the sample viability by dividing readouts for each sample, for each time point and modulated condition, by the associated readout for the un-stimulated condition at experimental time 0 or at the matched experimental timepoint, e.g., see Figure 5. An extension of this metric utilizes the normalized metrics but also integrates the various time points associated with the specific treatment (such as the use of an apoptosis inducing agent, such as etoposide) into a unified metric. This extended, and normalized, measurement can be designed to measure the total experimental effect of the specific treatment on the sample over the time points of the experiment. See Figure 5 (calculations). Time zero for testing may occur at 6 hours, as in Figure 5, as the samples may need to be thawed and brought to a state ready for analysis.

[0096] The above calculations are also useful to select nodes that are less affected by apoptosis. For example, in one embodiment data are collected and then adjusted as set out above. Then, the adjusted values are plotted versus the unadjusted values to determine and the nodes are selected which are above the X/Y line.

Activatable elements

[0097] The methods and compositions described herein may be employed to examine and profile the status or activation level of any activatable element in a cellular pathway, or collections of such activatable elements. Single or multiple distinct pathways can be profiled (e.g., sequentially or simultaneously), or subsets of activatable elements within a single pathway or across multiple pathways can be examined (e.g., sequentially or simultaneously).

[0098] In some embodiments, apoptosis, signaling, cell cycle and/or DNA damage

pathways are characterized in order to classify one or more cells in an individual. The characterization of multiple pathways can reveal operative pathways in a condition that Atty Dkt o. 33118-747601 can then be used to classify one or more cells in an individual. In some embodiments, the classification includes classifying the cell as a cell that is correlated with a clinical outcome. The clinical outcome can be the prognosis and/or diagnosis of a condition, and/or staging or grading of a condition. In some embodiments, the classifying of the cell includes classifying the cell as a cell that is correlated with a patient response to a treatment. In some embodiments, the classifying of the cell includes classifying the cell as a cell that is correlated with minimal residual disease or emerging resistance. In some embodiments, the cell classification includes correlating a response to a potential drug treatment. See also U.S. Ser. Nos. 12/432,720 and 61/048,886 for activatable elements.

[0099] As will be appreciated by those in the art, a wide variety of activation events can find use in the methods described herein. In general, activation can result in a change in the activatable protein that is detectable by some indication (termed an "activation state indicator"), e.g., by altered binding of a labeled binding element or by changes in detectable biological activities (e.g., the activated state has an enzymatic activity which can be measured and compared to a lack of activity in the non-activated state). Using one or more detectable events or moieties, two or more activation states (e.g., "off and "on") can be differentiated.

[00100] The activation state of an individual activatable element can be in the on or off state. As an illustrative example, and without intending to be limited to any theory, an individual phosphorylatable site on a protein can activate or deactivate the protein.

Phosphorylation of an adapter protein can promote its interaction with other components/proteins of distinct cellular signaling pathways. In another embodiment, the difference in enzymatic activity in a protein can reflect a different activation state. The terms "on" and "off," when applied to an activatable element that is a part of a cellular constituent, can be used here to describe the state of the activatable element, and not the overall state of the cellular constituent of which it is a part.

[00101] The activation state of an individual activatable element can be represented as continuous numeric values representing a quantity of the activatable element or can be discretized into categorical variables. For instance, the activation state may be discretized into a binary value indicating that the activatable element is either in the on or off state. As an illustrative example, and without intending to be limited to any theory, an individual phosphorylatable site on a protein will either be phosphorylated and then be in the "on" state or it will not be phosphorylated and hence, it will be in the "off state. See Blume- Jensen and Hunter, Nature, vol 411, 17 May 2001, p 355-365. Atty Dkt o. 33118-747601

[00102] Typically, a cell possesses a plurality of a particular protein or other constituent with a particular activatable element and this plurality of proteins or constituents usually has some proteins or constituents whose individual activatable element is in the on state and other proteins or constituents whose individual activatable element is in the off state. Since the activation state of each activatable element can be measured through the use of a binding element that recognizes a specific activation state, only those activatable elements in the specific activation state recognized by the binding element, representing some fraction of the total number of activatable elements, will be bound by the binding element to generate a measurable signal. The measurable signal corresponding to the summation of individual activatable elements of a particular type that are activated in a single cell can be the "activation level" for that activatable element in that cell.

[00103] Activation levels for a particular activatable element may vary among individual cells so that when a plurality of cells is analyzed, the activation levels follow a distribution. The distribution may be a normal distribution, also known as a Gaussian distribution, or it may be of another type. Different populations of cells may have different distributions of activation levels that can then serve to distinguish between the populations. For more information on the measurement of activatable elements, specific activatable elements, signaling pathways, and drug transporters, see U.S. Ser. No.

61/350,864 or U.S. Pub. No. 2009/0269773, which are hereby incorporated by reference in their entireties.

[00104] In some embodiments, the activation levels of one or more activatable elements of a cell from a first population of cells and the activation levels of one or more activatable elements of a cell from a second population of cells are correlated with a condition. In some embodiments, the first and second homogeneous populations of cells are hematopoietic cell populations. In some embodiments, the activation levels of one or more activatable elements of a cell from a first population of hematopoietic cells and the activation levels of one or more activatable elements of cell from a second population of hematopoietic cells are correlated with a neoplastic, autoimmune or hematopoietic condition as described herein. Examples of different populations of hematopoietic cells include, but are not limited to, pluripotent hematopoietic stem cells, B-lymphocyte lineage progenitor or derived cells, T-lymphocyte lineage progenitor or derived cells, NK cell lineage progenitor or derived cells, granulocyte lineage progenitor or derived cells, Atty Dkt o. 33118-747601 monocyte lineage progenitor or derived cells, megakaryocyte lineage progenitor or derived cells and erythroid lineage progenitor or derived cells.

[00105] In some embodiments, the activation level of one or more activatable elements in single cells in the sample is determined. Cellular constituents that may include activatable elements include without limitation proteins, carbohydrates, lipids, nucleic acids and metabolites. The activatable element may be a portion of the cellular constituent, for example, an amino acid residue in a protein that may undergo phosphorylation, or it may be the cellular constituent itself, for example, a protein that is activated by translocation, change in conformation (due to, e.g., change in pH or ion concentration), by proteolytic cleavage, and the like. Upon activation, a change can occur to the activatable element, such as covalent modification of the activatable element (e.g., binding of a molecule or group to the activatable element, such as phosphorylation) or a conformational change. Such changes generally contribute to changes in particular biological, biochemical, or physical properties of the cellular constituent that contains the activatable element. The state of the cellular constituent that contains the activatable element is determined to some degree, though not necessarily completely, by the state of a particular activatable element of the cellular constituent. For example, a protein may have multiple activatable elements, and the particular activation states of these elements may overall determine the activation state of the protein; the state of a single activatable element is not necessarily determinative. Additional factors, such as the binding of other proteins, pH, ion concentration, interaction with other cellular constituents, and the like, can also affect the state of the cellular constituent.

[00106] In some embodiments, the activation levels of a plurality of intracellular

activatable elements in single cells are determined. The term "plurality" as used herein refers to two or more. In some embodiments, the activation level of at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 intracellular activatable elements are determined.

[00107] Activation states of activatable elements can may result from chemical additions or modifications of biomolecules and include biochemical processes such as glycosylation, phosphorylation, acetylation, methylation, biotinylation, glutamylation, glycylation, hydroxylation, isomerization, prenylation, myristoylation, lipoylation, phosphopantetheinylation, sulfation, ISGylation, nitrosylation, palmitoylation, SUMOylation, ubiquitination, neddylation, citrullination, amidation, and disulfide bond formation, disulfide bond reduction. Other possible chemical additions or modifications of biomolecules include the formation of protein carbonyls, direct modifications of Atty Dkt o. 33118-747601 protein side chains, such as o-tyrosine, chloro-, nitrotyrosine, and dityrosine, and protein adducts derived from reactions with carbohydrate and lipid derivatives. Other modifications may be non-covalent, such as binding of a ligand or binding of an allosteric modulator.

[00108] In some embodiments, the activatable element is a protein. Examples of proteins that can include activatable elements include, but are not limited to kinases, phosphatases, lipid signaling molecules, adaptor/scaffold proteins, cytokines, cytokine regulators, ubiquitination enzymes, adhesion molecules, cyto skeletal/contractile proteins, heterotrimeric G proteins, small molecular weight GTPases, guanine nucleotide exchange factors, GTPase activating proteins, caspases, proteins involved in apoptosis, cell cycle regulators, molecular chaperones, metabolic enzymes, vesicular transport proteins, hydroxylases, isomerases, deacetylases, methylases, demethylases, tumor suppressor genes, proteases, ion channels, molecular transporters, transcription factors/DNA binding factors, regulators of transcription, and regulators of translation. Examples of activatable elements, activation states and methods of determining the activation level of activatable elements are described in US Publication Number 20060073474 entitled "Methods and compositions for detecting the activation state of multiple proteins in single cells" and US Publication Number 20050112700 entitled "Methods and compositions for risk stratification" the content of which are incorporate here by reference. See also U.S.S.Nos. 61/048,886, 61/048,920 and Shulz et al, Current Protocols in Immunology 2007, 7:8.17.1-20.

[00109] In some embodiments, the protein that may be activated is selected from the

group consisting of HER receptors, PDGF receptors, FLT3 receptor, Kit receptor, FGF receptors, Eph receptors, Trk receptors, IGF receptors, Insulin receptor, Met receptor, Ret, VEGF receptors, erythropoetin receptor, thromobopoetin receptor, CD114, CD116, TIE1, TIE2, FAK, Jakl, Jak2, Jak3, Tyk2, Src, Lyn, Fyn, Lck, Fgr, Yes, Csk, Abl, Btk, ZAP70, Syk, IRAKs, cRaf, ARaf, BRAF, Mos, Lim kinase, ILK, Tpl, ALK, TGFp receptors, BMP receptors, MEKKs, ASK, MLKs, DLK, PAKs, Mek 1, Mek 2, MKK3/6, MKK4/7, ASKl,Cot, NIK, Bub, Myt 1, Weel, Casein kinases, PDK1, SGK1, SGK2, SGK3, Aktl, Akt2, Akt3, p90Rsks, p70S6Kinase, Prks, PKCs, PKAs, ROCK 1, ROCK 2, Auroras, CaMKs, MNKs, AMPKs, MELK, MARKs, Chkl, Chk2, LKB-1, MAPKAPKs, Piml, Pim2, Pim3, IKKs, Cdks, Jnks, Erks, IKKs, GSK3 , GSK3p, Cdks, CLKs, PKR, PI3-Kinase class 1, class 2, class 3, mTor, SAPK/JNK1,2,3, p38s, PKR, DNA-PK, ATM, ATR, Receptor protein tyrosine phosphatases (RPTPs), LAR Atty Dkt o. 33118-747601 phosphatase, CD45, Non receptor tyrosine phosphatases (NPRTPs), SHPs, MAP kinase phosphatases (MKPs), Dual Specificity phosphatases (DUSPs), CDC25 phosphatases, Low molecular weight tyrosine phosphatase, Eyes absent (EYA) tyrosine phosphatases, Slingshot phosphatases (SSH), serine phosphatases, PP2A, PP2B, PP2C, PP1, PP5, inositol phosphatases, PTEN, SHIPs, myotubularins, phosphoinositide kinases, phopsho lipases, prostaglandin synthases, 5- lipoxygenase, sphingosine kinases, sphingomyelinases, adaptor/scaffold proteins, She, Grb2, BLNK, LAT, B cell adaptor for PI3-kinase (BCAP), SLAP, Dok, KSR, MyD88, Crk, CrkL, GAD, Nek, Grb2 associated binder (GAB), Fas associated death domain (FADD), TRADD, TRAF2, RIP, T-Cell leukemia family, IL-2, IL-4, IL-8, IL-6, interferon γ, interferon a, suppressors of cytokine signaling (SOCs), Cbl, SCF ubiquitination ligase complex, APC/C, adhesion molecules, integrins, Immunoglobulin-like adhesion molecules, selectins, cadherins, catenins, focal adhesion kinase, pl30CAS, fodrin, actin, paxillin, myosin, myosin binding proteins, tubulin, eg5/KSP, CENPs, β-adrenergic receptors, muscarinic receptors, adenylyl cyclase receptors, small molecular weight GTPases, H-Ras, K-Ras, N-Ras, Ran, Rac, Rho, Cdc42, Arfs, RABs, RHEB, Vav, Tiam, Sos, Dbl, PRK, TSC1,2, Ras-GAP, Arf-GAPs, Rho-GAPs, caspases, Caspase 2, Caspase 3, Caspase 6, Caspase 7, Caspase 8, Caspase 9, Be 1-2, Mcl-1, Bel -XL, Bcl-w, Bcl-B, Al, Bax, Bak, Bok, Bik, Bad, Bid, Bim, Bmf, Hrk, Noxa, Puma, IAPs, XIAP, Smac, Cdk4, Cdk 6, Cdk 2, Cdkl, Cdk 7, Cyclin D, Cyclin E, Cyclin A, Cyclin B, Rb, pl6, pl4Arf, p27KIP, p21CIP, molecular chaperones, Hsp90s, Hsp70, Hsp27, metabolic enzymes, Acetyl-CoAa Carboxylase, ATP citrate lyase, nitric oxide synthase, caveolins, endosomal sorting complex required for transport (ESCRT) proteins, vesicular protein sorting (Vsps), hydroxylases, prolyl- hydroxylases PHD-1, 2 and 3, asparagine hydroxylase FIH transferases, Pinl prolyl isomerase, topoisomerases, deacetylases, Histone deacetylases, sirtuins, histone acetylases, CBP/P300 family, MYST family, ATF2, DNA methyl transferases, Histone H3K4 demethylases, H3K27, JHDM2A, UTX, VHL, WT-1, p53, Hdm, PTEN, ubiquitin proteases, urokinase-type plasminogen activator (uPA) and uPA receptor (uPAR) system, cathepsins, metalloproteinases, esterases, hydrolases, separase, potassium channels, sodium channels, multi-drug resistance proteins, P-Gycoprotein, nucleoside transporters, Ets, Elk, SMADs, Rel-A (p65-NFKB), CREB, NFAT, ATF-2, AFT, Myc, Fos, Spl, Egr-1, T-bet, β - catenin, HIFs, FOXOs, E2Fs, SRFs, TCFs, Egr-1, β-catenin, FOXO STAT1, STAT 3, STAT 4, STAT 5, STAT 6, p53, Ets-1, Ets-2, SPDEF, GABPa, Tel, Tel2, WT-1, Atty Dkt o. 33118-747601

HMGA, pS6, 4EPB-1, eIF4E-binding protein, R A polymerase, initiation factors, elongation factors.

[00110] In some embodiments, the methods described herein are employed to determine the activation level of an activatable element, e.g., in a cellular pathway. Methods and compositions are provided for the determination of a cell signaling profile (e.g., activation level of an activatable element) of a cell according to the activation level of an activatable element in a cellular pathway. Methods and compositions are provided for the determination of the cell signaling profile of a cell in a first cell population and a cell in a second cell population according to the activation level of an activatable element in a cellular pathway in each cell. The cells can be a hematopoietic cell.

[00111] In some embodiments, the determination of the cell signaling profile of cells in different populations according to activation level of an activatable element, e.g., in a cellular pathway comprises classifying at least one of the cells as a cell that is correlated with a clinical outcome. Examples of clinical outcomes, staging, as well as patient responses are also shown above.

Signaling Pathways

[00112] In some embodiments, the methods described herein are employed to determine the activation level of an activatable element in a signaling pathway. In some embodiments, the cell signaling profile of a cell is determined, as described herein, according to the activation level of one or more activatable elements in one or more signaling pathways. Signaling pathways and their members have been extensively described. See (Hunter T. Cell Jan. 7, 2000;100(1): 13-27; Weinberg, 2007; and Blume- Jensen and Hunter, Nature, vol 411, 17 May 2001, p 355-365 cited above). Exemplary signaling pathways include the following pathways and their members: the JAK-STAT pathway including JAKs, STATs 2,3 4 and 5, the FLT3L signaling pathway, the MAP kinase pathway including Ras, Raf, MEK, ER and Elk; the PI3K/Akt pathway including PI-3 -kinase, PDKl, Akt and Bad; the NF-κΒ pathway including IKKs, IkB and NF-KB and the Wnt pathway including frizzled receptors, beta-catenin, APC and other co-factors and TCF (see Cell Signaling Technology, Inc. 2002 Catalog pages 231-279 and Hunter T., supra.). In some embodiments, the correlated activatable elements being assayed (or the signaling proteins being examined) are members of the MAP kinase, Akt, NFkB, WNT, STAT and/or PKC signaling pathways.

[00113] In some embodiments, methods are employed to determine the activation level of a signaling protein in a signaling pathway known in the art including those described Atty Dkt o. 33118-747601 herein. Exemplary types of signaling proteins include, but are not limited to, kinases, kinase substrates (i.e., phosphorylated substrates), phosphatases, phosphatase substrates, binding proteins (such as 14-3-3), receptor ligands and receptors (cell surface receptor tyrosine kinases and nuclear receptors)). Kinases and protein binding domains, for example, have been well described (see, e.g., Cell Signaling Technology, Inc., 2002 Catalogue "The Human Protein Kinases" and "Protein Interaction Domains" pgs. 254- 279).

