ANTIBODY-BASED METHOD TO IDENTIFY, PURIFY, AND MANIPULATE

CELL TYPES AND PROCESSES

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

[0001] This invention was made with government support under U01GM094665, U54GM094662, RC1GM090825, and U01CA241981, awarded by the National Institutes of Health (NIH). The government has certain rights in the invention. FIELD OF THE INVENTION

[0002] The invention relates to compositions and methods of identifying, isolating, and modulating cells and tissues based on their cellular glycosaminoglycan pattern.

BACKGROUND

[0003] The surface characteristics of cells in multicellular organisms are a direct reflection of their function. Sensitive methods for detecting and defining the unique surface

characteristics of cells offer great opportunities for gaining new mechanistic insights and developing new therapeutic strategies. Glycosaminoglycans (GAG) such as heparan sulfates (HS) or chondroitin/dermatan sulfates (CS/DS) are ubiquitous on the cell surface of metazoans and are expressed with extraordinary temporal and spatial resolution. Since HS and CS/DS may be amongst the most diverse molecules in nature, they provide the potential to strongly discriminate between different cell types.

[0004] However, current analytical methods for HS and CS/DS glycan structure determination are expensive, technically challenging and often low resolution, thus limiting their discriminatory power and widespread use. Thus, novel tools to define structural characteristics of HS or CS/DS on the surface of cells and to use these characteristics to distinguish between cells for diagnostic and therapeutic applications are urgently needed.

SUMMARY OF THE INVENTION

[0005] The invention relates to anti-GAG motif binding agents, including, but not limited to anti-GAG motif antibodies and antigen binding fragments thereof, as well as method of using these anti-GAG motif binding agents thereof for the identification, isolation, and manipulation of cells and tissues based on cellular glycotypes.

[0006] In one aspect, provided is a method of identifying a glycosaminoglycan (GAG) glycotype for a cell, the method comprising:

(a) contacting the cell with one or more anti-GAG motif antibodies or antigen-binding fragments thereof;

(b) assessing the binding of the one or more anti-GAG motif antibodies or antigen- binding fragments thereof to the cell; and

(c) assigning a GAG glycotype to the cell based on binding of the one or more antibodies or antigen-binding fragments thereof to the cell.

[0007] In one aspect, provided is a method of isolating a target cell from a mixture of cells based on the target cell’s GAG glycotype, the method comprising:

(a) contacting the mixture of cells with one or more anti-GAG motif antibodies or antigen-binding fragments thereof that bind to one or more GAG motifs on the surface of the target cell; and

(b) separating the target cell from the cell mixture.

[0008] In one embodiment, the one or more anti-GAG motif antibodies or antigen-binding fragments thereof comprises an affinity tag. In one embodiment, the method further comprises a step of contacting the target cell bound to the one or more anti-GAG motif antibodies or antigen binding fragments thereof with a medium that has a higher affinity for the affinity tag than the remainder of the mixture or composition.

[0009] In one aspect, provided is a method of identifying a cell based on its GAG glycotype, the method comprising:

(a) contacting the cell to one or more anti-GAG motif antibodies or antigen-binding

fragments thereof;

(b) assessing the binding of the one or more anti-GAG motif antibodies or antigen- binding fragments thereof to the cell; and

(c) comparing the binding of the one or more anti-GAG motif antibodies or antigen- binding fragments thereof to the cell to the binding of the one or more anti-GAG motif antibodies or antigen-binding fragments thereof to a reference cell.

[0010] In one aspect, provided is a method of detecting a disease or disorder in a subject, the method comprising:

(a) providing one or more cells derived from the subject; (b) contacting the one or more cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof;

(c) measuring binding of the one or more anti-GAG motif antibodies or antigen binding fragments to the one or more cells; and

(d) detecting the disease or disorder if binding of the one or more anti-GAG motif

antibodies or antigen binding fragments to the one or more cells is detected.

[0011] In one aspect, provided is a method of detecting a disease or disorder in a subject, the method comprising:

(a) providing one or more cells derived from the subject;

(b) contacting the one or more cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof;

(c) measuring binding of the one or more anti-GAG motif antibodies or antigen binding fragments thereof to the one or more cells; and

(d) detecting the disease or disorder if binding of the one or more anti-GAG motif

antibodies or antigen binding fragments thereof to the one or more cells is not detected.

[0012] In some embodiments, the one or more cells are provided in a sample. In some embodiments, the sample is a blood, bone marrow, serum, plasma, urine, feces, or tissue biopsy sample.

[0013] In one aspect, provided is a method of monitoring the progression of a disease or disorder in a subject, the method comprising:

(a) providing one or more cells derived from the subject;

(b) contacting one or more cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof;

(c) measuring binding of the one or more anti-GAG motif antibodies or antigen binding fragments thereof to the one or more cells; and

(d) comparing the binding of the one or more anti-GAG motif antibodies or antigen

binding fragments thereof to the one or more cells with the binding of the one or more anti-GAG motif antibodies or antigen binding fragments thereof to one or more cells obtained from the same patient at an earlier time.