[00114] Exemplary signaling proteins include, but are not limited to, kinases, HER

receptors, PDGF receptors, Kit receptor, FGF receptors, Eph receptors, Trk receptors, IGF receptors, Insulin receptor, Met receptor, Ret, VEGF receptors, TIE1, TIE2, FAK, Jakl, Jak2, Jak3, Tyk2, Src, Lyn, Fyn, Lck, Fgr, Yes, Csk, Abl, Btk, ZAP70, Syk, IRAKs, cRaf, ARaf, BRAF, Mos, Lim kinase, ILK, Tpl, ALK, TGFp receptors, BMP receptors, MEKKs, ASK, MLKs, DLK, PAKs, Mek 1, Mek 2, MKK3/6, MKK4/7, ASKl,Cot, NIK, Bub, Myt 1, Weel, Casein kinases, PDK1, SGK1, SGK2, SGK3, Aktl, Akt2, Akt3, p90Rsks, p70S6Kinase,Prks, PKCs, PKAs, ROCK 1, ROCK 2, Auroras, CaMKs, MNKs, AMPKs, MELK, MARKs, Chkl, Chk2, LKB-1, MAPKAPKs, Piml, Pim2, Pim3, IKKs, Cdks, Jnks, Erks, Erkl, Erk2, IKKs, GSK3a, GSK3P, Cdks, CLKs, PKR, PI3-Kinase class 1, class 2, class 3, mTor, SAPK/JNK1,2,3, p38s, PKR, DNA-PK, ATM, ATR, phosphatases, Receptor protein tyrosine phosphatases (RPTPs), LAR phosphatase, CD45, Non receptor tyrosine phosphatases (NPRTPs), SHPs, MAP kinase phosphatases

(MKPs), Dual Specificity phosphatases (DUSPs), CDC25 phosphatases, low molecular weight tyrosine phosphatase, Eyes absent (EYA) tyrosine phosphatases, Slingshot phosphatases (SSH), serine phosphatases, PP2A, PP2B, PP2C, PP1, PP5, inositol phosphatases, PTEN, SHIPs, myotubularins, lipid signaling, phosphoinositide kinases, phopsho lipases, prostaglandin synthases, 5 -lipoxygenase, sphingosine kinases, sphingomyelinases, adaptor/scaffold proteins, She, Grb2, BLNK, LAT, B cell adaptor for PI3-kinase (BCAP), SLAP, Dok, KSR, MyD88, Crk, CrkL, GAD, Nek, Grb2 associated binder (GAB), Fas associated death domain (FADD), TRADD, TRAF2, RIP, T-Cell leukemia family, cytokines, IL-2, IL-4, IL-8, IL-6, interferon , interferon a, cytokine regulators, suppressors of cytokine signaling (SOCs), ubiquitination enzymes, Cbl, SCF ubiquitination ligase complex, APC/C, adhesion molecules, integrins, Immunoglobulin- like adhesion molecules, selectins, cadherins, catenins, focal adhesion kinase, pl30CAS, cytoskeletal/contractile proteins, fodrin, actin, paxillin, myosin, myosin binding proteins, tubulin, eg5/KSP, CENPs, heterotrimeric G proteins, β-adrenergic receptors, muscarinic Atty Dkt o. 33118-747601 receptors, adenylyl cyclase receptors, small molecular weight GTPases, H-Ras, K- Ras, N-Ras, Ran, Rac, Rho, Cdc42, Arfs, RABs, RHEB, guanine nucleotide exchange factors, Vav, Tiam, Sos, Dbl, PRK, TSC1,2, GTPase activating proteins, Ras-GAP, Arf-GAPs, Rho-GAPs, caspases, Caspase 2, Caspase 3, Caspase 6, Caspase 7, Caspase 8, Caspase 9, proteins involved in apoptosis, Bcl-2, Mcl-l, Bcl-XL, Bcl-w, Bcl-B, Al, Bax, Bak, Bok, Bik, Bad, Bid, Bim, Bmf, Hrk, Noxa, Puma, IAPs, XIAP, Smac, cell cycle regulators, Cdk4, Cdk 6, Cdk 2, Cdkl, Cdk 7, Cyclin D, Cyclin E, Cyclin A, Cyclin B, Rb, pi 6, pl4Arf, p27KIP, p21CIP, molecular chaperones, Hsp90s, Hsp70, Hsp27, metabolic enzymes, Acetyl-CoAa Carboxylase, ATP citrate lyase, nitric oxide synthase, vesicular transport proteins, caveolins, endosomal sorting complex required for transport (ESCRT) proteins, vesicular protein sorting (Vsps), hydroxylases, prolyl- hydroxylases PHD-1, 2 and 3, asparagine hydroxylase FIH transferases, isomerases, Pinl prolyl isomerase, topoisomerases, deacetylases, Histone deacetylases, sirtuins, acetylases, histone acetylases, CBP/P300 family, MYST family, ATF2, methylases, DNA methyl transferases, demethylases, Histone H3K4 demethylases, H3K27, JHDM2A, UTX, tumor suppressor genes, VHL, WT-1, p53, Hdm, PTEN, proteases, ubiquitin proteases, urokinase-type plasminogen activator (uPA) and uPA receptor (uPAR) system, cathepsins, metalloproteinases, esterases, hydrolases, separase, ion channels, potassium channels, sodium channels, molecular transporters, multi-drug resistance proteins, P- Gycoprotein, nucleoside transporters, transcription factors/ DNA binding proteins, Ets, Elk, SMADs, Rel-A (p65-NFKB), CREB, NFAT, ATF-2, AFT, Myc, Fos, Spl, Egr-1, T- bet,P-catenin, HIFs, FOXOs, E2Fs, SRFs, TCFs, Egr-1, β - catenin, FOXO STAT1, STAT 3, STAT 4, STAT 5, STAT 6, p53, WT-1, HMGA, regulators of translation, pS6, 4EPB-1, eIF4E-binding protein, regulators of transcription, RNA polymerase, initiation factors, and elongation factors.

[00115] In some embodiments the protein is selected from the group consisting of PI3- Kinase (p85, pi 10a, pi 10b, pi lOd), Jakl, Jak2, SOCs, Rac, Rho, Cdc42, Ras-GAP, Vav, Tiam, Sos, Dbl, Nek, Gab, PRK, SHP1, and SHP2, SHIP1, SHIP2, sSHIP, PTEN, She, Grb2, PDK1, SGK, Aktl, Akt2, Akt3, TSC1,2, Rheb, mTor, 4EBP-1, p70S6Kinase, S6, LKB-1, AMPK, PFK, Acetyl-CoAa Carboxylase, DokS, Rafs, Mos, Tpl2, MEK1/2, MLK3, TAK, DLK, MKK3/6, MEKK1,4, MLK3, ASK1, MKK4/7, SAPK/JNK1,2,3, p38s, Erkl/2, Syk, Btk, BLNK, LAT, ZAP70, Lck, Cbl, SLP-76, PLCyi, PLCy 2, STAT1, STAT 3, STAT 4, STAT 5, STAT 6, FAK, pl30CAS, PAKs, LIMK1/2, Hsp90, Hsp70, Hsp27, SMADs, Rel-A (p65-NFKB), CREB, Histone H2B, HATs, HDACs, Atty Dkt o. 33118-747601

PKR, Rb, Cyclin D, Cyclin E, Cyclin A, Cyclin B, PI 6, pWArf, p27KIP, p21CIP, Cdk4, Cdk6, Cdk7, Cdkl, Cdk2, Cdk9, Cdc25,A/B/C, Abl, E2F, FADD, TRADD, TRAF2, RIP, Myd88, BAD, Bcl-2, Mcl-1, Bcl-XL, Caspase 2, Caspase 3, Caspase 6, Caspase 7, Caspase 8, Caspase 9, IAPs, Smac, Fodrin, Actin, Src, Lyn, Fyn, Lck, NIK, ΙκΒ, p65(RelA), IKKa, PKA, PKCa, PKC β, PKC9, PKC5, CAMK, Elk, AFT, Myc, Egr-1, NFAT, ATF-2, Mdm2, p53, DNA-PK, Chkl, Chk2, ATM, ATR, Pcatenin, CrkL, GSK3a, GSK3P, and FOXO.

[00116] In some embodiments, the methods described herein are employed to determine the activation level of an activatable element in a signaling pathway. See U.S.S.Nos. 61/048,886 and 61/048,920 which are incorporated by reference in their entireties.

Methods and compositions are provided for the determination of a cell signaling profile of a cell according to the status of an activatable element in a signaling pathway.

Methods and compositions are provided for the determination of a cell signaling profile of cells in different populations of cells according to the status of an activatable element in a signaling pathway. The cells can be a hematopoietic cells. Examples of hematopoietic cells are shown above. In some embodiments, the determination of a cell signaling profile of cells in different populations of cells according to the activation level of an activatable element in a signaling pathway comprises classifying the cell populations as cells that are correlated with a clinical outcome. Examples of clinical outcome, staging, patient responses and classifications are shown above.

Binding Element

[00117] In some embodiments, the activation level of an activatable element is

determined. One embodiment makes this determination by contacting a cell from a cell population with a binding element that is specific for an activation state of the activatable element. The term "binding element" includes any molecule, e.g., peptide, nucleic acid, small organic molecule which is capable of detecting an activation state of an activatable element over another activation state of the activatable element. Binding elements and labels for binding elements are shown in U.S. S.N. 61/048,886; 61/048,920 and 61/048,657.

[00118] In some embodiments, the binding element is a peptide, polypeptide, oligopeptide or a protein. The peptide, polypeptide, oligopeptide or protein may be made up of naturally occurring amino acids and peptide bonds, or synthetic peptidomimetic structures. Thus "amino acid", or "peptide residue", as used herein include both naturally occurring and synthetic amino acids. For example, homo-phenylalanine, citrulline and Atty Dkt o. 33118-747601 noreleucine are considered amino acids. The side chains may be in either the (R) or the (S) configuration. In some embodiments, the amino acids are in the (S) or reconfiguration. If non-naturally occurring side chains are used, non-amino acid substituents may be used, for example to prevent or retard in vivo degradation. Proteins including non-naturally occurring amino acids may be synthesized or in some cases, made recombinantly; see van Hest et al, FEBS Lett 428:(l-2) 68-70 May 22, 1998 and Tang et al, Abstr. Pap Am. Chem. S218: U138 Part 2 Aug. 22, 1999, both of which are expressly incorporated by reference herein.

[00119] Methods described herein may be used to detect any particular activatable

element in a sample that is antigenically detectable and antigenically distinguishable from other activatable element which is present in the sample. For example, activation state- specific antibodies can be used in the present methods to identify distinct signaling cascades of a subset or subpopulation of complex cell populations and the ordering of protein activation (e.g., kinase activation) in potential signaling hierarchies. Hence, in some embodiments the expression and phosphorylation of one or more polypeptides are detected and quantified using methods described herein. In some embodiments, the expression and phosphorylation of one or more polypeptides that are cellular components of a cellular pathway are detected and quantified using methods described herein. As used herein, the term "activation state-specific antibody" or "activation state antibody" or grammatical equivalents thereof, can refer to an antibody that specifically binds to a corresponding and specific antigen. The corresponding and specific antigen can be a specific form of an activatable element. The binding of the activation state-specific antibody can be indicative of a specific activation state of a specific activatable element.

[00120] In some embodiments, the binding element is an antibody. In some embodiment, the binding element is an activation state-specific antibody.

[00121] The term "antibody" includes full length antibodies and antibody fragments, and can refer to a natural antibody from any organism, an engineered antibody, or an antibody generated recombinantly for experimental, therapeutic, or other purposes as further defined below. Examples of antibody fragments, as are known in the art, such as Fab, Fab', F(ab')2, Fv, scFv, or other antigen-binding subsequences of antibodies, either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA technologies. The term "antibody" comprises monoclonal and polyclonal antibodies. Antibodies can be antagonists, agonists, neutralizing, inhibitory, or stimulatory. They can be humanized, glycosylated, bound to solid supports, and Atty Dkt o. 33118-747601 posses other variations. See U.S.S.Nos. 61/048,886; 61/048,920 and 61/048,657 for more information about antibodies as binding elements.

[00122] Activation state specific antibodies can be used to detect kinase activity; however additional means for determining kinase activation are provided herein. For example, substrates that are specifically recognized by protein kinases and phosphorylated thereby are known. Antibodies that specifically bind to such phosphorylated substrates but do not bind to such non-phosphorylated substrates (phospho-substrate antibodies) can be used to determine the presence of activated kinase in a sample.

[00123] The antigenicity of an activated isoform of an activatable element can be

distinguishable from the antigenicity of non-activated isoform of an activatable element or from the antigenicity of an isoform of a different activation state. In some embodiments, an activated isoform of an element possesses an epitope that is absent in a non-activated isoform of an element, or vice versa. In some embodiments, this difference is due to covalent addition of a moiety to an element, such as a phosphate moiety, or due to a structural change in an element, as through protein cleavage, or due to an otherwise induced conformational change in an element which causes the element to present the same sequence in an antigenically distinguishable way. In some embodiments, such a conformational change causes an activated isoform of an element to present at least one epitope that is not present in a non-activated isoform, or to not present at least one epitope that is presented by a non-activated isoform of the element. In some embodiments, the epitopes for the distinguishing antibodies are centered around the active site of the element, although as is known in the art, conformational changes in one area of an element may cause alterations in different areas of the element as well.

[00124] Many antibodies, many of which are commercially available (for example, see Cell Signaling Technology, www.cellsignal.com or Becton Dickinson, www.bd.com) have been produced which specifically bind to the phosphorylated isoform of a protein but do not specifically bind to a non-phosphorylated isoform of a protein. Many such antibodies have been produced for the study of signal transducing proteins which are reversibly phosphorylated. Particularly, many such antibodies have been produced which specifically bind to phosphorylated, activated iso forms of protein. Examples of proteins that can be analyzed with the methods described herein include, but are not limited to, kinases, HER receptors, PDGF receptors, FLT3 receptor, Kit receptor, FGF receptors, Eph receptors, Trk receptors, IGF receptors, Insulin receptor, Met receptor, Ret, VEGF receptors, TIE1, TIE2, erythropoetin receptor, thromobopoetin receptor, CD114, CD116, Atty Dkt o. 33118-747601

FAK, Jakl, Jak2, Jak3, Tyk2, Src, Lyn, Fyn, Lck, Fgr, Yes, Csk, Abl, Btk, ZAP70, Syk, IRAKs, cRaf, ARaf, BRAF, Mos, Lim kinase, ILK, Tpl, ALK, TGFp receptors, BMP receptors, MEKKs, ASK, MLKs, DLK, PAKs, Mek 1, Mek 2, MKK3/6, MKK4/7, ASKl,Cot, NIK, Bub, Myt 1, Weel, Casein kinases, PDK1, SGK1, SGK2, SGK3, Aktl, Akt2, Akt3, p90Rsks, p70S6Kinase,Prks, PKCs, PKAs, ROCK 1, ROCK 2, Auroras, CaMKs, MNKs, AMPKs, MELK, MARKs, Chkl, Chk2, LKB-1, MAPKAPKs, Piml, Pim2, Pim3, IKKs, Cdks, Jnks, Erks, IKKs, GSK3a, GSK3p, Cdks, CLKs, PKR, PI3- Kinase class 1, class 2, class 3, mTor, SAPK/JNK1,2,3, p38s, PKR, DNA-PK, ATM, ATR, phosphatases, Receptor protein tyrosine phosphatases (RPTPs), LAR phosphatase, CD45, Non receptor tyrosine phosphatases (NPRTPs), SHPs, MAP kinase phosphatases (MKPs), Dual Specificity phosphatases (DUSPs), CDC25 phosphatases, Low molecular weight tyrosine phosphatase, Eyes absent (EYA) tyrosine phosphatases, Slingshot phosphatases (SSH), serine phosphatases, PP2A, PP2B, PP2C, PP1, PPS, inositol phosphatases, PTEN, SHIPs, myotubularins, lipid signaling, phosphoinositide kinases, phopsho lipases, prostaglandin synthases, 5 -lipoxygenase, sphingosine kinases, sphingomyelinases, adaptor/scaffold proteins, She, Grb2, BLNK, LAT, B cell adaptor for PI3-kinase (BCAP), SLAP, Dok, KSR, MyD88, Crk, CrkL, GAD, Nek, Grb2 associated binder (GAB), Fas associated death domain (FADD), TRADD, TRAF2, RIP, T-Cell leukemia family, cytokines, IL-2, IL-4, IL-8, IL-6, interferon , interferon a, cytokine regulators, suppressors of cytokine signaling (SOCs), ubiquitination enzymes, Cbl, SCF ubiquitination ligase complex, APC/C, adhesion molecules, integrins, Immunoglobulin- like adhesion molecules, selectins, cadherins, catenins, focal adhesion kinase, pl30CAS, cytoskeletal/contractile proteins, fodrin, actin, paxillin, myosin, myosin binding proteins, tubulin, eg5/KSP, CENPs, heterotrimeric G proteins, β-adrenergic receptors, muscarinic receptors, adenylyl cyclase receptors, small molecular weight GTPases, H-Ras, K- Ras, N-Ras, Ran, Rac, Rho, Cdc42, Arfs, RABs, RHEB, guanine nucleotide exchange factors, Vav, Tiam, Sos, Dbl, PRK, TSC1,2, GTPase activating proteins, Ras-GAP, Arf-GAPs, Rho-GAPs, caspases, Caspase 2, Caspase 3, Caspase 6, Caspase 7, Caspase 8, Caspase 9, proteins involved in apoptosis, Bcl-2, Mcl-1, Bcl-XL, Bcl-w, Bcl-B, Al, Bax, Bak, Bok, Bik, Bad, Bid, Bim, Bmf, Hrk, Noxa, Puma, IAPs, XIAP, Smac, cell cycle regulators, Cdk4, Cdk 6, Cdk 2, Cdkl, Cdk 7, Cyclin D, Cyclin E, Cyclin A, Cyclin B, Rb, pi 6, pl4Arf, p27KIP, p21CIP, molecular chaperones, Hsp90s, Hsp70, Hsp27, metabolic enzymes, Acetyl-CoAa Carboxylase, ATP citrate lyase, nitric oxide synthase, vesicular transport proteins, caveolins, endosomal sorting complex required for transport (ESCRT) Atty Dkt o. 33118-747601 proteins, vesicular protein sorting (Vsps), hydroxylases, prolyl- hydroxylases PHD-1, 2 and 3, asparagine hydroxylase FIH transferases, isomerases, Pinl prolyl isomerase, topoisomerases, deacetylases, Histone deacetylases, sirtuins, acetylases, histone acetylases, CBP/P300 family, MYST family, ATF2, methylases, DNA methyl transferases, demethylases, Histone H3K4 demethylases, H3K27, JHDM2A, UTX, tumor suppressor genes, VHL, WT-1, p53, Hdm, PTEN, proteases, ubiquitin proteases, urokinase-type plasminogen activator (uPA) and uPA receptor (uPAR) system, cathepsins, metalloproteinases, esterases, hydrolases, separase, ion channels, potassium channels, sodium channels, molecular transporters, multi-drug resistance proteins, P- Gycoprotein, nucleoside transporters, transcription factors/ DNA binding proteins, Ets family transcription factors, Ets-1, Ets-2, Tel, Tel2, Elk, SMADs, Rel-A (p65-NFKB), CREB, NFAT, ATF-2, AFT, Myc, Fos, Spl, Egr-1, T-bet, β-catenin, HIFs, FOXOs, E2Fs, SRFs, TCFs, Egr-1, β-FOXO STAT1, STAT 3, STAT 4, STAT 5, STAT 6, p53, WT-1, HMGA, regulators of translation, pS6, 4EPB-1, eIF4E-binding protein, regulators of transcription, RNA polymerase, initiation factors, elongation factors. In some embodiments, the protein is S6.