[0014] In one aspect, provided is a method of treating and/or preventing a disease in a subject in need thereof, the method comprising administering to the subject an effective amount of one or more anti-GAG motif antibodies or antigen binding fragments thereof, wherein at least one anti-GAG motif antibody or antigen binding fragments thereof is conjugated to a therapeutic moiety, and wherein the one or more anti-GAG motif antibodies or antigen binding fragments thereof bind to one or more GAG motifs on the surface of the target cell or target tissue. In some embodiments, at least one of the one or more GAG motif antibodies or antigen-binding fragments thereof is conjugated to a detectable moiety. In some embodiments, the detectable moiety is fluorescent.

[0015] In some embodiments of the methods disclosed herein, at least one of the one or more GAG motif antibodies or antigen-binding fragments thereof is conjugated to an affinity tag.

[0016] In some embodiments of the methods disclosed herein, at least one of the one or more GAG motif antibodies or antigen-binding fragments thereof is conjugated to a magnetic moiety.

[0017] In some embodiments of the methods disclosed herein, at least one of the one or more GAG motif antibodies or antigen-binding fragments thereof is conjugated to a Sortase motif.

[0018] In one aspect, provided is a method of delivering a payload to a target cell based on the target cell’s glycotype, the method comprising contacting a cell with an anti-GAG motif antibody or antigen binding fragment thereof, wherein the anti-GAG motif antibody or antigen-binding fragment thereof is conjugated to the payload and wherein the anti-GAG motif antibody or antigen-binding fragment thereof bind to one or more GAG motifs on the surface of the target cell.

BRIEF DESCRIPTION OF THE FIGURES

[0019] Figure 1 illustrates the organization of a heparan sulfate (HS) glycan chain (Figure 1A) and HS disaccharide (Figure 1B). In Figure 1A, HS domain structure is indicated (NS, N-sulfated; NS/NA, N-sulfated/ acetylated; NA, N-acetylated) as well as putative protein binding motifs (e.g. FGF-1). HS is attached to core proteins via a tetrasaccharide linker region. In Figure 1B, a characteristic HS disaccharide is shown as well as the linkages that connect them. Gene names of enzymes that introduce various HS modifications are shown. GLCE, HS C5-glucuronyl-epimerase; HS6ST, HS 6-O-sulfotransferase; HS2ST, HS 2-O- sulfotransferase; HS3ST, HS 3-O-sulfotransferase; NDST, N-deacetylase-N-sulfotransferase. [0020] Figure 2 illustrates that anti-GAG motif scFvs expressed on the surface of reporter cells can be used to glycotype cell lines by measuring cell-cell interactions. Figure 2A Anti- HS motif scFvs were fused to a transmembrane domain, which is turn fused to a green fluorescent protein. The fusion proteins were then expressed on the surface of HEK cells (“reporter cells”). The reporter cells were mixed with suspension adapted HEK or CHO cells (“sample cells”), respectively, which were fluorescently labeled with cyto-tracker dye.

Binding (double positive events) were detected by flow cytometry. Figure 2B Representative experimental data from flow cytometry with reporter cells expressing anti-HS motif scFvs HS4C3. Figure 2C. Adherent MIA PaCa-2 cancer cells (“Cancer”) or immortalized primary pancreatic duct control cells (“Control”) were interrogated by reporter cells expressing scFv LKIV69.

[0021] Figure 3 illustrates the concept of“glycotyping”. Figure 3A illustrates a suite of anti-GAG motif antibodies or antigen binding fragments thereof. Figure 3B illustrates differential binding of a suite of anti-GAG motif antibodies or antigen binding fragments thereof to different cell types. Figure 3C shows the“glycotype” of four homogeneous cell populations as determined by using the cell-cell interaction assay with reporter and sample cells used in Figure 2. Black square indicates binding. Crossed square = intermediate binding, white square = no binding. ND, not determined.

[0022] Figure 4 shows the binding profile of 5 hematopoietic cell lines (as indicated: HEL, MEL, MOLM-14, THP-1, K-562) using purified, His-tagged scFvs. Signal was detected using a secondary anti-HIS-PE (Phycoerythrin) antibody. Cell lines 32D and BAF3- EpoR, which do not express HS proteoglycans were used as controls. scFv MPB49, which does not bind to HS, served as a control.

[0023] Figure 5 illustrates that anti-HS motif antibodies or antigen binding fragments can be used to characterize primary hematopoietic cell lineages. Figure 5A shows the gating schema for the isolation of hematopoietic bone marrow stem and progenitor cell (HSPC) populations. Figure 5B shows HS profiling of various HSPC populations using different purified, His-tagged anti-HS motif antibodies in scFv format. MPB49 served as a negative control. Signal was detected using a secondary anti-His-PE antibody. HSC = hematopoietic stem cells. MPP = multipotent progenitor cells. Pre-GM: Granulocyte/monocyte progenitor cells. GMP = Committed granulocyte/monocyte progenitor cells. Pre-MegE =

Megakaryocyte/Erythrocyte progenitor cells. MkP = Committed megakaryocyte progenitor cells. Pre-CFU-E = Immature committed erythrocyte progenitor cells. CFU-E = Committed erythrocyte progenitor cells.