[00125] In some embodiments, an epitope-recognizing fragment of an activation state antibody rather than the whole antibody is used. In some embodiments, the epitope- recognizing fragment is immobilized. In some embodiments, the antibody light chain that recognizes an epitope is used. A recombinant nucleic acid encoding a light chain gene product that recognizes an epitope can be used to produce such an antibody fragment by recombinant means well known in the art.

[00126] In alternative embodiments, aromatic amino acids of protein binding elements can be replaced with other molecules. See U.S. S. Nos. 61/048,886; 61/048,920 and

61/048,657.

[00127] In some embodiments, the activation state-specific binding element is a peptide comprising a recognition structure that binds to a target structure on an activatable protein. A variety of recognition structures are well known in the art and can be made using methods known in the art, including by phage display libraries (see e.g., Gururaja et al. Chem. Biol. (2000) 7:515-27; Houimel et al, Eur. J. Immunol. (2001) 31 :3535-45; Cochran et al. J. Am. Chem. Soc. (2001) 123:625-32; Houimel et al. Int. J. Cancer (2001) 92:748-55, each incorporated herein by reference). Further, fluorophores can be attached to such antibodies for use in the methods described herein. Atty Dkt o. 33118-747601

[00128] A variety of recognitions structures are known in the art (e.g., Cochran et al, J.

Am. Chem. Soc. (2001) 123:625-32; Boer et al, Blood (2002) 100:467-73, each expressly incorporated herein by reference)) and can be produced using methods known in the art (see e.g., Boer et al, Blood (2002) 100:467-73; Gualillo et al, Mol. Cell Endocrinol. (2002) 190:83-9, each expressly incorporated herein by reference)), including for example combinatorial chemistry methods for producing recognition structures such as polymers with affinity for a target structure on an activatable protein (see e.g., Barn et al, J. Comb. Chem. (2001) 3:534-41; Ju et al, Biotechnol. (1999) 64:232-9, each expressly incorporated herein by reference). In another embodiment, the activation state-specific antibody is a protein that only binds to an isoform of a specific activatable protein that is phosphorylated and does not bind to the isoform of this activatable protein when it is not phosphorylated or nonphosphorylated. In another embodiment the activation state-specific antibody is a protein that only binds to an isoform of an activatable protein that is intracellular and not extracellular, or vice versa. In some embodiments, the recognition structure is an anti-laminin single-chain antibody fragment (scFv) (see e.g., Sanz et al, Gene Therapy (2002) 9: 1049-53; Tse et al, J. Mol. Biol. (2002) 317:85-94, each expressly incorporated herein by reference).

[00129] In some embodiments the binding element is a nucleic acid. The term "nucleic acid" include nucleic acid analogs, for example, phosphoramide (Beaucage et al, Tetrahedron 49(10): 1925 (1993) and references therein; Letsinger, J. Org. Chem.

35:3800 (1970); Sprinzl et al, Eur. J. Biochem. 81 :579 (1977); Letsinger et al, Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem. Lett. 805 (1984), Letsinger et al, J. Am. Chem. Soc. 110:4470 (1988); and Pauwels et al, Chemica Scripta 26: 141 91986)), phosphorothioate (Mag et al, Nucleic Acids Res. 19: 1437 (1991); and U.S. Pat. No. 5,644,048), phosphorodithioate (Briu et al, J. Am. Chem. Soc. 111 :2321 (1989), O- methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press), and peptide nucleic acid backbones and linkages (see Egholm, J. Am. Chem. Soc. 114: 1895 (1992); Meier et al, Chem. Int. Ed. Engl. 31 : 1008 (1992); Nielsen, Nature, 365:566 (1993); Carlsson et al, Nature 380:207 (1996), all of which are incorporated by reference). Other analog nucleic acids include those with positive backbones (Denpcy et al, Proc. Natl. Acad. Sci. USA 92:6097 (1995); non-ionic backbones (U.S. Pat. Nos. 5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al, Angew. Chem. Intl. Ed. English 30:423 (1991);

Letsinger et al, J. Am. Chem. Soc. 110:4470 (1988); Letsinger et al, Nucleoside & Atty Dkt o. 33118-747601

Nucleotide 13: 1597 (1994); Chapters 2 and 3, ASC Symposium Series 580, "Carbohydrate Modifications in Antisense Research", Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker et al, Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffs et al, J. Biomolecular NMR 34: 17 (1994); Tetrahedron Lett. 37:743 (1996)) and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, "Carbohydrate Modifications in Antisense Research", Ed. Y. S. Sanghui and P. Dan Cook. Nucleic acids containing one or more carbocyclic sugars are also included within the definition of nucleic acids (see Jenkins et al, Chem. Soc. Rev. (1995) ppl69- 176). Several nucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997 page 35. All of these references are hereby expressly incorporated by reference. These modifications of the ribose-phosphate backbone may be done to facilitate the addition of additional moieties such as labels, or to increase the stability and half-life of such molecules in physiological environments.

[00130] In some embodiment the binding element is a small organic compound. Binding elements can be synthesized from a series of substrates that can be chemically modified. "Chemically modified" herein includes traditional chemical reactions as well as enzymatic reactions. These substrates generally include, but are not limited to, alkyl groups (including alkanes, alkenes, alkynes and heteroalkyl), aryl groups (including arenes and heteroaryl), alcohols, ethers, amines, aldehydes, ketones, acids, esters, amides, cyclic compounds, heterocyclic compounds (including purines, pyrimidines, benzodiazepins, beta-lactams, tetracylines, cephalosporins, and carbohydrates), steroids (including estrogens, androgens, cortisone, ecodysone, etc.), alkaloids (including ergots, vinca, curare, pyrollizdine, and mitomycines), organometallic compounds, hetero-atom bearing compounds, amino acids, and nucleosides. Chemical (including enzymatic) reactions may be done on the moieties to form new substrates or binding elements that can then be used.

[00131] In some embodiments the binding element is a carbohydrate. As used herein the term carbohydrate can include any compound with the general formula (CH20)n.

Examples of carbohydrates are mono-, di-, tri- and oligosaccharides, as well polysaccharides such as glycogen, cellulose, and starches.

[00132] In some embodiments the binding element is a lipid. As used herein the term

lipid herein can include any water insoluble organic molecule that is soluble in nonpolar organic solvents. Examples of lipids are steroids, such as cholesterol, and phospholipids such as sphingomeylin, and fatty acyls, glycero lipids, glycerophospho lipids, Atty Dkt o. 33118-747601 sphingo lipids, saccharolipids, and polyketides, including tri-, di- and monoglycerides and phospholipids. The lipid can be a hydrophobic molecule or amphiphilic molecule.

[00133] Examples of activatable elements, activation states and methods of determining the activation level of activatable elements are described in US publication number 20060073474 entitled "Methods and compositions for detecting the activation state of multiple proteins in single cells" and US publication number 20050112700 entitled "Methods and compositions for risk stratification" the content of which are incorporate here by reference.

DNA Damage and Apoptosis

[00134] The response to DNA damage is a protective measure taken by cells to prevent or delay genetic instability and tumorigenesis. It allows cells to undergo cell cycle arrest and gives them an opportunity to either: repair the broken DNA and resume passage through the cell cycle or, if the breakage is irreparable, trigger senescence or an apoptotic program leading to cell death (Wade Harper et al, Molecular Cell, (2007) 28 p739 - 745, Bartek J et al, Oncogene (2007)26 p7773-9). See also Reed J. "Apoptosis and Cancer". Cancer Medicine. 7th edition. Holland, Frei, Kufe DW, Pollock RE, Weichselbaum RR, et al, editors; Hamilton (ON): BC Decker; 2006; and Danial NN. "BCL-2 Family Proteins: Critical Checkpoints of Apoptotic Cell Death" Clinical Cancer Research. 2007; 13 (24). 7254.

[00135] Several protein complexes are positioned at strategic points within the DNA

damage response pathway and act as sensors, transducers or effectors of DNA damage. Depending on the nature of DNA damage for example; double stranded breaks, single strand breaks, single base alterations due to alkylation, oxidation etc, there is an assembly of specific DNA damage sensor protein complexes in which activated ataxia telangiectasia mutated (ATM) and ATM- and Rad3 related (ATR) kinases phosphorylate and subsequently activate the checkpoint kinases Chkl and Chk2. Both of these DNA- signal transducer kinases amplify the damage response by phosphorylating a multitude of substrates. Both checkpoint kinases have overlapping and distinct roles in orchestrating the cell's response to DNA damage.

[00136] Maximal kinase activation of Chk2 involves phosphorylation and homo- dimerization with ATM-mediated phosphorylation of T68 on Chk2 as a preliminary event. This in turn activates DNA repair. As mentioned above, in order for DNA repair to proceed, there must be a delay in the cell cycle. Chk2 seems to have a role at the Gl/S and G2/M junctures and may have overlapping functions with Chkl . There are multiple Atty Dkt o. 33118-747601

ways in which Chkl and Chk2 mediate cell cycle suspension. In one mechanism Chk2 phosphorylates the CDC25A and CDC25C phosphatases resulting in their removal from the nucleus either by proteosomal degradation or by sequestration in the cytoplasm by 14-3-3. These phosphatases are no longer able to act on their nuclear CDK substrates. If DNA repair is successful, cell cycle progression is resumed (Antoni et al, Nature reviews cancer (2007) 7, p925-936).

[00137] When DNA repair is no longer possible the cell undergoes apoptosis with

participation from Chk2 in p53 independent and dependent pathways. Chk2 substrates that operate in a p53 -independent manner include the E2F1 transcription factor, the tumor suppressor promyelocytic leukemia (PML) and the polo-like kinases 1 and 3 (PLK1 and PLK3). E2F1 drives the expression of a number of apoptotic genes including caspases 3, 7, 8 and 9 as well as the pro-apoptotic Bcl-2 related proteins (e.g., Bim, Noxa, PUMA).

[00138] In its response to DNA damage, p53 activates the transcription of a program of genes that regulate DNA repair, cell cycle arrest, senescence and apoptosis. The overall functions of p53 are to preserve fidelity in DNA replication such that when cell division occurs, tumorigenic potential can be avoided. In such a role, p53 is described as "The Guardian of the Genome" (Riley et al, Nature Reviews Molecular Cell Biology (2008) 9 pp. 402-412). The diverse alarm signals that impinge on p53 result in a rapid increase in its levels through a variety of post translational modifications. Worthy of mention is the phosphorylation of amino acid residues within the amino terminal portion of p53 such that p53 is no longer under the regulation of Mdm2. The responsible kinases are ATM, Chkl, and Chk2. The subsequent stabilization of p53 permits it to transcriptionally regulate multiple pro-apoptotic members of the Bcl-2 family, including Bax, Bid, Puma, and Noxa (discussion below).

[00139] The series of events that are mediated by p53 to promote apoptosis, including DNA damage, anoxia and imbalances in growth-promoting signals, are sometimes termed the 'intrinsic apoptotic" program since the signals triggering it originate within the cell. An alternate route of activating the apoptotic pathway can occur from the outside of the cell mediated by the binding of ligands to transmembrane death receptors. This extrinsic or receptor mediated apoptotic program acting through their receptor death domains eventually converges on the intrinsic, mitochondrial apoptotic pathway as discussed below (Sprick et al, Biochim Biophys Acta. (2004) 1644 pi 25-32).

[00140] Regulators of apoptosis include proteins of the Bcl-2 family. The founding

member, the Bcl-2 proto-oncogene, was first identified at the chromosomal breakpoint of Atty Dkt o. 33118-747601

t(14: 18) bearing human follicular B cell lymphoma. Expression of Bcl-2 can block rather than promote cell death following multiple pathological and physiological stimuli (Danial and Korsemeyer, Cell (2004) 116, p205-219). The Bcl-2 family has members which can be regulators of apoptosis, functioning to control mitochondrial permeability as well as the release of proteins that play a role in the apoptotic program. The ratio of anti- to pro- apoptotic molecules such as Bcl-2/Bax constitutes a rheostat that can set the threshold of susceptibility to apoptosis for the intrinsic pathway, which utilizes organelles such as the mitochondrion to amplify death signals. The family can be divided into 3 subclasses based on structure and impact on apoptosis. Family members of subclass 1 (Bcl-2) including Bcl-2, Bcl-w, BC1-X _L , Mcl-1 and Al are characterized by the presence of 4 Bcl-

2 homology domains (BH1, BH2, BH3 and BH4) and can be anti-apoptotic. The structure of the second subclass members (Bax) is marked for containing 3 BH domains and family members, such as Bax, Bak and Bok, possess pro-apoptotic activities. The third subclass, termed the BH3-only proteins include Noxa, Puma, Bid, Bad, Blk, Hrk, BNIP3 and BimL. They can function to promote apoptosis either by activating the pro- apoptotic members of group 2 or by inhibiting the anti-apoptotic members of subclass 1 (Er et al, Biochimica et Biophysica Act (2006) 1757, pl301-1311, Fernandez-Luna Cellular Signaling (2008) Advance Publication Online; and Adams and Cory, 1998, Science, 281 : 1322-1326; Brown, 1997, Brit. Med. Bullet., 53(3): 466-477.).

[00141] The role of mitochondria in the apoptotic process can involve an apoptotic

stimulus resulting in depolarization of the outer mitochondrial membrane leading to a leak of cytochrome C into the cytoplasm. Association of Cytoplasmic cytochrome C molecules with adaptor apoptotic protease activating factor (APAF) forms a structure called the apoptosome which can activate enzymatically latent procaspase 9 into a cleaved activated form. Caspase 9 is one member of a family of cysteine aspartyl- specific proteases; genes encoding 11 of these proteases have been mapped in the human genome. Activated caspase 9, classified as an intiator caspase, can then cleave procaspase

3 which cleaves more downstream procaspases, classified as executioner caspases, which canresult in an amplification cascade that can promote cleavage of death substrates including poly(ADP-ribose) polymerase 1 (PARP). The cleavage of PARP produces 2 fragments both of which have a role in apoptosis (Soldani and Scovassi Apoptosis (2002) 7, p321). A further level of apoptotic regulation is provided by smac/Diablo, a mitochondrial protein that inactivates a group of anti-apoptotic proteins termed inhibitors of apoptosis (IAPs) (Huang et al, Cancer Cell (2004) 5 pi -2). IAPs operate to block Atty Dkt o. 33118-747601 caspase activity in 2 ways; they can bind directly to and inhibit caspase activity and in certain cases they can mark caspases for ubiquitination and degradation.

[00142] Members of the caspase gene family (cysteine proteases with aspartate

specificity) can play roles in both inflammation and apoptosis. Caspases can exhibit catalytic and substrate recognition motifs that have been highly conserved. These characteristic amino acid sequences allow caspases to interact with both positive and negative regulators of their activity. The substrate preferences or specificities of individual caspases have been exploited for the development of peptides that successfully compete for caspase binding. In addition to their distinctive aspartate cleavage sites at the PI position, the catalytic domains of the caspases can require at least four amino acids to the left of the cleavage site with P4 as the prominent specificity-determining residue. WEHD, VDVAD, and DEVD are examples of peptides that can preferentially bind caspase- 1, caspase-2 and caspase-3, respectively. It is possible to generate reversible or irreversible inhibitors of caspase activation by coupling caspase-specific peptides to certain aldehyde, nitrile or ketone compounds. These caspase inhibitors can inhibit the induction of apoptosis in various tumor cell lines as well as normal cells. Fluoromethyl ketone (FMK)-derivatized peptides act as effective irreversible inhibitors with no added cytotoxic effects. Inhibitors synthesized with a benzyloxycarbonyl group (also known as BOC or Z) at the N-terminus and O-methyl side chains can exhibit enhanced cellular permeability thus facilitating their use in both in vitro cell culture as well as in vivo animal studies. Benzyloxycarbonyl-Val-Ala-Asp (OMe)

fluoromethylketone (ZVAD) is a caspase inhibitor. See Misaghi, et al, z-VAD-fmk inhibits peptide :N-glycanase and may result in ER stress Cell Death and Differentiation (2006) 13, 163-165.

[00143] The balance of pro- and anti-apoptotic proteins is tightly regulated under normal physiological conditions. Tipping of this balance either way can result in disease. An oncogenic outcome can result from the inability of tumor cells to undergo apoptosis and this can be caused by over-expression of anti-apoptotic proteins or reduced expression or activity of pro-apoptotic protein.

[00144] In some embodiments, the status or activation level of an activatable element within an apoptosis pathway in response to a modulator that slows or stops the growth of cells and/or induces apoptosis of cells is determined. In some embodiments, the activatable element within the apoptosis pathway is selected from the group consisting of Cleaved PARP+, Cleaved Caspase 3, Cleaved Caspase 8, and Cytoplasmic Cytochrome Atty Dkt o. 33118-747601

C, and the modulator that slows or stops the growth of cells and/or induces apoptosis of cells is a chemotherapeutic, such as one selected from the group consisting of Staurosporine, Etoposide, Mylotarg, Vidaza, Dacogen, Clofarabine, (Gemtuzumab Ozogamicin, or GO), Fludarabine, Bendamustine, PARP inhibitors, Temozolomide, Cisplatin, Carboplatin, Daunorubicin, and AraC.