[0024] Figure 6 shows differential HS profiling of erythrocytes and megakaryotes by anti- HS motif antibodies. HS profiling was performed using purified, His-tagged anti-HS motif antibodies in scFv format. Signal was detected using a secondary anti-His-PE antibody.

[0025] Figure 7 illustrates that anti-HS motif antibodies can be used to identify functionally distinct cell populations that cannot be distinguished based on the existing CD system. Figure 7A shows sorting of total c-kit ⁺ bone marrow cells using the HS-specific scFv EW4E9. Figure 7B shows the results of a megakaryocyte forming assay for the two cell populations shown in Figure 7A. Statistical significance is indicated (* = 0.02).

[0026] Figure 8 illustrates conserved HS scFv patterning within human megakaryocyte and erythroid differentiation. Figure 8A shows representative FACS density plot (upper panel) and morphology (lower panel) of human CD34 ⁺ cells. Figure 8B shows histograms of HS scFv binding to human CD34 ⁺ cells.

[0027] Figure 9 illustrates that HS-related genes are significantly differentially expressed within human common myeloid progenitor cell (CMP), granulocyte-monocyte progenitor (GMP), and megakaryocyte-erythrocyte progenitors (MEP) populations from GSE19599 (gene expression profiling of normal hematopoietic cell subpopulations; Andersson et al. BMC Med Genomics 2010 Mar 8;3:6).

[0028] Figure 10 illustrates HS modification alteration of the TF-1 cell line upon erythroid and megakaryocyte differentiation. Figure 10A provides a schematic of TF-1 differentiation into erythroid and megakaryocytic cells. Figure 10B illustrates the

morphological (upper panels) and immunophenotypic (lower panels) validation of erythroid and megakaryocyte differentiation of TF-1 cells. Figure 10C shows representative histograms of HS scFv binding of TF-1 cells in parental (grey), megakaryocyte (green) and erythroid (red) differentiation conditions. (n = 3).

DETAILED DESCRIPTION OF THE INVENTION

[0029] The invention relates to anti-glycosaminoglycans (GAG) motif antibodies and antigen binding fragments thereof as well as method of using these antibodies and antigen binding fragments thereof for the identification, isolation, and manipulation of cells and tissues based on cellular glycotypes. [0030] After binding of anti-GAG motif antibodies or antigen binding fragments thereof to cells, the cells remain intact and alive, allowing isolation, downstream analysis and manipulation of the isolated cells. Conversely, conjugation of anti-GAG motif antibodies or antigen binding fragments to cytotoxic agents allows targeted killing of undesired and/or pathogenic cells.

[0031] The surface characteristics of cells in multicellular organisms are a direct reflection of their function within the organism and are often used to classify them. Sensitive methods for detecting and defining novel or unique cell surface features at“higher resolution” and with greater dynamic precision could offer great mechanistic insight and therapeutic potential for the detection of malignancies and development of novel therapeutic approaches. For example, the cluster of differentiation (CD) marker system has revolutionized

characterization, isolation, and targeting of hematopoietic, and many other cells. However, the number of reliable CD markers to isolate or target specific and homogenous cell types, and the resolution of separation of different cell types, widely varies between markers used and cell populations studied.

[0032] GAGs such as heparan sulfate (HS) are ubiquitous, essential glycans, which are invariably attached to proteins (to form e.g. HS proteoglycans (HSPG)) and, are common to all cellular surfaces in multicellular organisms. HS glycans comprise long, unbranched polymers of disaccharides (glucuronic/iduronic acid– N-Acetyl-glucosamine for HS (see Figure 1) and contribute to a multitude of functions in metazoan development, homeostasis, microbial infection, and immunity. An evolutionarily conserved network of HS modifying enzymes catalyzes the partial modification of the HS glycan polymer by de-acetylation, epimerization and sulfation (see Figure 1). As a consequence, HS are often described as the most chemically and physically complex macromolecules in nature. Genetic and biochemical evidence demonstrate that many functions of HSPGs are controlled by specific HS modification patterns. These modification patterns are characteristic of specific cell and tissue types and states, and govern a wide spectrum of glycan-protein interactions.

[0033] The above said applies also to chondroitin/dermatan sulfate (CS/DS), which differs from HS only in that glucosamine is replaced by galactosamine. A conceptually similar, but molecularly distinct set of modification enzymes modifies CS/DS in various positions along the glycan chains to create a comparable molecular diversity. [0034] GAG glycotype

[0035] In one aspect, disclosed herein are methods of determining the GAG glycotype of a cell, a cell type and/or a tissue. As used herein, a“GAG glycotype”, or short,“glycotype” is a classification system that classifies cells or tissues based on their binding to one or more antibodies or antigen-binding fragments thereof that bind to HS motifs or CS/DS motifs. As such, the GAG glycotype is a characterization of the sum of HS and CS/DS cell surface characteristics.