[00145] In some embodiments, the status of an activatable element within a DNA damage pathway in response to a modulator that slows or stops the growth of cells and/or induces apoptosis of cells is determined. In some embodiments, the activatable element within a DNA damage pathway is selected from the group consisting of DNA-PK, 53BP1, p53, BRCAl, RPA-2(RPA-32), Chkl, Chk2, ATM, and ATR and the modulator that slows or stops the growth of cells and/or induces apoptosis of cells is selected from the group consisting of Staurosporine, Etoposide, Mylotarg (GO), Vidaza, Dacogen, Clofarabine, Fludarabine, Bendamustine, PARP inhibitors, Temozolomide, Cisplatin, Carboplatin, Daunorubicin, and AraC.

[00146] In some embodiments, interrogation of the apoptotic machinery will also be

performed by etoposide with or without ZVAD, an inhibitor of caspases, or a combination of Cytarabine and Daunorubicin at clinically relevant concentrations based on peak plasma drug levels. The standard dose of Cytarabine, 100 mg/m2, yields a peak plasma concentration of approximately 40 nM, whereas high dose Cytarabine, 3 g/m2, yields a peak plasma concentration of 2 uM. Daunorubicin at 25 mg/m2 yields a peak plasma concentration of 50 ng/ml and at 50 mg/m2 yields a peak plasma concentration of 200 ng/ml. An in vitro apoptosis assay will use concentrations of Cytarabine up to 2 uM, and concentrations of Daunorubicin up to 200 ng/ml.

[00147] PARP (Poly-ADP-Ribose-Polymerase) is a DNA polymerase associated with DNA damage repair. When a cell undergoes apoptosis, a caspase cleaves PARP and deactivates its DNA damage repair function. Without DNA damage repair, cells cannot fix DNA damage caused by other apoptotic pathways. The deactivation of PARP facilitates cell death. Cleaved PARP is therefore an indicator for apoptosis. Detecting cleaved PARP with anti-cleaved PARP antibody after induction/stimulation (with an apoptosis inducing agent) can allow measurement of apoptosis caused by therapeutic treatments.

[00148] PARP is composed of four domains: a DNA-binding domain, a caspase-cleaved domain domain, an auto -modification domain, and a catalytic domain. The DNA-binding domain is composed of two zinc finger motifs. In the presence of damaged DNA (base Atty Dkt o. 33118-747601

pair-excised), the DNA-binding domain can bind DNA and induce a conformational shift. This binding can occur independent of the other domains. This is integral in a programmed cell death model based on Caspase cleavage inhibition of PARP. The auto- modification domain is responsible for releasing the protein from the DNA after catalysis. Also, it plays a role in cleavage-induced inactivation.

[00149] PARP is found in the cell's nucleus, and a role for PARP is to detect and signal single strand DNA breaks (SSB) to the enzymatic machinery involved in the SSB repair. PARP activation can be an immediate cellular response to metabolic, chemical, or radiation-induced DNA SSB damage. Once PARP detects a SSB it can bind to the DNA, and, after a structural change, PARP can begin the synthesis of a poly(ADP-ribose)chain (PAR) as a signal for the other DNA repairing enzymes such as DNA ligase III (Liglll), DNA polymerase beta (ροΐβ) and scaffolding proteins such as x-ray repair

complementing gene 1 (XRCCl). After repair, the PAR chains can be degraded via PAR glyco hydrolase (PARG). Interestingly, NAD+ is can be used as substrate for generating ADP-ribose monomers. The overactivation of PARP may deplete the stores of cellular NAD+ and induce a progressive ATP depletion, resulting in inhibited glucose oxidation and necrotic cell death. In this regard, PARP is inactivated by caspase-3 cleavage (in a specific domain of the enzyme) during programmed cell death. PARP enzymes are essential in a number of cellular functions, including expression of inflammatory genes: PARPl plays a role inthe induction of ICAM-1 gene expression by smooth muscle cells, in response to TNF.

[00150] BC1-X _L is a transmembrane molecule in the mitochondria. It is involved in the signal transduction pathway of the FAS-L. It is one of several anti-apoptotic proteins which are members of the Bcl-2 family of proteins. It has been implicated in the survival of cancer cells. "BC1-X _L " stands for "B-cell lymphoma-extra large". Other Bcl-2 proteins include Bcl-2, Bcl-w, Bcl-xs, and MCL-1. BC1-X _L is the dominant regulator of apoptosis, or active cell suicide. It is known as the survival protein because the long form of BC1-X _L has cell death repressor activity. Bak accelerates programmed cell death by binding to and antagonizing the repressor Bcl-2. It is a membrane-bound protein found mainly in the heart and skeletal muscle. BC1-X _L is 181 amino acid residues long. It consists of 10 alpha helices, 2 of which are 310 alpha helices. The Bak peptide is 16 residues long and is as follows: Gly-Gln-Val-Gly-Arg-Gln-Leu-Ala-Ile-Ile-Gly-Asp-Asp-Ile-Asn- Arg.

[00151] Bcl-2 (B-cell lymphoma 2) is the founding member of the Bcl-2 family of

apoptosis regulator proteins encoded by the BCL2 gene. Bcl-2 derives its name from B- Atty Dkt o. 33118-747601 cell lymphoma 2, as it is the second member of a range of proteins initially described in chromosomal translocations involving chromosomes 14 and 18 in follicular lymphomas. Bcl-2 orthologs have been identified in numerous mammals for which complete genome data are available. Bcl-2 has been shown to interact with RAD9A, BAK1, Reticulon 4, Bcl-2-associated X protein, Caspase 8, BECN1, SOD1, Bcl-2-interacting killer, BH3 interacting domain death agonist, RRAS, C-Raf, BCL2L11, BNIPL, HRK, PSEN1, BMF, BNIP2, BNIP3, Nerve Growth factor IB, BCL2-like 1, Myc, BCAP31, SMN1, CAPN2, PPP2CA, Noxa, Cdkl, TP53BP2, Bcl-2-associated death promoter and IRS1.

[00152] APO-1 (Fas/CD95), a member of the tumor necrosis factor receptor superfamily, induces apoptosis upon receptor oligomerization. See F. C. Kischkel, et. al, EMBO J. 1995 November 15; 14(22): 5579-5588. The Apo-l/Fas (CD95) antigen is known to be involved in the process of T cell-mediated target cell killing and has recently been shown to be expressed on myeloma cell lines and native malignant plasma cells. Several cytokines have been reported to interfere with spontaneous and even Apo-l/Fas-induced apoptosis. See A. Egle, Eur. Jour. Imm. Vol 26, Issue 12, 3119-3126, Dec. 1996.

[00153] Apoptosis inducing factor (AIF) is involved in initiating a caspase-independent pathway of apoptosis (positive intrinsic regulator of apoptosis) by causing DNA fragmentation and chromatin condensation. It can also act as an NADH oxidase. Another AIF function is to regulate the permeability of the mitochondrial membrane upon apoptosis. Normally it is found behind the outer membrane of the mitochondria and is therefore secluded from the nucleus. However, when the mitochondria is damaged, it moves to the cytosol and to the nucleus. Inactivation of AIF can lead to resistance of embryonic stem cells to death following the withdrawal of growth factors indicating that it can be involved in apoptosis. Ye H, (September 2002). Nat. Struct. Biol. 9 (9): 680-4.

[00154] The mitochondrial AIF protein was found to be a capasase-independent death effector that can allow independent nuclei to undergo apoptotic changes. The process triggering apoptosis starts when the mitochondria releases AIF, which exits through the mitochondrial membrane, enters the cytosol, and finally ends up in the cell nucleus where it signals the cell to condense its chromosomes and fragment its DNA molecules in order to prepare for cell death. AIF activity can be dependent upon the type of cell, the apoptotic insult, and its DNA binding ability. AIF also can play a role in the mitochondrial respiratory chain as well as in metabolic redox reactions. Hangen E, (May 2010). Trends Biochem. Sci. 35 (5): 278-87. Atty Dkt o. 33118-747601

[00155] MCL-1 is a member of the Bcl-2 family. The gene for MCL-1 (Myeloid Cell Leukemia Sequence) is publically known and shown at

http://www.ncbi.nlm.mh.gov/gene/4170. The gene encodes an anti-apoptotic protein.

[00156] MCL-1 is also known as TM; EAT; MCL1L; MCL1S; Mcl-1 ; BCL2L3; MCL1- ES; MGC1839; bcl2-L-3; mcll/EAT; or MGC104264. MCLl has been shown to interact with BAK1, Noxa, BCL2L11, Bcl-2-associated death promoter, PCNA, DAD1, TNKS and BH3 interacting domain death agonist. MCL-1 is a pro-survival member of the Bcl-2 family. Normally, MCL-1 functions to block oligomerization or activation of pro- apoptotic Bak and Bax proteins. During apoptosis, MCL-1 is inhibited and degraded, leading to Bax/Bak pore formation and permeabilization of the mitochondrial membrane and apoptosome/caspase activation. Thus, MCL-1 represents an upstream indicator of apoptosis before the majority of caspase activation, i.e. PARP cleavage.

[00157] Antibodies directed to an activatable element that can be a cell health marker (anti-cleaved PARP antibody for example) can identify cells undergoing apoptosis.

Antibodies are commercially available from sources such as Becton Dickinson (San Jose, CA), Cell Signaling Technology (Danvers, MA), and Beckman Coulter (Brea, CA) among others. In one embodiment of the methods described herein, a cleaved PARP or MCL-1 antibody is used in combination with phospho-specific and cell lineage specific antibodies to allow for the identification and exclusion of apoptotic cells from the analysis of single cell network profiling assays. As apoptotic cells can have reduced responsiveness and/or different basal levels of phosphorylated signaling proteins, excluding cleaved PARP positive cells "in silico" can result in improvements in signal- to-noise for measuring evoked or inhibited signaling to exogenous modulators. This method can be used to assess the general quality of the cells after removal from the body, such as after sample shipment or after cryogenic storage, or in response to apoptosis inducing agents.

Modulators

[00158] In some embodiments, the methods and composition utilize a modulator. A

modulator can be an activator, a therapeutic compound, an inhibitor or a compound capable of impacting a cellular pathway. Modulators can also take the form of environmental cues and inputs.

[00159] Modulation can be performed in a variety of environments. In some

embodiments, cells are exposed to a modulator immediately after collection. In some embodiments where there is a mixed population of cells, purification of cells is Atty Dkt o. 33118-747601 performed after modulation. In some embodiments, whole blood is collected to which a modulator is added. In some embodiments, cells are modulated after processing for single cells or purified fractions of single cells. As an illustrative example, whole blood can be collected and processed for an enriched fraction of lymphocytes that is then exposed to a modulator. Modulation can include exposing cells to more than one modulator. For instance, in some embodiments, a sample of cells is exposed to at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more modulators. See U.S. Patent Applications 12/432,239 and 12/910,769 which are incorporated by reference in their entireties. See also U.S. Patent Nos. 7,695,926 and 7,381,535 and U.S. Pub. No. 2009/0269773.

[00160] In some embodiments, cells are cultured post collection in a suitable media before exposure to a modulator. In some embodiments, the media is a growth media. In some embodiments, the growth media is a complex media that may include serum. In some embodiments, the growth media comprises serum. In some embodiments, the serum is selected from the group consisting of fetal bovine serum, bovine serum, human serum, porcine serum, horse serum, and goat serum. In some embodiments, the serum level ranges from 0.0001% to 30 %, about 0.001% to 30%, about 0.01% to 30%, about 0.1% to 30% or 1% to 30%. In some embodiments, the growth media is a chemically defined minimal media and is without serum. In some embodiments, cells are cultured in a differentiating media.

[00161] Modulators include chemical and biological entities, and physical or

environmental stimuli. Modulators can act extracellularly or intracellularly. Chemical and biological modulators include growth factors, mitogens, cytokines, drugs, immune modulators, ions, neurotransmitters, adhesion molecules, hormones, small molecules, inorganic compounds, polynucleotides, antibodies, natural compounds, lectins, lactones, chemotherapeutic agents, biological response modifiers, carbohydrate, proteases and free radicals. Modulators include complex and undefined biologic compositions that may comprise cellular or botanical extracts, cellular or glandular secretions, physiologic fluids such as serum, amniotic fluid, or venom. Physical and environmental stimuli include electromagnetic, ultraviolet, infrared or particulate radiation, redox potential and pH, the presence or absences of nutrients, changes in temperature, changes in oxygen partial pressure, changes in ion concentrations and the application of oxidative stress. Modulators can be endogenous or exogenous and may produce different effects depending on the concentration and duration of exposure to the single cells or whether they are used in combination or sequentially with other modulators. Modulators can act Atty Dkt o. 33118-747601 directly on the activatable elements or indirectly through the interaction with one or more intermediary biomolecule. Indirect modulation includes alterations of gene expression wherein the expressed gene product is the activatable element or is a modulator of the activatable element. A modulator can include, e.g., a psychological stressor.

[00162] In some embodiments the modulator is selected from the group consisting of growth factors, mitogens, cytokines, adhesion molecules, drugs, hormones, small molecules, polynucleotides, antibodies, natural compounds, lactones, chemotherapeutic agents, immune modulators, carbohydrates, proteases, ions, reactive oxygen species, peptides, and protein fragments, either alone or in the context of cells, cells themselves, viruses, and biological and non-biological complexes (e.g., beads, plates, viral envelopes, antigen presentation molecules such as major histocompatibility complex). In some embodiments, the modulator is a physical stimuli such as heat, cold, UV radiation, and radiation. Examples of modulators include but are not limited to SDF-Ι , IFN-a, IFN-γ, IL-10, IL-6, IL-27, G-CSF, FLT-3L, IGF-1, M-CSF, SCF, PMA, Thapsigargin, H ₂ 0 ₂ , Etoposide, Mylotarg, AraC, daunorubicin, staurosporine, benzyloxycarbonyl-Val- Ala- Asp (OMe) fluoromethylketone (ZVAD), lenalidomide, EPO, azacitadine, decitabine, IL- 3, IL-4, GM-CSF, EPO, LPS, TNF-a, and CD40L. Below are descriptions of some examples of modulators.

[00163] In one embodiment, the modulator is etoposide phosphate. Etoposide phosphate (brand names: Eposin, Etopophos, Vepesid, VP- 16) can inhibit enzyme topoisomerase II. Etoposide phosphate is a semisynthetic derivative of podophyllotoxin, a substance extracted from the mandrake root Podophyllum peltatum. Etoposide can possess antineoplastic properties. Etoposide can bind to and inhibit topoisomerase II and its function in ligating cleaved DNA molecules, resulting in the accumulation of single- or double-strand DNA breaks, the inhibition of DNA replication and transcription, and apoptotic cell death. Etoposide can act primarily in the G2 and S phases of the cell cycle. See the NCI Drug Dictionary at

http ://www. cancer . go v/Templates/drugdictionary. aspx?CdrID=39207.

[00164] In one embodiment, the modulator is Mylotarg. Mylotarg® (gemtuzumab

ozogamicin for Injection) is a chemotherapy agent composed of a recombinant humanized IgG4, kappa antibody conjugated with a cytotoxic antitumor antibiotic, calicheamicin, isolated from fermentation of a bacterium, Micromonospora echinospora subsp. calichensis. The antibody portion of Mylotarg can bind specifically to the CD33 antigen, a sialic acid-dependent adhesion protein found on the surface of leukemic blasts Atty Dkt o. 33118-747601 and immature normal cells of myelomonocytic lineage, but not on normal hematopoietic stem cells. See U.S. Patent Nos. 7,727,968, 5,773,001, and 5,714,586.

[00165] In one embodiment, the modulator is staurosporine. Staurosporine (antibiotic AM-2282 or STS) is a natural product originally isolated in 1977 from bacterium

Streptomyces staurosporeus. Staurosporine can have biological activities ranging from anti-fungal to anti-hypertensive. See e.g.,Ruegg UT, Burgess GM. (1989) Staurosporine, K-252 and UCN-01 : potent but nonspecific inhibitors of protein kinases. Trends in Pharmacological Science 10 (6): 218-220. Staruosporine can be an anticancer treatment. Staurosporine can inhibit protein kinases through the prevention of ATP binding to the kinase. This inhibition can be achieved because of the higher affinity of staurosporine for the ATP-binding site on the kinase. Staurosporine is a prototypical ATP-competitive kinase inhibitor in that it can bind to many kinases with high affinity, though with little selectivity. Staurosporine can be used to induce apoptosis. One way in which staurosporine can induce apoptosis is by activating caspase-3.

[00166] In another embodiment, the modulator is AraC. Ara-C (cytosine arabinoside or cytarabine) is an antimetabolic agent with the chemical name of 1β- arabinofuranosylcytosine. Its mode of action can be due to its rapid conversion into cytosine arabinoside triphosphate, which damages DNA when the cell cycle holds in the S phase (synthesis of DNA). Rapidly dividing cells, which require DNA replication for mitosis, are therefore affected by treatment with cytosine arabinoside. Cytosine arabinoside can also inhibit both DNA and RNA polymerases and nucleotide reductase enzymes needed for DNA synthesis. Cytarabine can be used in the treatment of acute myeloid leukaemia, acute lymphocytic leukaemia (ALL) and in lymphomas where it is the backbone of induction chemotherapy.

[00167] In another embodiment, the modulator is daunorubicin. Daunorubicin or

daunomycin (daunomycin cerubidine) is a chemotherapeutic of the anthracycline family that can be given as a treatment for some types of cancer. It can be used to treat specific types of leukaemia (acute myeloid leukemia and acute lymphocytic leukemia). It was initially isolated from Streptomyces peucetius. Daunorubicin can also used to treat neuroblastoma. Daunorubicin has been used with other chemotherapy agents to treat the blastic phase of chronic myelogenous leukemia. On binding to DNA, daunomycin can intercalate, with its daunosamine residue directed toward the minor groove. It has the highest preference for two adjacent G/C base pairs fianked on the 5' side by an A/T base Atty Dkt o. 33118-747601 pair. Daunomycin effectively binds to every 3 base pairs and induces a local unwinding angle of 11°, but negligible distortion of helical conformation.

[00168] In some embodiments, the modulator is an activator. In some embodiments the modulator is an inhibitor. In some embodiments, cells are exposed to one or more modulators. In some embodiments, cells are exposed to at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 modulators. In some embodiments, cells are exposed to at least two modulators, wherein one modulator is an activator and one modulator is an inhibitor. In some embodiments, cells are exposed to at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 modulators, where at least one of the modulators is an inhibitor.

[00169] In some embodiments, the inhibitor is an inhibitor of a cellular factor or a

plurality of factors that participates in a cellular pathway (e.g., signaling cascade) in the cell. In some embodiments, the inhibitor is a phosphatase inhibitor. Examples of phosphatase inhibitors include, but are not limited to H2O2, siRNA, miRNA, Cantharidin, (-)-p-Bromotetramisole, Microcystin LR, Sodium Orthovanadate, Sodium Pervanadate, Vanadyl sulfate, Sodium oxodiperoxo( 1,10-phenanthroline)vanadate,

bis(maltolato)oxovanadium(IV), Sodium Molybdate, Sodium Perm olybdate, Sodium Tartrate, Imidazole, Sodium Fluoride, β-Glycerophosphate, Sodium Pyrophosphate Decahydrate, Calyculin A, Discodermia calyx, bpV(phen), mpV(pic), DMHV, Cypermethrin, Dephostatin, Okadaic Acid, NIPP-1, N-(9,10-Dioxo-9,10-dihydro- phenanthren-2-yl)-2,2-dimethyl-propionamide, a-Bromo-4-hydroxyacetophenone, 4- Hydroxyphenacyl Br, a-Bromo-4-methoxyacetophenone, 4-Methoxyphenacyl Br, a- Bromo-4-(carboxymethoxy)acetophenone, 4-(Carboxymethoxy)phenacyl Br, and bis(4- Trifluoromethylsulfonamidophenyl)- 1 ,4-diisopropylbenzene, phenylarsine oxide, Pyrrolidine Dithiocarbamate, and Aluminium fluoride. In some embodiments, the phosphatase inhibitor is H2O2.

[00170] In some embodiments, a phenotypic profile of a population of cells is determined by measuring the activation level of an activatable element when the population of cells is exposed to a plurality of modulators in separate cultures. In some embodiments, the modulators include H ₂ 0 ₂ , PMA, SDFl , CD40L, IGF-1, IL-7, IL-6, IL-10, IL-27, IL-4, IL-2, IL-3, thapsigardin and/or a combination thereof. For instance a population of cells can be exposed to one or more, all or a combination of the following combination of modulators: H ₂ 0 _2; PMA; SDFla; CD40L; IGF-1; IL-7; IL-6; IL-10; IL-27; IL-4; IL-2; IL-3; thapsigardin. In some embodiments, the phenotypic profile of the population of cells is used to classify the population as described herein. Atty Dkt o. 33118-747601

[00171] In some embodiments, the activation level of an activatable element in a cell is determined by contacting the cell with at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 modulators. In some embodiments, the activation level of an activatable element in a cell is determined by contacting the cell with at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 modulators where at least one of the modulators is an inhibitor. In some embodiments, the activation level of an activatable element in a cell is determined by contacting the cell with an inhibitor and a modulator, where the modulator can be an inhibitor or an activator. In some embodiments, the activation level of an activatable element in a cell is determined by contacting the cell with an inhibitor and an activator. In some embodiments, the activation level of an activatable element in a cell is determined by contacting the cell with two or more modulators.

[00172] In some embodiments, the cell signaling profile a population of cells is

determined by measuring the activation level of an activatable element when the population of cells is exposed to one or more modulators. The population of cells can be divided into a plurality of samples, and the physiological status of the population can be determined by measuring the activation level of at least one activatable element in the samples after the samples have been exposed to one or more modulators. In some embodiments, the signaling profile of different populations of cells is determined by measuring the activation level of an activatable element in each population of cells when each of the populations of cells is exposed to a modulator.

Methods

[00173] The methods described herein are suitable for any condition for which a

correlation between the cell signaling profile of a cell and the determination of a disease predisposition, diagnosis, prognosis, and/or course of treatment in samples from individuals may be ascertained. In some embodiments, the methods described herein are directed to methods for analysis, drug screening, diagnosis, prognosis, and for methods of disease treatment and prediction. In some embodiments, the methods described herein comprise methods of analyzing experimental data. In some embodiments, the cell signaling profile of a cell population comprising a genetic alteration is used, e.g., in diagnosis or prognosis of a condition, patient selection for therapy, e.g., using some of the agents identified herein, to monitor treatment, modify therapeutic regimens, and/or to further optimize the selection of therapeutic agents which may be administered as one or a combination of agents. In some embodiments, the cell population is not associated Atty Dkt o. 33118-747601 and/or is not causative of the condition. In some embodiments, the cell population is associated with the condition but it has not yet developed the condition. The cell signaling profile of a cell population can be determined by determining the activation level of at least one activatable element in response to at least one modulator in one or more cells belonging to the cell population. The cell signaling profile of a cell population can be determined by adjusting the profile based on the presence of unhealthy cells in a sample.

[00174] In one embodiment, the methods described herein can be used to prevent disease, e.g., cancer by identifying a predisposition to the disease for which a medical intervention is available. In another embodiment, an individual afflicted with a condition can be treated. In another embodiment, methods are provided for assigning an individual to a risk group. In another embodiment, methods of predicting the increased risk of relapse of a condition are provided. In another embodiment, methods of predicting the risk of developing secondary complications are provided. In another embodiment, methods of choosing a therapy for an individual are provided. In another embodiment, methods of predicting the duration of response to a therapy are provided. In another embodiment, methods are provided for predicting a response to a therapy. In another embodiment, methods are provided for determining the efficacy of a therapy in an individual. In another embodiment, methods are provided for determining the prognosis for an individual.

[00175] The cell signaling profile of a cell population can serve as a prognostic indicator of the course of a condition, e.g. whether a person will develop a certain tumor or other pathologic conditions, whether the course of a neoplastic or a hematopoietic condition in an individual will be aggressive or indolent. The prognostic indicator can aid a healthcare provider, e.g., a clinician, in managing healthcare for the person and in evaluating one or more modalities of treatment that can be used. In another embodiment, the methods provided herein provide information to a healthcare provider, e.g., a physician, to aid in the clinical management of a person so that the information may be translated into action, including treatment, prognosis or prediction.

[00176] In some embodiments, the methods described herein are used to screen candidate compounds useful in the treatment of a condition or to identify new druggable targets.

[00177] In another embodiment, the cell signaling profile of a cell population can be used to confirm or refute a diagnosis of a pre-pathological or pathological condition. Atty Dkt o. 33118-747601

[00178] In instances where an individual has a known pre-patho logic or pathologic

condition, the cell signaling profile of the cell population can be used to predict the response of the individual to available treatment options. In one embodiment, an individual treated with the intent to reduce in number or ablate cells that are causative or associated with a pre-pathological or pathological condition can be monitored to assess the decrease in such cells and the state of a cellular network over time. A reduction in causative or associated cells may or may not be associated with the disappearance or lessening of disease symptoms. If the anticipated decrease in cell number and/or improvement in the state of a cellular network do not occur, further treatment with the same or a different treatment regiment may be warranted.

[00179] In another embodiment, an individual treated to reverse or arrest the progression of a pre-pathological condition can be monitored to assess the reversion rate or percentage of cells arrested at the pre-pathological status point. If the anticipated reversion rate is not seen or cells do not arrest at the desired pre-pathological status point further treatment with the same or a different treatment regime can be considered.

[00180] In a further embodiment, cells of an individual can be analyzed to see if treatment with a differentiating agent has pushed a cell type along a specific tissue lineage and to terminally differentiate with subsequent loss of proliferative or renewal capacity. Such treatment may be used preventively to keep the number of dedifferentiated cells associated with disease at a low level, thereby preventing the development of overt disease. Alternatively, such treatment may be used in regenerative medicine to coax or direct pluripotent or multipotent stem cells down a desired tissue or organ specific lineage and thereby accelerate or improve the healing process.

[00181] Individuals may also be monitored for the appearance or increase in cell number of another cell population(s) that are associated with a good prognosis. If a beneficial population of cells is observed, measures can be taken to further increase their numbers, such as the administration of growth factors. Alternatively, individuals may be monitored for the appearance or increase in cell number of another cells population(s) associated with a poor prognosis. In such a situation, renewed therapy can be considered including continuing, modifying the present therapy or initiating another type of therapy.

Computational Identification of Cell Populations

[00182] In some embodiments, the activation state data of a cell population is determined by contacting the cell population with one or more modulators, generating activation state data for the cell population and using computational techniques to identify one or more Atty Dkt o. 33118-747601 discrete cell populations based on the data. These techniques are implemented using computers comprising memory and hardware. In one embodiment, algorithms for generating metrics based on raw activation state data are stored in the memory of a computer and executed by a processor of a computer. These algorithms are used in conjunction with gating and binning algorithms, which are also stored and executed by a computer, to identify the discrete cell populations.

[00183] The data can be analyzed using various metrics. For example, the median

fluorescence intensity (MFI) is computed for each activatable element from the intensity levels for the cells in the cell population gate. The MFI values are then used to compute a variety of metrics by comparing them to the various baseline or background values, e.g., the unstimulated condition, autofluorescence, and isotype control. The following metrics are examples of metrics that can be used in the methods described herein: 1) a metric that measures the difference in the log of the median fluorescence value between an unstimulated fluorochrome-antibody stained sample and a sample that has not been treated with a stimulant or stained (log (MFIUnstimulated Stained) - log (MFIGated Unstained)), 2) a metric that measures the difference in the log of the median fluorescence value between a stimulated fluorochrome-antibody stained sample and a sample that has not been treated with a stimulant or stained (log (MFI Stimulated Stained) - log(MFIGated Unstained)), 3) a metric that measures the change between the stimulated fluorochrome-antibody stained sample and the unstimulated fluorochrome- antibody stained sample log (MFI Stimulated Stained) - log (MFIUnstimulated Stained), also called "fold change in median fluorescence intensity", 4) a metric that measures the percentage of cells in a Quadrant Gate of a contour plot which measures multiple populations in one or more dimension 5) a metric that measures MFI of phosphor positive population to obtain percentage positivity above the background and 6) use of multimodality and spread metrics for large sample population and for subpopulation analysis.

[00184] In a specific embodiment, the equivalent number of reference fluorophores value (ERF) is generated. The ERF is a transformed value of the median fluorescent intensity values. The ERF value is computed using a calibration line determined by fitting observations of a standardized set of 8-peak rainbow beads for all fluorescent channels to standardized values assigned by the manufacturer. The ERF values for different samples can be combined in any way to generate different activation state metric. Different metrics can include: 1) a fold value based on ERF values for samples that have been Atty Dkt o. 33118-747601

treated with a modulator (ERFm) and samples that have not been treated with a modulator (ERFu), log2 (ERFm/ERFu); 2) a total phospho value based on ERF values for samples that have been treated with a modulator (ERFm) and samples from autofluorecsent wells (ERFa), log2 (ERFm/ERFa); 3) a basal value based on ERF values for samples that have not been treated with a modulator (ERFu) and samples from auto fluorescent wells (ERFa), log2 (ERFu/ERFa); 4) A Mann- Whitney statistic Uu comparing the ERFm and ERFu values that has been scaled down to a unit interval (0,1) allowing inter-sample comparisons; 5) A Mann- Whitney statistic Uu comparing the ERFm and ERFu values that has been scaled down to a unit interval (0,1) allowing inter- sample comparisons; 5) a Mann- Whitney statistic Ua comparing the ERFa and ERFm values that has been scaled down to a unit interval (0,1); and 6) A Mann- Whitney statistic U75. U75 is a linear rank statistic designed to identify a shift in the upper quartile of the distribution of ERFm and ERFu values. ERF values at or below the 75th percentile of the ERFm and ERFu values are assigned a score of 0. The remaining ERFm and ERFu values are assigned values between 0 and 1 as in the Uu statistic. For activatable elements that are surface markers on cells, the following metrics may be further generated: 1) a relative protein expression metric log2(ERF stain) - log2(ERFcontrol) based on the ERF value for a stained sample (ERFstain) and the ERF value for a control sample (ERFcontrol); and 2) A Mann- Whitney statistic Ui comparing the ERFm and ERFi values that has been scaled down to a unit interval (0,1), where the ERFi values are derived from an isotype control.

[00185] The activation state data for the different markers is "gated" in order to identify discrete subpopulations of cells within the data. In gating, activation state data is used to identify discrete sub-populations of cells with distinct activation levels of an activatable element. These discrete sub-populations of cells can correspond to cell types, cell subtypes, cells in a disease or other physiological state and/or a population of cells having any characteristic in common.

[00186] In some embodiments, the activation state data is displayed as a two-dimensional scatter-plot and the discrete subpopulations are "gated" or demarcated within the scatter- plot. According to the embodiment, the discrete subpopulations may be gated automatically, manually or using some combination of automatic and manual gating methods. In some embodiments, a user can create or manually adjust the demarcations or "gates" to generate new discrete sub-populations of cells. Suitable methods of gating Atty Dkt o. 33118-747601 discrete sub-populations of cells are described in U.S. Patent Application No. 12/501295, the entirety of which is incorporated by reference herein, for all purposes.

[00187] In some embodiments, the homogenous cell populations are gated according to markers that are known to segregate different cell types or cell sub-types. In a specific embodiment, a user can identify discrete cell populations based on surface markers. For example, the user could look at: "stem cell populations" by CD34+ CD38- or CD34+ CD33- expressing cells; memory CD4 T lymphocytes; e.g., CD4+CD45RA+CD291ow cells; or multiple leukemic sub-clones based on CD33, CD45, HLA-DR, CD1 lb and analyzing signaling in each discrete population/subpopulation. In another alternative embodiment, a user may identify discrete cell populations/subpopulations based on intracellular markers, such as transcription factors or other intracellular proteins; based on a functional assay (e.g., dye efflux assay to determine drug transporter + cells or fluorescent glucose uptake) or based on other fluorescent markers. In some embodiments, gates are used to identify the presence of specific discrete populations and/or subpopulations in existing independent data. The existing independent data can be data stored in a computer from a previous patient, or data from independent studies using different patients.

Gating

[00188] Gating can be used to focus on healthy cells or to analyze cell signaling. For example, in one embodiment gating is used to identify the healthy cell subpopulation. In one embodiment, cells are identified using Forward and Side Scatter, live cells are identified using Amine Aqua, leukemic blasts are identified using Side Scatter and CD45, and non apoptotic leukemic blasts (Healthy PI) are identified by assaying for cleaved PARP. This embodiment focuses the analysis on healthy cells.

[00189] In another embodiment, a user will gate cells for the cell signaling component.

For example, a user may analyze the signaling in subpopulations based on surface markers. For example, the user can look at: "stem cell populations" by CD34+ CD38- or CD34+ CD33- expressing cells; drug transporter positive cells; i.e. C-KIT+ (SCF

Receptor, CD 117) cells+; FLT3+ cells; CD44+ cells, CD47+ cells, CD 123+ cells, or multiple leukemic subpopulations based on CD33, CD45, HLA-DR, CD1 lb and analyzing signaling in each subpopulation. In another alternative embodiment, a user may analyze the data based on intracellular markers, such as transcription factors or other intracellular proteins; based on a functional assay (e.g., dye negative "side population" aka drug transporter + cells, or fluorescent glucose uptake, or based on other fluorescent Atty Dkt o. 33118-747601 markers). In some embodiments, a gate is established after learning from a responsive subpopulation. That is, a gate is developed from one data set after finding a population that correlates with a clinical outcome. This gate can then be applied restrospectively or prospectively to other data sets. See U.S. Ser. No. 12/501,295 for an example of gating.

[00190] Both gating embodiments can be run at the same time when a user is analyzing each well/aliquot for the activatable element that relates to cell health, for example, if each well has the reagent used for detecting the activatable element related to cell health.

[00191] In some embodiments where flow cytometry is used, prior to analyzing data the populations of interest and the method for characterizing these populations are determined. For instance, there are at least two general ways of identifying populations for data analysis: (i) "Outside-in" comparison of Parameter sets for individual samples or subset (e.g., patients in a trial). In this more common case, cell populations are homogenous or lineage gated in such a way as to create distinct sets considered to be homogenous for targets of interest. An example of sample-level comparison would be the identification of signaling profiles in tumor cells of a patient and correlation of these profiles with non-random distribution of clinical responses. This is considered an outside-in approach because the population of interest is pre-defined prior to the mapping and comparison of its profile to other populations, (ii) "Inside-out" comparison of Parameters at the level of individual cells in a heterogeneous population. An example of this would be the signal transduction state mapping of mixed hematopoietic cells under certain conditions and subsequent comparison of computationally identified cell clusters with lineage specific markers. This could be considered an inside-out approach to single cell studies as it does not presume the existence of specific populations prior to classification.

[00192] Each of these techniques capitalizes on the ability of flow cytometry to deliver large amounts of multiparameter data at the single cell level. For cells associated with a condition (e.g., neoplastic or hematopoetic condition), a third "meta-level" of data exists because cells associated with a condition (e.g., cancer cells) are generally treated as a single entity and classified according to historical techniques. These techniques have included organ or tissue of origin, degree of differentiation, proliferation index, metastatic spread, and genetic or metabolic data regarding the patient.

[00193] In some embodiments, methods described herein use variance mapping

techniques for mapping condition signaling space. These methods represent a significant advance in the study of condition biology because they enable comparison of conditions Atty Dkt o. 33118-747601

independent of a putative normal control. Traditional differential state analysis methods (e.g., DNA microarrays, subtractive Northern blotting) generally rely on the comparison of cells associated with a condition from each patient sample with a normal control, generally adjacent and theoretically untransformed tissue. Alternatively, they rely on multiple clusterings and reclusterings to group and then further stratify patient samples according to phenotype. In contrast, variance mapping of condition states compares condition samples first with themselves and then against the parent condition population. As a result, activation states with the most diversity among conditions provide the core parameters in the differential state analysis. Given a pool of diverse conditions, this technique allows a researcher to identify the molecular events that underlie differential condition pathology (e.g., cancer responses to chemotherapy), as opposed to differences between conditions and a proposed normal control.