[0036] In one aspect, provided are antibodies or antigen-binding fragments thereof that recognize GAG motifs (such as a HS motif or a CS/DS motif) and that can be used for determining a GAG glycotype. As used herein, an“HS motif” is a combination of different HS modifications that are spatially arranged along a glycan chain attached to a protein on a cell’s surface to provide a binding motif (antigen) for an anti-HS-motif-antibody or antigen- binding fragment thereof. As used herein, a“CS/DS motif” is a combination of different CS/DS modifications that are spatially arranged along a glycan chain attached to a protein on a cell’s surface to provide a binding motif (antigen) for an anti-CS-motif-antibody or antigen- binding fragment thereof. In vivo, some HS motifs appear quite common and are widely distributed across tissues, whereas others seem less common, and can be as rare as single cell-specific in the nematode C. elegans. [0037] Antibodies and antibody fragments that bind to GAG motifs

[0038] In one aspect, provided are antibodies or antigen-binding fragments thereof that bind to GAG motifs. In some embodiments, the anti-GAG motif antibodies or antigen- binding fragments thereof bind to an HS motif. In some embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof bind to a CS/DS motif.

[0039] In some embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is an anti-HS motif antibody or an anti-CD/DS motif antibody in scFv format previously described, see Table 1 and Table 2. For a limited number of scFvs listed in Table 1, individual HS modifications required for binding have been determined in vitro and in vivo. Table 1 Selected anti-HS motif antibodies (scFv format). Indicated are individual anti-HS motif antibodies (in scFv format), the parental heavy chain from the antibody is derived from, the sequence of heavy chain CDR3 (CDR3H), known HS modification that are part of the HS motif recognized by the indicated antibody, and the corresponding scientific reference (Ref.). “+” = required.”–“ = not required. in. = inhibitory. (+) = partially required. # control antibody shown to not bind to HS. NAc = N-acetylated glucosamine. NS = N-sulfated glucosamine. C5 = C5-epimerization.2S = 2-O-sulfation.6S = 6-O-sulfation.3S = 3-O- sulfation. [1] Dennissen et al (2002). J Biol Chem 277, 10982-10986. [2] Attreed et al (2012). Nat Methods 9, 477-479. [3] van de Westerlo et al (2002). Blood 99, 2427-2433. [4] Attreed et al (2015). Methods Mol Biol 1229, 253-268. [5] Attreed et al (2016). Glycobiology 26, 862-870. [6] van Kuppevelt et al (1998). J Biol Chem 273, 12960-12966. [7] Smits, N.C., Lensen et al (2006). Methods Enzymol 416, 61-87. [8] Wijnhoven et al (2008). Glycoconj J 25, 177-185. [9] ten Dam et al (2004). J Biol Chem 279, 38346-38352. [10] Smits et al (2010). J Biol Chem 285, 41143-41151. [11] Jenniskens et al (2000). J Neurosci 20, 4099- 4111.

Table 2 Selected anti-CS motif antibodies (scFv format). Indicated are individual anti-CS motif antibodies (in scFv format), the parental heavy chain from the antibody is derived from, the sequence of heavy chain CDR3, and the corresponding scientific reference. [12] Smetsers et al (2004). J Invest Dermatol 122, 707-716. [13] Purushothaman et al (2007). J Biol Chem 282, 19442-19452.

[0040] Also provided are scFvs generated based on information available in the references listed in Tables 1 and Table 2 as well as references therein (e.g. Tomlinson et al., J. Mol. Biol. (1992), 227:776-798; Nissim et al., EMBO (1994), 13(3):692-698; Marks et al., J. Mol. Biol. (1991) 222:581-597). The variable light chain of the scFvs was synthesized de novo based on the V ^3-BSA sequence from Marks et al. (J. Mol. Biol. (1991) 222:581-597) and the linker on Huston et al. (PNAS (1988) 85:5879-5883). In some embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof are scFvs and comprise one or more of the SEQ ID NOs:1-42. Variable heavy chains are indicated in bold and the variable light chain in regular font, respectively. The linker is underlined as follows: linker. Each heavy and light variable chain comprises three CDRs. The heavy chain CDRs are CDR1H, CDR2H, and CDR3H. The light chain CDRs are CDR1L, CDR2L, and CDR3L. The complementary regions are underlined as follows: CDR1, CDR2, and CDR3.

[0041] Anti-HS motif scFvs

[0042] SEQ ID NO 1 (AO4B08)

[0079] A iCS if F

[0080]

[0085] In some embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein comprise one, two, or three of the heavy and/or of the light chain CDRs of SEQ ID NOs:1-42. In some embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein comprise CDR1H, CDR2H, and CDR3H of any of SEQ ID NOs:1-42. In some embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein comprise CDR1L, CDR2L, and CDR3L of any of SEQ ID NOs:1-42. In some embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein comprise CDR1H, CDR2H, CDR3H, CDR1L, CDR2L, and CDR3L of any of SEQ ID NOs:1-42.

[0086] Based on the anti-GAG motif-antibodies or antigen-binding fragments thereof disclosed herein, it would be a routine matter for those skilled in the art to design and produce additional anti-GAG motif-antibodies or antigen-binding fragments thereof for use in the present methods by, e.g., designing and producing additional anti-GAG motif-antibodies that comprise the variable region sequences and/or CDRs of the anti-GAG motif-antibodies disclosed herein. Moreover, it would be a routine matter to design additional anti-GAG motif-antibodies that comprise variable region sequences or CDRs that have certain specified levels of identity in amino acid sequence to the variable region sequences or CDRs of the anti-GAG motif-antibodies disclosed herein.