[00194] In some embodiments, when variance mapping is used to profile the signaling space of patient samples, conditions whose signaling response to modulators is similar are grouped together, regardless of tissue or cell type of origin. Similarly, two conditions (e.g., two tumors) that are thought to be relatively alike based on lineage markers or tissue of origin could have vastly different abilities to interpret environmental stimuli and would be profiled in two different groups.

[00195] When groups of signaling profiles have been identified it is frequently useful to determine whether other factors, such as clinical responses, presence of gene mutations, and protein expression levels, are non-randomly distributed within the groups. If experiments or literature suggest such a hypothesis in an arrayed flow cytometry experiment, it can be judged with simple statistical tests, such as the Student's t-test and the X ² test. Similarly, if two variable factors within the experiment are thought to be related, the Pearson, and/or Spearman is used to measure the degree of this relationship.

[00196] Examples of analysis for activatable elements are described in US publication number 20060073474 entitled "Methods and compositions for detecting the activation state of multiple proteins in single cells" and US publication number 20050112700 entitled "Methods and compositions for risk stratification" the content of which are incorporated herein by reference.

Labels

[00197] The methods and compositions provided herein provide binding elements

comprising a label or tag. A label can be a molecule that can be directly (i.e., a primary label) or indirectly (i.e., a secondary label) detected; for example a label can be visualized Atty Dkt o. 33118-747601 and/or measured or otherwise identified so that its presence or absence can be known. Binding elements and labels for binding elements are shown, e.g., in

U.S. S.N. 61/048,886; 61/048,920 and 61/048,657.

[00198] A compound can be directly or indirectly conjugated to a label which provides a detectable signal, e.g., radioisotopes, fluorescers, enzymes, antibodies, particles such as magnetic particles, chemiluminescers, molecules that can be detected by mass spectrometry, or specific binding molecules, etc. Specific binding molecules include pairs, such as biotin and streptavidin, digoxin and antidigoxin etc. Examples of labels include, but are not limited to, optical fluorescent and chromogenic dyes including labels, label enzymes and radioisotopes. In some embodiments, a label can be conjugated to a binding element.

[00199] In some embodiments, one or more binding elements are uniquely labeled. Using the example of two activation state specific antibodies, "uniquely labeled" can mean that a first activation state antibody recognizing a first activated element comprises a first label, and second activation state antibody recognizing a second activated element comprises a second label, wherein the first and second labels are detectable and distinguishable, making the first antibody and the second antibody uniquely labeled.

[00200] In general, labels can fall into four classes: a) iso topic labels, which can be

radioactive or heavy isotopes; b) magnetic, electrical, thermal labels; c) colored, optical labels including luminescent, phosphorous and fluorescent dyes or moieties; and d) binding partners. Labels can also include enzymes (e.g., horseradish peroxidase, etc.) and magnetic particles. In some embodiments, the detection label is a primary label. A primary label is one that can be directly detected, such as a fluorophore.

[00201] Labels include optical labels such as fluorescent dyes or moieties. Fluorophores can be "small molecule" fluors or proteinaceous fluors (e.g., green fluorescent proteins and all variants thereof).

[00202] In some embodiments, activation state-specific antibodies are labeled with

quantum dots as disclosed by Chattopadhyay, P.K. et al. Quantum dot semiconductor nanocrystals for immunophenotyping by polychromatic flow cytometry. Nat. Med. 12, 972-977 (2006). Quantum dot labels are commercially available through Invitrogen, http://probes.invitrogen.com/products/qdot/.

[00203] Quantum dot labeled antibodies can be used alone or they can be employed in conjunction with organic fluorochrome— conjugated antibodies to increase the total number of labels available. As the number of labeled antibodies increase so does the Atty Dkt o. 33118-747601

ability for subtyping known cell populations. Additionally, activation state-specific antibodies can be labeled using chelated or caged lanthanides as disclosed by Erkki, J. et al. Lanthanide chelates as new fluorochrome labels for cytochemistry. J. Histochemistry Cytochemistry, 36: 1449-1451, 1988, and U.S. Patent No. 7,018850, entitled Salicy lamide-Lanthanide Complexes for Use as Luminescent Markers. Other methods of detecting fluorescence may also be used, e.g., Quantum dot methods (see, e.g., Goldman et al, J. Am. Chem. Soc. (2002) 124:6378-82; Pathak et al. J. Am. Chem. Soc. (2001) 123:4103-4; and Remade et al, Proc. Natl. Sci. USA (2000) 18:553-8, each expressly incorporated herein by reference) as well as confocal microscopy.

[00204] In some embodiments, activatable elements are labeled with tags suitable for Inductively Coupled Plasma Mass Spectrometer (ICP-MS) as disclosed in Tanner et al. Spectrochimica Acta Part B: Atomic Spectroscopy, 2007 Mar;62(3): 188-195.

[00205] Detection systems based on FRET, discussed in detail below, can be used. FRET can be used in the methods described herein, for example, in detecting activation states that involve clustering or multimerization wherein the proximity of two FRET labels is altered due to activation. In some embodiments, at least two fluorescent labels are used which are members of a fluorescence resonance energy transfer (FRET) pair.

[00206] The methods and compositions described herein can also make use of label

enzymes. A label enzyme can be an enzyme that can be reacted in the presence of a label enzyme substrate that produces a detectable product. Suitable label enzymes include but are not limited to horseradish peroxidase, alkaline phosphatase and glucose oxidase. Methods for the use of such substrates are well known in the art. The presence of a label enzyme can generally be revealed through the enzyme's catalysis of a reaction with a label enzyme substrate, producing an identifiable product. Such products may be opaque, such as the product resulting from the reaction of horseradish peroxidase with tetramethyl benzedine, and may have a variety of colors. Other label enzyme substrates, such as Luminol (available from Pierce Chemical Co.), have been developed that produce fluorescent reaction products. Methods for identifying label enzymes with label enzyme substrates are well known in the art and many commercial kits are available. Examples and methods for the use of various label enzymes are described in Savage et al, Previews 247:6-9 (1998), Young, J. Virol. Methods 24:227-236 (1989), which are each hereby incorporated by reference in their entirety. Atty Dkt o. 33118-747601

[00207] By radioisotope is meant any radioactive molecule. Suitable radioisotopes

include, but are not limited to 14C, 3H, 32P, 33P, 35S, 1251 and 1311. The use of radioisotopes as labels is well known in the art.

[00208] Labels can be indirectly detected, that is, the tag is a partner of a binding pair.

"Partner of a binding pair" can mean one of a first and a second moiety, wherein the first and the second moiety have a specific binding affinity for each other. Suitable binding pairs include, but are not limited to, antigens/antibodies (for example, digoxigenin/anti- digoxigenin, dinitrophenyl (DNP)/anti-DNP, dansyl-X-anti-dansyl, Fluorescein/anti- fluorescein, lucifer yellow/anti-lucifer yellow, and rhodamine anti-rhodamine), biotin/avidin (or biotin/streptavidin) and calmodulin binding protein (CBP)/calmodulin. Other suitable binding pairs include polypeptides such as the FLAG-peptide [Hopp et al, BioTechnology, 6: 1204-1210 (1988)]; the KT3 epitope peptide [Martin et al, Science, 255: 192-194 (1992)]; tubulin epitope peptide [Skinner et al, J. Biol. Chem., 266: 15163- 15166 (1991)]; and the T7 gene 10 protein peptide tag [Lutz-Freyermuth et al, Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990)] and the antibodies each thereto. As will be appreciated by those in the art, binding pair partners may be used in applications other than for labeling, as is described herein.

[00209] As will be appreciated by those in the art, a partner of one binding pair may also be a partner of another binding pair. For example, an antigen (first moiety) can bind to a first antibody (second moiety) that can, in turn, be an antigen for a second antibody (third moiety). It will be further appreciated that such a circumstance allows indirect binding of a first moiety and a third moiety via an intermediary second moiety that is a binding pair partner to each.

[00210] As will be appreciated by those in the art, a partner of a binding pair can comprise a label, as described above. It will further be appreciated that a label allows for a tag to be indirectly labeled upon the binding of a binding partner comprising a label. Attaching a label to a tag that is a partner of a binding pair, as just described, can be referred to herein as "indirect labeling".

[00211] "Surface substrate binding molecule" or "attachment tag" and grammatical

equivalents thereof can mean a molecule have binding affinity for a specific surface substrate, which substrate is generally a member of a binding pair applied, incorporated or otherwise attached to a surface. Suitable surface substrate binding molecules and their surface substrates include, but are not limited to, poly-histidine (poly-his) or poly- histidine-glycine (poly-his-gly) tags and Nickel substrate; the Glutathione-S Transferase Atty Dkt o. 33118-747601 tag and its antibody substrate (available from Pierce Chemical); the flu HA tag polypeptide and its antibody 12CA5 substrate [Field et al, Mol. Cell. Biol, 8:2159-2165 (1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibody substrates thereto [Evan et al, Molecular and Cellular Biology, 5:3610-3616 (1985)]; and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody substrate [Paborsky et al, Protein Engineering, 3(6):547-553 (1990)]. In general, surface binding substrate molecules include, but are not limited to, polyhistidine structures (His-tags) that bind nickel substrates, antigens that bind to surface substrates comprising antibody, haptens that bind to avidin substrate (e.g., biotin) and CBP that binds to surface substrate comprising calmodulin.

Detection

[00212] In practicing the methods described herein, the detection of the status of the one or more activatable elements can be carried out by a person, such as a technician in the laboratory. Alternatively, the detection of the status of the one or more activatable elements can be carried out using automated systems. In either case, the detection of the status of the one or more activatable elements for use according to the methods described herein can be performed according to standard techniques and protocols well-established in the art.

[00213] One or more activatable elements can be detected and/or quantified by any

method that detects and/or quantitates the presence of the activatable element of interest. Such methods may include flow cytometry, mass spectrometry, radioimmunoassay (RIA) or enzyme linked immunoabsorbance assay (ELISA), immunohistochemistry, immuno fluorescent histochemistry with or without confocal microscopy, reversed phase assays, homogeneous enzyme immunoassays, and related non-enzymatic techniques, Western blots, Far Western, Northern Blot, Southern blot, whole cell staining, immunoelectronmicroscopy, nucleic acid amplification, gene array, protein array, mass spectrometry, nucleic acid sequencing, next generation sequencing, patch clamp, 2- dimensional gel electrophoresis, differential display gel electrophoresis, microsphere- based multiplex protein assays, label-free cellular assays, etc. These techniques are particularly useful for modified protein parameters. Cell readouts for proteins and other cell determinants can be obtained using fluorescent or otherwise tagged reporter molecules. Flow cytometry and mass spectrometry methods are useful for measuring intracellular parameters. See e.g., U.S. Pat. App. No. 10/898,734 and Shulz et al, Atty Dkt o. 33118-747601

Current Protocols in Immunology, 2007, 78:8.17.1-20 which are incorporated by reference in their entireties.

[00214] In some embodiments, provided herein are methods for determining an

activatable element's activation profile for a single cell. The methods may comprise analyzing cells by flow cytometry on the basis of the activation level of at least two activatable elements. Binding elements (e.g., activation state-specific antibodies) can be used to analyze cells on the basis of activatable element activation level, and can be detected as described herein. Alternatively, non-binding element systems as described above can be used in any system described herein.

[00215] Detection of cell signaling states may be accomplished using binding elements and labels. Cell signaling states may be detected by a variety of methods known in the art. They generally involve a binding element, such as an antibody, and a label, such as a fiuorochrome to form a detection element. Detection elements do not need to have both of the above agents, but can be one unit that possesses both qualities. These and other methods are well described in U.S. Patent Nos. 7,381535 and 7,393,656 and U.S. Ser. Nos. 10/193,462; 11/655,785; 11/655,789; 11/655,821; 11/338,957, 61/048,886;

61/048,920; and 61/048,657 (as well as the applications listed above) which are all incorporated by reference in their entireties.

[00216] In one embodiment, it is advantageous to increase the signal to noise ratio by contacting the cells with the antibody and label for a time greater than 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24 or up to 48 or more hours.

[00217] When using fluorescent labeled components in the methods and compositions described herein, it will recognized that different types of fluorescent monitoring systems, e.g., cytometric measurement device systems, can be used. In some embodiments, flow cytometric systems are used or systems dedicated to high throughput screening, e.g., 96 well or greater microtiter plates. Methods of performing assays on fluorescent materials are well known in the art and are described in, e.g., Lakowicz, J. R., Principles of Fluorescence Spectroscopy, New York: Plenum Press (1983); Herman, B., Resonance energy transfer microscopy, in: Fluorescence Microscopy of Living Cells in Culture, Part B, Methods in Cell Biology, vol. 30, ed. Taylor, D. L. & Wang, Y.-L., San Diego: Academic Press (1989), pp. 219-243; Turro, N. J., Modern Molecular Photochemistry, Menlo Park: Benjamin/Cummings Publishing Col, Inc. (1978), pp. 296- 361. Commercial instruments are available through Becton Dickinson and Beckman Coulter, among others. Atty Dkt o. 33118-747601

[00218] Fluorescence in a sample can be measured using a fluorimeter. In general,

excitation radiation, from an excitation source having a first wavelength, passes through excitation optics. The excitation optics cause the excitation radiation to excite the sample. In response, fluorescent proteins in the sample emit radiation that has a wavelength that is different from the excitation wavelength. Collection optics then collect the emission from the sample. The device can include a temperature controller to maintain the sample at a specific temperature while it is being scanned. According to one embodiment, a multi-axis translation stage moves a microtiter plate holding a plurality of samples in order to position different wells to be exposed. The multi-axis translation stage, temperature controller, auto-focusing feature, and electronics associated with imaging and data collection can be managed by an appropriately programmed digital computer. The computer also can transform the data collected during the assay into another format for presentation. In general, known robotic systems and components can be used.

[00219] Other methods of detecting fluorescence may also be used, e.g., Quantum dot methods (see, e.g., Goldman et al, J. Am. Chem. Soc. (2002) 124:6378-82; Pathak et al. J. Am. Chem. Soc. (2001) 123:4103-4; and Remade et al, Proc. Natl. Sci. USA (2000) 18:553-8, each expressly incorporated herein by reference) as well as confocal microscopy. In general, flow cytometry involves the passage of individual cells through the path of a laser beam. The scattering the beam and excitation of any fluorescent molecules attached to, or found within, the cell is detected by photomultiplier tubes to create a readable output, e.g., size, granularity, or fluorescent intensity.

[00220] In some embodiments, the activation level of an activatable element is measured using Inductively Coupled Plasma Mass Spectrometer (ICP-MS). A binding element that has been labeled with a specific element binds to the activatable element. When the cell is introduced into the ICP, it is atomized and ionized. The elemental composition of the cell, including the labeled binding element that is bound to the activatable element, can be measured. The presence and intensity of the signals corresponding to the labels on the binding element indicates the level of activation of the activatable element on that cell (Tanner et al. Spectrochimica Acta Part B: Atomic Spectroscopy, 2007 Mar;62(3): 188- 195.).

[00221] The detecting, sorting, or isolating step of the methods described herein can entail fluorescence-activated cell sorting (FACS) techniques, where FACS is used to select cells from the population containing a particular surface marker, or the selection step can Atty Dkt o. 33118-747601 entail the use of magnetically responsive particles as retrievable supports for target cell capture and/or background removal. A variety of FACS systems are known in the art and can be used in the methods described herein (see e.g., W099/54494, filed Apr. 16, 1999; U.S. Ser. No. 20010006787, filed Jul. 5, 2001, each expressly incorporated herein by reference).

[00222] In some embodiments, a FACS cell sorter (e.g., a FACSVantage™ Cell Sorter, Becton Dickinson Immuno cytometry Systems, San Jose, Calif.) is used to sort and collect cells based on their activation profile (positive cells) in the presence or absence of an increase in activation level of an activatable element in response to a modulator. Other flow cytometers that are commercially available include the LSR II and the Canto II both available from Becton Dickinson. See Shapiro, Howard M., Practical Flow Cytometry, 4th Ed., John Wiley & Sons, Inc., 2003 for additional information on flow cytometers.

[00223] In some embodiments, the cells are first contacted with fluorescent-labeled

activation state-specific binding elements (e.g., antibodies) directed against a specific activation state of specific activatable elements. In such an embodiment, the amount of bound binding element on each cell can be measured by passing droplets containing the cells through the cell sorter. By imparting an electromagnetic charge to droplets containing the positive cells, the cells can be separated from other cells. The positively selected cells can then be harvested in sterile collection vessels. These cell-sorting procedures are described in detail, for example, in the FACSVantage™ manual, with particular reference to sections 3-11 to 3-28 and 10-1 to 10-17, which is hereby incorporated by reference in its entirety. See the patents, applications and articles referred to, and incorporated above for detection systems.

[00224] In another embodiment, positive cells can be sorted using magnetic separation of cells based on the presence of an isoform of an activatable element. In such separation techniques, cells to be positively selected are first contacted with specific binding element (e.g., an antibody or reagent that binds an isoform of an activatable element). The cells are then contacted with retrievable particles (e.g., magnetically responsive particles) that are coupled with a reagent that binds the specific element. The cell- binding element-particle complex can then be physically separated from non-positive or non-labeled cells, for example, using a magnetic field. When using magnetically responsive particles, the positive or labeled cells can be retained in a container using a magnetic filed while the negative cells are removed. These and similar separation Atty Dkt o. 33118-747601 procedures are described, for example, in the Baxter Immunotherapy Isolex manual which is hereby incorporated in its entirety.

[00225] In some embodiments, methods for the determination of a receptor element

activation state profile for a single cell are provided. The methods comprise providing a population of cells and analyzing the population of cells by flow cytometry. Preferably, cells are analyzed on the basis of the activation level of at least two activatable elements. In some embodiments, a multiplicity of activatable element activation-state antibodies is used to simultaneously determine the activation level of a multiplicity of elements.