[0087] In designing and producing additional anti-GAG motif-antibodies those skilled in the art may be guided by certain well known features of antibodies. The structure of typical naturally occurring antibodies is well known and includes two identical heavy chains and two identical light chains, with each light chain covalently linked to a heavy chain by an interchain disulfide bond. The two heavy chains are linked to one another by additional disulfide bonds. Individual heavy and light chains can fold into domains having similar sizes (e.g.110-125 amino acids) and structures, but different functions. Light chains can comprise one variable domain (VL) and/or one constant domain (CL). Heavy chains can also comprise one variable domain (VH) and/or three or four constant domains (CH1, CH2, CH3 and CH4), depending on the class or isotype of antibody. In humans, the isotypes are IgA, IgD, IgE, IgG, and IgM, with IgA and IgG further subdivided into subclasses or subtypes (IgA1-2 and IgG1-4).

[0088] It has been found to be convenient to consider certain portions of antibody molecules individually. The portion of an antibody consisting of VL and VH domains is designated Fv (fragment variable) and constitutes the antigen-binding site. An antibody fragment containing a VL domain and a VH domain on one polypeptide chain is referred to as a single chain Fv (scFv) and generally contains the N terminus of one domain and the C terminus of the other domain joined by a flexible linker (see, e.g., U.S. Patent No.4,946,778 and International Patent Publication WO 88/09344. Accordingly, in some embodiments of the aspects described herein, the anti-GAG motif antibody fragment is an Fv fragment comprising or consisting essentially of the VL and VH domains of a single arm of an antibody. For certain embodiments disclosed herein, it may be advantageous to employ scFv fragments because scFv fragments lack some or all of the constant domains of whole antibodies. Therefore, they can overcome some of the disadvantages associated with the use of whole antibodies. For example, scFv fragments tend to be free of certain undesired interactions between heavy-chain constant regions and other biological molecules.

[0089] In certain embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein are multivalent single chain antibodies, where multiple single chain antibodies, each single chain having one VH and one VL domain covalently linked by a first peptide linker, are covalently linked by at least one or more second peptide linkers to form a multivalent single chain antibody. Each chain of a multivalent single chain antibody includes a variable light chain fragment and a variable heavy chain fragment, and is linked by the second peptide linker to at least one other chain. The second peptide linker is preferably composed of at least fifteen and fewer than one hundred amino acid residues.

[0090] In certain embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein are diabodies, where two single chain antibodies are combined to form a diabody. Diabodies have two chains and two binding sites, each specific for a GAG motif. Each chain of the diabody includes a VH domain connected to a VL domain. The domains are connected with linkers that are short enough to prevent pairing between domains on the same chain, thus driving the pairing between complementary domains on different chains to recreate the two antigen-binding sites.

[0091] In certain embodiments, anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein are triabodies, where three single chain antibodies are combined to form a triabody. In triabodies, the amino acid terminus of a VL or VH domain is directly fused to the carboxyl terminus of a VL or VH domain, i.e., without any linker sequence. The triabody has three Fv heads with the polypeptides arranged in a cyclic, head-to-tail fashion.

[0092] In certain embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is a Fab fragment, which comprises or consist essentially a variable (VL) and constant (CL) domain of the light chain and a variable domain (VH) and the first constant domain (CH1) of the heavy chain. In certain embodiments, the anti-GAG motif antibody or antigen- binding fragment thereof is a Fab' fragment, which refers to a Fab fragment having one or more cysteine residues at the C-terminus of the CH1 domain. In certain embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is a F(ab')2 fragment, which comprises a bivalent fragment comprising two Fab' fragments linked by a disulfide bridge at the hinge region.

[0093] In certain embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is an Fd fragment comprising or consisting essentially of VH and CH1 domains.

[0094] In certain embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is an Fd' fragment comprising VH and CH1 domains and one or more cysteine residues at the C-terminus of the CH1 domain.

[0095] In certain embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is a dAb fragment comprising or consisting essentially of a VH domain.

[0096] Linear antibodies refers to the antibodies as described in Zapata et al., Protein Engin., 8(10):1057-1062 (1995). Briefly, these antibodies comprise a pair of tandem Fd segments (VH-CH1-VH-CH1), which, together with complementary light chain

polypeptides, form a pair of antigen binding regions. Linear antibodies can be bispecific or monospecific.

[0097] In certain embodiments, the anti-GAG motif antibody or antigen-binding fragment thereof is a linear antibody comprising a pair of tandem Fd segments (VH-CH1-VH-CH1) which, together with complementary light chain polypeptides, form a pair of antigen binding regions.