[00226] In some embodiments, cell analysis by flow cytometry on the basis of the

activation level of at least two elements is combined with a determination of other flow cytometry readable outputs, such as the presence of surface markers, granularity and cell size to provide a correlation between the activation level of a multiplicity of elements and other cell qualities measurable by flow cytometry for single cells.

[00227] As will be appreciated, the methods described herein also provide for the ordering of element clustering events in signal transduction. Particularly, the methods described herein allow the artisan to construct an element clustering and activation hierarchy based on the correlation of levels of clustering and activation of a multiplicity of elements within single cells. Ordering can be accomplished by comparing the activation level of a cell or cell population with a control at a single time point, or by comparing cells at multiple time points to observe subpopulations arising out of the others.

[00228] Provided herein is a method of determining the presence of cellular subsets within cellular populations. Ideally, signal transduction pathways are evaluated in homogeneous cell populations to ensure that variances in signaling between cells do not qualitatively nor quantitatively mask signal transduction events and alterations therein. As the ultimate homogeneous system is the single cell, the methods described herein allow the individual evaluation of cells to allow true differences to be identified in a significant way.

[00229] Thus, provided herein aremethods of distinguishing cellular subsets within a

larger cellular population. As outlined herein, these cellular subsets often exhibit altered biological characteristics (e.g., activation levels, altered response to modulators) as compared to other subsets within the population. For example, as outlined herein, the methods described herein allow the identification of subsets of cells from a population such as primary cell populations, e.g., peripheral blood mononuclear cells that exhibit altered responses (e.g., response associated with presence of a condition) as compared to Atty Dkt o. 33118-747601

other subsets. In addition, this type of evaluation distinguishes between different activation states, altered responses to modulators, cell lineages, cell differentiation states, etc.

[00230] As will be appreciated, these methods provide for the identification of distinct signaling cascades for both artificial and stimulatory conditions in complex cell populations, such a peripheral blood mononuclear cells, or naive and memory lymphocytes.

[00231] When necessary cells are dispersed into a single cell suspension, e.g., by

enzymatic digestion with a suitable protease, e.g., collagenase, dispase, etc; and the like. An appropriate solution is used for dispersion or suspension. Such solution will generally be a balanced salt solution, e.g., normal saline, PBS, Hanks balanced salt solution, etc., conveniently supplemented with fetal calf serum or other naturally occurring factors, in conjunction with an acceptable buffer at low concentration, generally from 5-25 mM. Convenient buffers include HEPES, phosphate buffers, lactate buffers, etc. The cells may be fixed, e.g., with 3% paraformaldehyde, and are usually permeabilized, e.g., with ice cold methanol; HEPES-buffered PBS containing 0.1% saponin, 3% BSA; covering for 2 min in acetone at -200°C; and the like as known in the art and according to the methods described herein.

[00232] In some embodiments, one or more cells are contained in a well of a 96 well plate or other commercially available multiwell plate. In an alternate embodiment, the reaction mixture or cells are in a cytometric measurement device. Other multiwell plates useful in the methods described herein include, but are not limited to 384 well plates and 1536 well plates. Still other vessels for containing the reaction mixture or cells and useful for the methods described herein will be apparent to the skilled artisan. Methods to automate the analysis are shown in U.S. Ser. No. 12/606,869 which is hereby incorporated by reference in its entirety.

[00233] The addition of the components of the assay for detecting the activation level or activity of an activatable element, or modulation of such activation level or activity, may be sequential or in a predetermined order or grouping under conditions appropriate for the activity that is assayed for. Such conditions are described here and known in the art. Moreover, further guidance is provided below (see, e.g., in the Examples).

[00234] As will be appreciated by one of skill in the art, the instant methods and

compositions find use in a variety of other assay formats in addition to flow cytometry analysis. For example, DNA microarrays are commercially available through a variety of Atty Dkt o. 33118-747601

sources (Affymetrix, Santa Clara CA) or they can be custom made in the lab using arrayers which are also know (Perkin Elmer). In addition, protein chips and methods for synthesis are known. These methods and materials may be adapted for the purpose of affixing activation state binding elements to a chip in a prefigured array. In some embodiments, such a chip comprises a multiplicity of element activation state binding elements, and is used to determine an element activation state profile for elements present on the surface of a cell.

[00235] In some embodiments, the methods and compositions described herein can be used in conjunction with an "In-Cell Western Assay." In such an assay, cells are initially grown in standard tissue culture flasks using standard tissue culture techniques. Once grown to optimum confluency, the growth media is removed and cells are washed and trypsinized. The cells can then be counted and volumes sufficient to transfer the appropriate number of cells are aliquoted into microwell plates (e.g., Nunc™ 96

Microwell™ plates). The individual wells are then grown to optimum confluency in complete media whereupon the media is replaced with serum- free media. At this point controls are untouched, but experimental wells are incubated with a modulator, e.g., EGF. After incubation with the modulator cells are fixed and stained with labeled antibodies to the activation elements being investigated. Once the cells are labeled, the plates can be scanned using an imager such as the Odyssey Imager (LiCor, Lincoln Nebr.) using techniques described in the Odyssey Operator's Manual vl .2., which is hereby incorporated in its entirety. Data obtained by scanning of the multiwell plate can be analyzed and activation profiles determined as described herein.

[00236] In some embodiments, the detecting is by high pressure liquid chromatography (HPLC), for example, reverse phase HPLC, and in a further aspect, the detecting is by mass spectrometry.

[00237] These instruments can fit in a sterile laminar flow or fume hood, or are enclosed, self-contained systems, for cell culture growth and transformation in multi-well plates or tubes and for hazardous operations. The living cells may be grown under controlled growth conditions, with controls for temperature, humidity, and gas for time series of the live cell assays. Automated transformation of cells and automated colony pickers may facilitate rapid screening of desired cells.

[00238] Flexible hardware and software allow instrument adaptability for multiple

applications. The software program modules allow creation, modification, and running of methods. The system diagnostic modules allow instrument alignment, correct Atty Dkt o. 33118-747601 connections, and motor operations. Customized tools, labware, and liquid, particle, cell and organism transfer patterns allow different applications to be performed. Databases allow method and parameter storage. Robotic and computer interfaces allow communication between instruments.

[00239] In some embodiments, the methods described herein include the use of liquid handling components. The liquid handling systems can include robotic systems comprising any number of components. In addition, any or all of the steps outlined herein may be automated; thus, for example, the systems may be completely or partially automated. See U.S. Ser. Nos. 12/606,869 and 12/432,239.

[00240] As will be appreciated by those in the art, there are a wide variety of components which can be used, including, but not limited to, one or more robotic arms; plate handlers for the positioning of microplates; automated lid or cap handlers to remove and replace lids for wells on non-cross contamination plates; tip assemblies for sample distribution with disposable tips; washable tip assemblies for sample distribution; 96 well loading blocks; cooled reagent racks; microtiter plate pipette positions (optionally cooled);

stacking towers for plates and tips; and computer systems.

[00241] Fully robotic or micro fluidic systems include automated liquid-, particle-, cell- and organism-handling including high throughput pipetting to perform all steps of screening applications. This includes liquid, particle, cell, and organism manipulations such as aspiration, dispensing, mixing, diluting, washing, accurate volumetric transfers; retrieving, and discarding of pipet tips; and repetitive pipetting of identical volumes for multiple deliveries from a single sample aspiration. These manipulations are cross- contamination- free liquid, particle, cell, and organism transfers. This instrument performs automated replication of microplate samples to filters, membranes, and/or daughter plates, high-density transfers, full-plate serial dilutions, and high capacity operation.

[00242] In some embodiments, chemically derivatized particles, plates, cartridges, tubes, magnetic particles, or other solid phase matrix with specificity to the assay components are used. The binding surfaces of microplates, tubes or any solid phase matrices include non-polar surfaces, highly polar surfaces, modified dextran coating to promote covalent binding, antibody coating, affinity media to bind fusion proteins or peptides, surface- fixed proteins such as recombinant protein A or G, nucleotide resins or coatings, and other affinity matrix are useful. Atty Dkt o. 33118-747601

[00243] In some embodiments, platforms for multi-well plates, multi-tubes, holders,

cartridges, minitubes, deep-well plates, micro fuge tubes, cryovials, square well plates, filters, chips, optic fibers, beads, and other solid-phase matrices or platform with various volumes are accommodated on an upgradable modular platform for additional capacity. This modular platform includes a variable speed orbital shaker, and multi-position work decks for source samples, sample and reagent dilution, assay plates, sample and reagent reservoirs, pipette tips, and an active wash station. In some embodiments, the methods described herein include the use of a plate reader.

[00244] In some embodiments, thermocycler and thermoregulating systems are used for stabilizing the temperature of heat exchangers such as controlled blocks or platforms to provide accurate temperature control of incubating samples from 0°C to 100°C.

[00245] In some embodiments, interchangeable pipet heads (single or multi-channel) with single or multiple magnetic probes, affinity probes, or pipetters robotically manipulate the liquid, particles, cells, and organisms. Multi-well or multi-tube magnetic separators or platforms manipulate liquid, particles, cells, and organisms in single or multiple sample formats.

[00246] In some embodiments, the instrumentation will include a detector, which can be a wide variety of different detectors, depending on the labels and assay. In some embodiments, useful detectors include a microscope(s) with multiple channels of fluorescence; plate readers to provide fluorescent, ultraviolet and visible

spectrophotometric detection with single and dual wavelength endpoint and kinetics capability, fluorescence resonance energy transfer (FRET), luminescence, quenching, two-photon excitation, and intensity redistribution; CCD cameras to capture and transform data and images into quantifiable formats; and a computer workstation.

[00247] In some embodiments, the robotic apparatus includes a central processing unit which communicates with a memory and a set of input/output devices (e.g., keyboard, mouse, monitor, printer, etc.) through a bus. Again, as outlined below, this may be in addition to or in place of the CPU for the multiplexing devices described herein. The general interaction between a central processing unit, a memory, input/output devices, and a bus is known in the art. Thus, a variety of different procedures, depending on the experiments to be run, are stored in the CPU memory.

[00248] These robotic fluid handling systems can utilize any number of different reagents, including buffers, reagents, samples, washes, assay components such as label probes, etc. Atty Dkt o. 33118-747601

[00249] Any of the steps above can be performed by a computer program product that comprises a computer executable logic that is recorded on a computer readable medium. For example, the computer program can execute some or all of the following functions: (i) exposing reference population of cells to one or more modulators, (ii) exposing reference population of cells to one or more binding elements, (iii) detecting the activation levels of one or more activatable elements, (iv) characterizing one or more cellular pathways, (v) classifying one or more cells into one or more classes based on the activation level (vi) determining cell health status of a cell, (vii) determining the percentage of viable cells in a sample; (viii) determining the percentage of healthy cells in a sample; (ix) determining a cell signaling profile; (x) adjusting a cell signaling profile based on the percentage of healthy cells in a sample; (xi) adjusting a cell signaling profile for an individual cell based on the health of the cell; (xii) excluding or including a cell or population of cells in a cell signaling analysis based on the health of the cell or population of cells; (xiii) assaying for one or more cell health markers; and/or (xiv) assaying for one or more apoptosis and/or necrosis markers.

[00250] The computer executable logic can work in any computer that may be any of a variety of types of general-purpose computers such as a personal computer, network server, workstation, or other computer platform now or later developed. In some embodiments, a computer program product is described comprising a computer usable medium having the computer executable logic (computer software program, including program code) stored therein. The computer executable logic can be executed by a processor, causing the processor to perform functions described herein. In other embodiments, some functions are implemented primarily in hardware using, for example, a hardware state machine. Implementation of the hardware state machine so as to perform the functions described herein will be apparent to those skilled in the relevant arts.

[00251] The program can provide a method of determining the status of an individual by accessing data that reflects the activation level of one or more activatable elements in the reference population of cells.

Analysis

[00252] Advances in flow cytometry have enabled the individual cell enumeration of up to thirteen simultaneous parameters (De Rosa et al, 2001) and are moving towards the study of genomic and proteomic data subsets (Krutzik and Nolan, 2003; Perez and Nolan, 2002). Likewise, advances in other techniques (e.g., microarrays) allow for the identification of multiple activatable elements. As the number of parameters, epitopes, Atty Dkt o. 33118-747601 and samples have increased, the complexity of experiments and the challenges of data analysis have grown rapidly. An additional layer of data complexity has been added by the development of stimulation panels which enable the study of activatable elements under a growing set of experimental conditions. See Krutzik et al, Nature Chemical Biology Feb. 2008. Methods for the analysis of multiple parameters are well known in the art. See U.S. Ser. Nos. 61/350,864, 12/293,081, 12/538,643, and 12/501,274 for more info on analysis. See U.S. Ser. No. 12/501,295 for gating analysis.

[00253] In some embodiments where flow cytometry is used, flow cytometry experiments are performed and the results are expressed as fold changes using graphical tools and analyses, including, but not limited to a heat map or a histogram to facilitate evaluation. One common way of comparing changes in a set of flow cytometry samples is to overlay histograms of one parameter on the same plot. Flow cytometry experiments ideally include a reference sample against which experimental samples are compared. Reference samples can include normal and/or cells associated with a condition (e.g., tumor cells). See also U.S. Ser. No. 12/501,295 for visualization tools.

[00254] The patients are stratified based on nodes that inform the clinical question using a variety of metrics. To stratify the patients between those patients with No Response (NR) versus a Complete Response (CR), a prioritization of the nodes can be made according to statistical significance (such as p-value from a t-test or Wilcoxon test or area under the receiver operator characteristic (ROC) curve) or their biological relevance.

Conditions

[00255] The methods described herein can be applicable to any condition in an individual involving, indicated by, and/or arising from, in whole or in part, an altered cell signaling profile in cells. In some embodiments, the cell signaling profile of a cell is determined by measuring characteristics of at least one cellular component of a cellular pathway in cells from different populations (e.g., different cell networks). Cellular pathways are well known in the art. In some embodiments the cellular pathway is a signaling pathway. Signaling pathways are also well known in the art (see, e.g., Hunter T., Cell 100(1): 113- 27 (2000); Cell Signaling Technology, Inc., 2002 Catalogue, Pathway Diagrams pgs. 232-253; Weinberg, Chapter 6, The biology of Cancer, 2007; and Blume- Jensen and Hunter, Nature, vol 411, 17 May 2001, p 355-365). A condition involving or characterized by altered cell signaling profile can be readily identified, for example, by determining the state of one or more activatable elements in cells from different populations, as taught herein. Atty Dkt o. 33118-747601

[00256] In certain embodiments, the condition is a neoplastic, immunologic or

hematopoietic condition. In some embodiments, the neoplastic, immunologic or hematopoietic condition is selected from the group consisting of solid tumors such as head and neck cancer including brain, thyroid cancer, breast cancer, lung cancer, mesothelioma, germ cell tumors, ovarian cancer, liver cancer, gastric carcinoma, colon cancer, prostate cancer, pancreatic cancer, melanoma, bladder cancer, renal cancer, prostate cancer, testicular cancer, cervical cancer, endometrial cancer, myosarcoma, leiomyosarcoma and other soft tissue sarcomas, osteosarcoma, Ewing's sarcoma, retinoblastoma, rhabdomyosarcoma, Wilm's tumor, and neuroblastoma, sepsis, allergic diseases and disorders that include but are not limited to allergic rhinitis, allergic conjunctivitis, allergic asthma, atopic eczema, atopic dermatitis, and food allergy, immunodeficiencies including but not limited to severe combined immunodeficiency (SCID), hypereosiniphic syndrome, chronic granulomatous disease, leukocyte adhesion deficiency I and II, hyper IgE syndrome, Chediak Higashi, neutrophilias, neutropenias, aplasias, agammaglobulinemia, hyper-IgM syndromes, DiGeorge/Velocardial- facial syndromes and Interferon gamma-THl pathway defects, autoimmune and immune dysregulation disorders that include but are not limited to rheumatoid arthritis, diabetes, systemic lupus erythematosus, Graves' disease, Graves ophthalmopathy, Crohn's disease, multiple sclerosis, psoriasis, systemic sclerosis, goiter and struma lymphomatosa

(Hashimoto's thyroiditis, lymphadenoid goiter), alopecia aerata, autoimmune myocarditis, lichen sclerosis, autoimmune uveitis, Addison's disease, atrophic gastritis, myasthenia gravis, idiopathic thrombocytopenic purpura, hemolytic anemia, primary biliary cirrhosis, Wegener's granulomatosis, polyarteritis nodosa, and inflammatory bowel disease, allograft rejection and tissue destructive from allergic reactions to infectious microorganisms or to environmental antigens, and hematopoietic conditions that include but are not limited to Non-Hodgkin Lymphoma, Hodgkin or other lymphomas, acute or chronic leukemias, polycythemias, thrombocythemias, multiple myeloma or plasma cell disorders, e.g., amyloidosis and Waldenstrom's macro globulinemia, myelodysplasia disorders, myeloproliferative disorders, myelofibroses, or atypical immune

lymphoproliferations. In some embodiments, the neoplastic or hematopoietic condition is non-B lineage derived, such as Acute myeloid leukemia (AML), Chronic Myeloid Leukemia (CML), non-B cell Acute lymphocytic leukemia (ALL ), non-B cell lymphomas, myelodysplasia disorders, myeloproliferative disorders, myelofibroses, polycythemias, thrombocythemias, or non-B atypical immune lymphoproliferations, Atty Dkt o. 33118-747601

Chronic Lymphocytic Leukemia (CLL), B lymphocyte lineage leukemia, B lymphocyte lineage lymphoma, Multiple Myeloma, or plasma cell disorders, e.g., amyloidosis or Waldenstrom's macroglobulinemia.

[00257] In some embodiments, the neoplastic or hematopoietic condition is a B-Cell or B cell lineage derived disorder. Examples of B-Cell or B cell lineage derived neoplastic or hematopoietic condition include but are not limited to Chronic Lymphocytic Leukemia (CLL), B lymphocyte lineage leukemia, B lymphocyte lineage lymphoma, Multiple Myeloma, and plasma cell disorders, including amyloidosis and Waldenstrom's macroglobulinemia.