[0098] It is noted that the methods of the invention are not limited to antibodies or antigen binding fragments thereof. Also disclosed is the use other anti-GAG motif binding agents that selectively bind GAG motifs, as such aptamers. As used herein,“binding” to a GAG motif includes the selective interaction of the binding agent with the GAG motif. Binding therefore includes, e.g., primary and secondary interactions including hydrogen bonds, ionic interactions, salt bridges, as well as hydrophilic and hydrophobic interactions. The terms “selective” and "selectivity" herein refer to the preferential binding of a binding agent (including, but not limited to an anti-GAG motif antibody or antigen binding fragment thereof) for a particular GAG motif, as opposed to binding to one or more other biological molecules. [0099] Antibody modifications

[0100] In some embodiments, the anti-GAG motif antibodies and antigen-binding fragments thereof disclosed herein are used in medium-throughput or high-throughout multiplex assays. As such, in some embodiments, the anti-GAG motif antibodies and antigen- binding fragments thereof disclosed herein may be covalently or non-covalently conjugated to a detectable moiety. Examples of detectable moieties provided herein include fluorescent moieties or labels, imaging agents, radioisotopic moieties, radiopaque moieties, and the like, e.g. detectable labels such as biotin, fluorophores, chromophores, spin resonance probes, or radiolabels. Exemplary fluorophores include fluorescent dyes and other luminescent molecules . A fluorophore may be environmentally sensitive such that its fluorescence changes if it is located close to one or more residues in the modified protein that undergo structural changes upon binding a substrate (e.g. dansyl probes). Exemplary radiolabels include small molecules containing atoms with one or more low sensitivity nuclei ( ¹³ C, ¹⁵ N, ² H, 125I, 123I, 99Tc, 43K, 52Fe, 67Ga, 68Ga, 111In and the like). Other useful moieties are known in the art.

[0101] In certain embodiments, the anti-GAG motif antibodies and antigen-binding fragments thereof are covalently or non-covalently linked to a fluorescent protein or tag. Examples of fluorescent tags and proteins include, but are not limited to, (3-F)Tyr-EGFP, A44-KR, aacuGFP1, aacuGFP2, aceGFP, aceGFP-G222E-Y220L, aceGFP-h, AcGFP1, AdRed, AdRed-C148S, aeurGFP, afraGFP, alajGFP1, alajGFP2, alajGFP3, amCyan1, amFP486, amFP495, amFP506, amFP515, amilFP484, amilFP490, amilFP497, amilFP504, amilFP512, amilFP513, amilFP593, amilFP597, anm1GFP1, anm1GFP2, anm2CP, anobCFP1, anobCFP2, anobGFP, apulFP483, AQ14, AQ143, Aquamarine, asCP562, asFP499, AsRed2, asulCP, atenFP, avGFP, avGFP454, avGFP480, avGFP509, avGFP510, avGFP514, avGFP523, AzamiGreen, Azurite, BDFP1.6, bfloGFPa1, bfloGFPc1, BFP, BFP.A5, BFP5, bsDronpa (On), ccalGFP1, ccalGFP3, ccalOFP1, ccalRFP1, ccalYFP1, cEGFP, cerFP505, Cerulean, CFP, cFP484, cfSGFP2, cgfmKate2, CGFP, cgfTagRFP, cgigGFP, cgreGFP, CheGFP1, CheGFP2, CheGFP4, Citrine, Citrine2, Clomeleon, Clover, cp-mKate, cpCitrine, cpT-Sapphire174-173, CyOFP1, CyPet, CyRFP1 (CyRFP1), d-RFP618, D10, d1EosFP (Green), d1EosFP (Red), d2EosFP (Green), d2EosFP (Red), deGFP1, deGFP2, deGFP3, deGFP4, dendFP (Green), dendFP (Red), Dendra (Green), Dendra (Red), Dendra2 (Green), Dendra2 (Red), Dendra2-M159A (Green), Dendra2-M159A (Orange), Dendra2-T69A (Green), Dendra2-T69A (Orange), dfGFP, dimer1, dimer2, dis2RFP, dis3GFP, dKeima, dKeima570, dLanYFP, DrCBD, Dreiklang (On), Dronpa (On), Dronpa-2 (On), Dronpa-3 (On), dsFP483, DspR1, DsRed, DsRed-Express, DsRed-Express2, DsRed- Max, DsRed.M1, DsRed.T3, DsRed.T4, DsRed2, DstC1, dTFP0.1, dTFP0.2, dTG, dTomato, dVFP, E2-Crimson, E2-Orange, E2-Red/Green, EaGFP, EBFP, EBFP1.2, EBFP1.5, EBFP2, ECFP, ECFPH148D, ECGFP, eechGFP1, eechGFP2, eechGFP3, eechRFP, efasCFP, efasGFP, eforCP, EGFP, eGFP203C, eGFP205C, Emerald, Enhanced Cyan-Emitting GFP, EosFP (Green), EosFP (Red), eqFP578, eqFP611, eqFP611V124T, eqFP650, eqFP670, EYFP, EYFP-Q69K, fabdGFP, ffDronpa (On), FoldingReporterGFP, FP586, FPrfl2.3, FR-1, FusionRed, FusionRed-M, G1, G2, G3, Gamillus (On), Gamillus0.1, Gamillus0.2,

Gamillus0.3, Gamillus0.4, GCaMP2, gfasGFP, GFP(S65T), GFP-151pyTyrCu, GFP- Tyr151pyz, GFPmut2, GFPmut3, GFPxm16, GFPxm161, GFPxm162, GFPxm163,

GFPxm18, GFPxm181uv, GFPxm18uv, GFPxm19, GFPxm191uv, GFPxm19uv, H9, HcRed, HcRed-Tandem, HcRed7, hcriGFP, hmGFP, HriCFP, HriGFP, iFP1.4, iFP2.0, iLov, iq- EBFP2, iq-mApple, iq-mCerulean3, iq-mEmerald, iq-mKate2, iq-mVenus, iRFP670, iRFP682, iRFP702, iRFP713, iRFP720, IrisFP (Green), IrisFP (Orange), IrisFP-M159A (Green), Jred, Kaede (Green), Kaede (Red), Katushka, Katushka-9-5, Katushka2S, KCY, KCY-G4219, KCY-G4219-38L, KCY-R1, KCY-R1-158A, KCY-R1-38H, KCY-R1-38L, KFP1 (On), KikGR1 (Green), KikGR1 (Red), KillerOrange, KillerRed, KO, Kohinoor (On), laesGFP, laGFP, LanFP1, LanFP2, lanRFP-DS83l, LanYFP, laRFP, LSS-mKate1, LSS- mKate2, LSSmOrange, M355NA, mAmetrine, mApple, Maroon0.1, mAzamiGreen, mBanana, mBeRFP, mBlueberry1, mBlueberry2, mc1, mc2, mc3, mc4, mc5, mc6, McaG1, McaG1ea, McaG2, mCardinal, mCarmine, mcavFP, mcavGFP, mcavRFP, mcCFP, mCerulean, mCerulean.B, mCerulean.B2, mCerulean.B24, mCerulean2, mCerulean2.D3, mCerulean2.N, mCerulean2.N(T65S), mCerulean3, mCherry, mCherry2, mCitrine, mClavGR2 (Green), mClavGR2 (Red), mClover3, mCyRFP1, mECFP, meffCFP, meffGFP, meffRFP, mEGFP, meleCFP, meleRFP, mEmerald, mEos2 (Green), mEos2 (Red), mEos2- A69T (Green), mEos2-A69T (Orange), mEos3.1 (Green), mEos3.1 (Red), mEos3.2 (Green), mEos3.2 (Red), mEos4a (Green), mEos4a (Red), mEos4b (Green), mEos4b (Red), mEosFP (Green), mEosFP (Red), mEosFP-F173S (Green), mEosFP-F173S (Red), mEosFP-M159A (Green), mEYFP, MfaG1, mGarnet, mGarnet2, mGeos-C (On), mGeos-E (On), mGeos-F (On), mGeos-L (On), mGeos-M (On), mGeos-S (On), mGinger1, mGinger2, mGrape1, mGrape2, mGrape3, mHoneydew, MiCy, mIFP, miniSOG, miniSOGQ103V, miniSOG2, miRFP, miRFP670, miRFP670nano, miRFP670v1, miRFP703, miRFP709, miRFP720, mIrisFP (Green), mIrisFP (Red), mK-GO (Early), mK-GO (Late), mKalama1, mKate, mKateM41GS158C, mKateS158A, mKateS158C, mKate2, mKeima, mKelly1, mKelly2, mKG, mKikGR (Green), mKikGR (Red), mKillerOrange, mKO, mKO2, mKOk, mLumin, mMaple (Green), mMaple (Red), mMaple2 (Green), mMaple2 (Red), mMaple3 (Green), mMaple3 (Red), mMaroon1, mmGFP, mMiCy, mmilCFP, mNectarine, mNeonGreen, mNeptune, mNeptune2, mNeptune2.5, mNeptune681, mNeptune684, Montiporasp.#20-9115, mOrange, mOrange2, moxBFP, moxCerulean3, moxDendra2 (Green), moxDendra2 (Red), moxGFP, moxMaple3 (Green), moxMaple3 (Red), moxNeonGreen, moxVenus, mPapaya, mPapaya0.7, mPlum, mPlum-E16P, mRaspberry, mRed7, mRed7Q1, mRed7Q1S1, mRed7Q1S1BM, mRFP1, mRFP1-Q66C, mRFP1-Q66S, mRFP1-Q66T, mRFP1.1, mRFP1.2, mRojoA, mRojoB, mRouge, mRtms5, mRuby, mRuby2, mRuby3, mScarlet, mScarlet-H, mScarlet-I, mStable, mStrawberry, mT-Sapphire, mTagBFP2, mTangerine, mTFP0.3, mTFP0.7 (On), mTFP1, mTFP1-Y67W, mTurquoise, mTurquoise2, muGFP, mUkG, mVenus, mVenus-Q69M, mVFP, mVFP1, mWasabi, Neptune, NijiFP (Green), NijiFP (Orange), NowGFP, obeCFP, obeGFP, obeYFP, OFP, OFPxm, oxBFP, oxCerulean, oxGFP, oxVenus, P11, P4, P4-1, P4-3E, P9, PA-GFP (On), Padron (On), Padron(star) (On), Padron0.9 (On), PAmCherry1 (On), PAmCherry2 (On), PAmCherry3 (On), PAmKate (On), PATagRFP (On), PATagRFP1297 (On), PATagRFP1314 (On), pcDronpa (Green), pcDronpa (Red), pcDronpa2 (Green), pcDronpa2 (Red), PdaC1, pdae1GFP, phiYFP, phiYFPv, pHluorin,ecliptic, pHluorin,ecliptic (acidic), pHluorin,ratiometric (acidic),