[00258] Other conditions can include, but are not limited to, cancers such as gliomas, lung cancer, colon cancer and prostate cancer. Specific signaling pathway alterations have been described for many cancers, including loss of PTEN and resulting activation of Akt signaling in prostate cancer (Whang Y E. Proc Natl Acad Sci USA Apr. 28, 1998;95(9):5246-50), increased IGF-1 expression in prostate cancer (Schaefer et al, Science October 9 1998, 282: 199a), EGFR overexpression and resulting ER activation in glioma cancer (Thomas C Y. Int J Cancer Mar. 10, 2003;104(1): 19-27), expression of HER2 in breast cancers (Menard et al. Oncogene. Sep 29 2003, 22(42):6570-8), and APC mutation and activated Wnt signaling in colon cancer (Bienz M. Curr Opin Genet Dev 1999 October, 9(5):595-603).

[00259] In certain embodiments, the condition Alzheimer's disease or dementia.

[00260] Diseases other than cancer involving altered cell signaling profiles are also

encompassed by the methods described herein. For example, it has been shown that diabetes involves underlying signaling changes, namely resistance to insulin and failure to activate downstream signaling through IRS (Burks D J, White M F. Diabetes 2001 February;50 Suppl 1 :S 140-5). Similarly, cardiovascular disease has been shown to involve hypertrophy of the cardiac cells involving multiple pathways such as the PKC family (Malhotra A. Mol Cell Biochem 2001 September;225 (l-):97-107). Inflammatory diseases, such as rheumatoid arthritis, are known to involve the chemokine receptors and disrupted downstream signaling (D'Ambrosio D. J Immunol Methods 2003 February;273 (l-2):3-13). The methods described herein are not limited to diseases presently known to involve altered cellular function, but includes diseases subsequently shown to involve physiological alterations or anomalies. Atty Dkt o. 33118-747601

Kits

[00261] In some embodiments, kits are provided. Kits may comprise one or more of the state-specific binding elements described herein, such as phospho-specific antibodies. A kit may also include other reagents, such as modulators, fixatives, containers, plates, buffers, therapeutic agents, instructions, and the like. A kit can be used to assay for one or more cell health markers. A kit can be used to assay for one or more markers of apoptosis and/or necrosis.

[00262] In some embodiments, the kit comprises one or more of the phospho-specific antibodies specific for the proteins selected from the group consisting of PI3-Kinase (p85, pi 10a, pi 10b, pi lOd), Jakl, Jak2, SOCs, Rac, Rho, Cdc42, Ras-GAP, Vav, Tiam, Sos, Dbl, Nek, Gab, PRK, SHP1, and SHP2, SHIP1, SHIP2, sSHIP, PTEN, She, Grb2, PDK1, SGK, Aktl, Akt2, Akt3, TSC1,2, Rheb, mTor, 4EBP-1, p70S6Kinase, S6, LKB- 1, AMPK, PFK, Acetyl-CoAa Carboxylase, DokS, Rafs, Mos, Tpl2, MEK1/2, MLK3, TAK, DLK, MKK3/6, MEKK1,4, MLK3, ASK1, MKK4/7, SAPK/JNK1,2,3, p38s, Erkl/2, Syk, Btk, BLNK, LAT, ZAP70, Lck, Cbl, SLP-76, PLCyi, PLCy 2, STAT1, STAT 3, STAT 4, STAT 5, STAT 6, FAK, pl30CAS, PAKs, LIMK1/2, Hsp90, Hsp70, Hsp27, SMADs, Rel-A (p65-NFKB), CREB, Histone H2B, HATs, HDACs, PKR, Rb, Cyclin D, Cyclin E, Cyclin A, Cyclin B, PI 6, pl4Arf, p27KIP, p21CIP, Cdk4, Cdk6, Cdk7, Cdkl, Cdk2, Cdk9, Cdc25, A/B/C, Abl, E2F, FADD, TRADD, TRAF2, RIP, Myd88, BAD, Bcl-2, Mcl-1, Bcl-XL, Caspase 2, Caspase 3, Caspase 6, Caspase 7, Caspase 8, Caspase 9, IAPs, Smac, Fodrin, Actin, Src, Lyn, Fyn, Lck, NIK, ΙκΒ, p65(RelA), IKKa, PKA, PKCa, PKC β, PKC9, PKC5, CAMK, Elk, AFT, Myc, Egr-1, NFAT, ATF-2, Mdm2, p53, DNA-PK, Chkl, Chk2, ATM, ATR, Bcatenin, CrkL, GSK3a, GSK3P, and FOXO. In some embodiments, the kit comprises one or more of the phospho-specific antibodies specific for the proteins selected from the group consisting of Erkl, Erk2, Syk, Zap70, Lck, Btk, BLNK, Cbl, PLCy2, Akt, RelA, p38, S6. In some embodiments, the kit comprises one or more of the phospho-specific antibodies specific for the proteins selected from the group consisting of Aktl, Akt2, Akt3,

SAPK/JNK1,2,3, p38s, Erkl/2, Syk, ZAP70, Btk, BLNK, Lck, PLCy, PLCy 2, STAT1, STAT 3, STAT 4, STAT 5, STAT 6, CREB, Lyn, p-S6, Cbl, NF-kB, GSK3p, CARMA BcllO and Tcl-1.

[00263] The state-specific binding element can be conjugated to a solid support and to detectable groups directly or indirectly. The reagents can also include ancillary agents such as buffering agents and stabilizing agents, e.g., polysaccharides and the like. The kit Atty Dkt o. 33118-747601

can further include, e.g., other members of the signal-producing system of which system the detectable group is a member (e.g., enzyme substrates), agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. The kit can be packaged in any suitable manner, typically with all elements in a single container along with a sheet of printed instructions for carrying out the test.

[00264] Such kits can enable the detection of activatable elements by sensitive cellular assay methods, such as IHC and flow cytometry, which are suitable for the clinical detection, prognosis, and screening of cells and tissue from patients, such as leukemia patients, having a disease involving altered pathway signaling.

[00265] Such kits can comprise one or more therapeutic agents. The kit can further

comprise a software package for data analysis of cell signaling profiles, which can include reference profiles for comparison with the test profile.

[00266] Such kits can also information, such as scientific literature references, package insert materials, clinical trial results, and/or summaries of these and the like, which indicate or establish the activities and/or advantages of the composition, and/or which describe dosing, administration, side effects, drug interactions, or other information useful to a health care provider. Such information can be based on the results of various studies, for example, studies using experimental animals involving in vivo models and studies based on human clinical trials. Kits described herein can be provided, marketed and/or promoted to health care providers, including physicians, nurses, pharmacists, formulary officials, and the like. Kits can also, in some embodiments, be marketed directly to the consumer.

Examples

[00267] One embodiment of the methods described herein is applied to single cell network profiling which is referenced above. Generally, the process involves treating or inducing cells with modulator, a staining step, and a flow cytometry step. The treatment with a modulator step can start with previously frozen cells and end with cells fixed and permeabilized with a compound, such as methanol. Then the cells can be stained with an antibody directed to a particular activated protein of interest and then analyzed using a flow cytometer. These general steps are disclosed in some references referred to above, including U.S. Ser. Nos. 61/350,864 and 12/460,029. Atty Dkt o. 33118-747601

[00268] Outline of the General method

[00269] Cell thawing, ficoll density gradient separation, and live/dead staining: Cells are thawed in a 37°C water bath in cryovials. Once the cells are thawed, 1 mL of pre- warmed thaw buffer (RPMI + 60% FBS) is added dropwise to the cryovials and then the entire contents of the cryovials are transferred to a 15 mL conical tube. The volume of each sample is brought up to 12 mL by adding the appropriate volume of thaw buffer. The 15 mL tubes are then capped and inverted 3 times.

[00270] A ficoll density gradient separation is then performed by underlaying 2 mL of ambient temperature ficoll using a Pasteur pipette on the samples. Next, the tubes are centrifuged at 400 x g for 30 minutes at room temperature, the "buffy coat" aspirated, and the mononuclear cell layer transferred to a new 15 mL conical tube containing 9 mL thaw buffer. The cell layers are centrifuged at 400 x g for 5 minutes, the liquid aspirated, the cell pellet gently resuspended. Subsequently, 10 mLs ambient temperature RPMI + 1% FBS is added to the cell pellets and the cells centrifuged at 400 x g for 5 minutes. The cell pellet is resuspended in 1 mL PBS and, if necessary, cell clumps removed by filtering (Celltrics filters) or by pipetting.

[00271] 1 mL of PBS/Amine Aqua solution is added to the samples, the samples are

mixed thoroughly by pipetting, and are incubated in a 37°C water bath for 15 minutes.

[00272] After 15 minute incubation, 1 ml RPMI + 10% FBS is added to the samples, a 150 aliquot removed from each sample and is placed in a 12X75mm FACSTube. A cell count is performed on the AcTIO hematology analyzer. 5 mL RPMI + 10% FBS are added to the samples, the cells are centrifuged at 400 x g for 5 minutes, the liquid is aspirated, and the cells are resuspended at 1.25xl0 ⁶ cells/mL in RPMI + 10% FCS. The cells are kept in a 37°C water bath until ready to array in deep-well plates.

[00273] Treatment of Cells with Modulators: A concentration for each modulator (e.g., stimulant) that is five fold (5X) more than the final concentration is prepared using Media A as diluents. The 5X modulators (e.g., stimulants) are arrayed in a standard 96 well v- bottom plate that corresponds to the well on the plate with the cells to be stimulated. Fixative is prepared by dilution of stock 16% paraformaldehyde with PBS to a concentration that is 2.4%, then placed in a 37°C water bath. Once the plated cells have completed their incubation, the plate(s) are taken out of the incubator and placed in a 37°C water bath next to the pipette apparatus. Prior to addition of stimulant, each plate of cells is taken from the water bath and gently swirled to resuspend any settled cells. The stimulant is pipetted into the cell plate, which is then held over a vortexer set to "7" Atty Dkt o. 33118-747601 and mixed for 5 seconds, and followed by the return of the deep well plate to the water bath. Modulation times can include 5, 10, and 15 minutes in a 37°C water bath. For longer incubation times, or for assays measuring induced apoptosis, cells are modulated for 6-72h and restained with Amine Aqua viability dye prior to the fixation steps below.

[00274] Fixing Cells and Cell Permeabilzation: Fixation is performed using

approximately 2.4% paraformaldehyde (Electron Microscopy Sciences, Hatfield, PA) diluted in PBS and is added to cells for a final concentration of 1.6%. The cells are pipetted up and down three times to mix and incubated for 10 minutes at 37 C. Next, the plates are centrifuged at 1000 x g for 5 minutes at room temperature, the liquid aspirated from the cell pellets, and cell pellets are resuspended and the cells are permeabilized with 200 μίΛνεΙΙ 100% ice cold methanol (SigmaAldrich), is added while vortexing. Cell plates are then covered with a foil seal and stored overnight at -80°C.

[00275] Surface and intracellular cell staining: Plates from -80°C storage are centrifuged at 1000 x g for 5 minutes at room temperature, the supernatant is aspirated, and the cell pellet is disrupted by vortexing for 10 seconds and a speed of "3000." Then, the cell pellets are washed two times with 1 mL FACS Buffer (PBS 0.5% BSA, 0.05% NaN ₃ ), and are incubated at room temperature at room temperature, centrifuged at 1000 x g for 5 minutes at room temperature, supernatant aspirated, and the cell disrupted by vortexing as above.

[00276] Next, 20 of antibody cocktail is added to each well in the cell plate, the

mixture is pipetted up and down 3 times to mix, and the cells are incubated at 25 °C for 1 fir or 4°C overnight (16 hours). After incubation, cells are washed twice by the same procedure as above.

[00277] Subsequently, 10 ul of secondary antibody mix is added the cells, the mixture is pipetted up and down three times to mix, the plate covered, and the cells incubated at 25°C for 30 minutes. After incubation, cells are washed twice by the same procedure as above.

[00278] Cell fixation and preparation for flow cytometry: The cells are then fixed by

addition 1 mL of 1.6% PFA, the cells are covered and incubated at room temperature for

5 minutes. The cells are then centrifuged at 1000 x g for 5 minutes, the supernatant is aspirated, the cell pellet is disrupted by vortexing as above, the cells are resuspended in

100 μΙ_, FACS Buffer, and are mixed by pipetting up and down 4 times. The mixed cells are transferred to a 96-well u-bottom plate and 100 of pre-diluted (40 μί into 1 mL of

FACS Buffer) Sphero Rainbow 8-peak fluorescent beads to all wells. The plates are Atty Dkt o. 33118-747601 sealed with foil and placed at 4°C in the dark until ready for acquisition on the flow cytometer.

[00279] Example 2: SCNP differs between cleaved-PARP ⁺ and cleaved-PARP ^" cell

populations

[00280] Intracellular network responses of AML patient samples were modulated by SCF and analyzed using flow-cytometry based Single Cell Network Profiling (SCNP). The protocol was similar to the protocols listed above and in U.S. Ser. Nos. 61/350,864 and 12/460,029. For each sample, the CD34+ cell population was further gated into cleaved- PARP ⁺ and cleaved-PARP ^" cell populations using software such as Flowjo, DIVA (available from Becton Dickinson), and/or Winlist (available from Verity Software). The Mean Fluorescence Intensity (MFI) of various signaling nodes (pAKT, pS6, and pER ) obtained by flow-cytometry based SCNP was examined in as function of cleaved-PARP gating.

[00281] Gating scheme 1 does not incorporate cleaved PARP as part of the analysis.

Gating scheme 2 excludes all cleaved PARP+ (apoptotic) cells. Gating scheme 3 incorporates only cleaved PARP+ cells. The utility of incorporating cleaved PARP in the gating analysis allows one to measure signaling changes in samples or cell populations with considerable numbers of apoptotic cells.

[00282] For cell populations that appeared to have relatively few apoptotic cells, the

adjusted results for the cPARP- cell population (gating scheme 2) are similar to the results for the population which does not correct for cPARP (gating scheme 1). However, a difference in the level of cell signaling is seen when looking at the cPARP+ cells as there was very little effect from the stimulation, (data not shown) Other samples showed different separation between the basal and induced state, (data not shown)

[00283] For cell populations that appeared to have a relatively high number of apoptotic cells, the signaling profiles of a gated region with a majority of cleaved-PARP ⁺ cells were analyzed in several donor samples. The data were also gated for cKIT ⁺ in addition to cleaved-PARP ⁺ or cleaved-PARP ^" cells. There is a difference in cell signaling when there are many apoptotic or dead cells but the cells that are cPARP- can evoke a signal. With pAKT there is more discrimination between basal and induced signaling states in the cPARP- population. There is no difference between the basal and induced states in cPARP + populations (gating scheme 3) or cell populations that do not adjust for cPARP (gating scheme 1). Atty Dkt o. 33118-747601

Example 3

[00284] Cells from cell line HL60 were contacted with Gemtuzumab Ozogamicin (GO, also known as Mylotarg) a cytotoxic agent. The SCNP process was used on these cells in a manner similar to that shown in Example 1.

[00285] An antibody recognizing MCL-1 was tested 24h after GO treatment and it was found to identify cell populations with degraded MCL-1 upon drug treatment. The antibody was anti-MCL-1, clone Y37, rabbit IgG, titre: 0.5 ng/100,000 cells (from Eptiromics, cat: 1239-l, lot YH081901C2). It was used to stain the cells for 1 hour at 25°C. This is consistent with the known biology of MCL-1 undergoing degradation with induction of apoptosis.

Example 4

[00286] Intracellular MCL-1 levels were examined in leukemia cell lines and primary samples using a process similar to that shown in Example 1. Briefly, cryopreserved AML samples were thawed and ficoll purified and treated for 6h, 24h, 48h, or 72h under conditions: 1) Untreated, 2) PSC833 (an MDR drug transporter inhibitor), 3) GO (Gemtuzumab Ozogamicin) and 4) GO + PSC833. Cells were then stained with Aqua viability dye, fixed and permeabilized. Intracellular staining for MCL-1 along with other measures of apoptosis (Cleaved PARP), DNA Damage (pH2AX) and surface markers to identify leukemic cells was then performed.

[00287] A number of observations follow: 1) MCL-1 levels seem to upregulate from 6h to 24h in AML samples, particularly in the cPARP- fraction of cells (data not shown); 2) drug induced MCL-1 degradation can be measured as early as 24h in primary AML samples (data not shown), 3) Multiple subpopulations of cells can be identified in primary AML samples or cell lines defined by MCL-1 expression and Aqua viability dye, or MCL-1 expression and cleaved PARP (data not shown), 4) MCL-1 degradation tracked with cleavage of PARP and Aqua staining, other later measures of apoptosis (data not shown). Mylotarg and Mylotarg+PSC833 treated patient cells have higher downregulation of MCL-1), 5) MCL-1 degradation also corresponds to decreases in CD34, CD45 staining (other measures of drug induced apoptosis) (data not shown).

[00288] Our results indicate that we can identify cells that are Cleaved PARP negative and MCL-1 positive (healthy cells), Cleaved PARP negative and MCL-1 Low (Early Apoptotic) and Cleaved PARP positive and MCL-1 negative (Late Apoptotic). Also, Atty Dkt o. 33118-747601 increased MCL-1 levels in the cleaved PARP negative (healthy cells fraction) of AML samples treated with GO may represent cells refractory to chemotherapy through the mechanism of MCL-1 upregulation (data not shown).

Example 5

[00289] Figure 2 shows that high cleaved PARP levels in cells correlates with low

induced signaling. Figure 3 shows that bone marrow (BM) and peripheral blood (PB) cell signaling can be low when basal apoptosis is high, and cell signaling can be higher when basal apoptosis is low. In this example, PMA, IL-27, G-CSF, and FLT3L were used as modulators. In similar experiments, lower Jak/Stat signaling and PI3K signaling is observed in non-viable and/or apoptotic samples. The SCNP process was used on these cells in a manner similar to that described in Example 1.