pHluorin,ratiometric (alkaline), pHluorin2 (acidic), pHluorin2 (alkaline), pHuji, PlamGFP, pmeaGFP1, pmeaGFP2, pmimGFP1, pmimGFP2, Pp2FbFP, Pp2FbFPL30M, ppluGFP1, ppluGFP2, pporGFP, pporRFP, PS-CFP (Cyan), PS-CFP (Green), PS-CFP2 (Cyan), PS- CFP2 (Green), psamCFP, PSmOrange (Far-red), PSmOrange (Orange), PSmOrange2 (Far- red), PSmOrange2 (Orange), ptilGFP, R3-2+PCB, RCaMP, RDSmCherry0.1,

RDSmCherry0.2, RDSmCherry0.5, RDSmCherry1, rfloGFP, rfloRFP, RFP611, RFP618, RFP630, RFP637, RFP639, roGFP1, roGFP1-R1, roGFP1-R8, roGFP2, rrenGFP, RRvT, rsCherry (On), rsCherryRev (On), rsCherryRev1.4 (On), rsEGFP (On), rsEGFP2 (On), rsFastLime (On), rsFolder (Green), rsFolder2 (Green), rsFusionRed1 (On), rsFusionRed2 (On), rsFusionRed3 (On), rsTagRFP (ON), Sandercyanin, Sapphire, sarcGFP, SBFP1, SBFP2, SCFP1, SCFP2, SCFP3A, SCFP3B, scubGFP1, scubGFP2, scubRFP, secBFP2, SEYFP, sg11, sg12, sg25, sg42, sg50, SGFP1, SGFP2, SGFP2(206A), SGFP2(E222Q), SGFP2(T65G), SHardonnay, shBFP, shBFP-N158S/L173I, ShG24, Sirius, SiriusGFP, Skylan-NS (On), Skylan-S (On), smURFP, SNIFP, SOPP, SOPP2, SOPP3, SPOON (on), stylGFP, SuperfolderGFP, SuperfoldermTurquoise2, SuperfoldermTurquoise2ox,

SuperNovaGreen, SuperNovaRed, SYFP2, T-Sapphire, TagBFP, TagCFP, TagGFP, TagGFP2, TagRFP, TagRFP-T, TagRFP657, TagRFP675, TagYFP, td-RFP611, td-RFP639, tdimer2(12), tdKatushka2, TDsmURFP, tdTomato, tKeima, Topaz, TurboGFP, TurboGFP- V197L, TurboRFP, Turquoise-GL, Ultramarine, UnaG, usGFP, Venus, VFP, vsfGFP-0, vsfGFP-9, W1C, W2, W7, WasCFP, Wi-Phy, YPet, zFP538, zoan2RFP, ZsGreen,

ZsYellow1, aGFP, 10B, 22G, 5B, 6C, A1a, aacuCP, acanFP, ahyaCP, amilCP, amilCP580, amilCP586, amilCP604, apulCP584, BFPsol, Blue102, CFP4, cgigCP, CheGFP3, Clover1.5, cpasCP, Cy11.5, dClavGR1.6, dClover2, dClover2A206K, dhorGFP, dhorRFP, dPapaya0.1, Dronpa-C62S, DsRed-Timer, echFP, echiFP, EYFP-F46L, fcFP, fcomFP, Fpaagar,

Fpag_frag, Fpcondchrom, FPmann, FPmcavgr7.7, Gamillus0.5, gdjiCP, gfasCP, GFPhal, gtenCP, hcriCP, hfriFP, KikG, LEA, mcFP497, mcFP503, mcFP506, mCherry1.5, mClavGR1, mClavGR1.1, mClavGR1.8, mClover1.5, mcRFP, meffCP, mEos2-NA, meruFP, mKate2.5, mOFP.T.12, mOFP.T.8, montFP, moxEos3.2, mPA-GFP, mPapaya0.3, mPapaya0.6, mRFP1.3, mRFP1.4, mRFP1.5, mTFP0.4, mTFP0.5, mTFP0.6, mTFP0.8, mTFP0.9, mTFP1-Y67H, mTurquoise-146G, mTurquoise-146S, mTurquoise-DR, mTurquoise-GL, mTurquoise-GV, mTurquoise-RA, mTurquoise2-G, NpR3784g, PDM1-4, psupFP, Q80R, rfloGFP2, RpBphP1, RpBphP2, RpBphP6, rrGFP, RSGFP1, RSGFP2, RSGFP3, RSGFP4, RSGFP6, RSGFP7, Rtms5, scleFP1, scleFP2, spisCP, stylCP, sympFP, TeAPCa, tPapaya0.01, Trp-lessGFP, vsGFP, Xpa, yEGFP, YFP3, zGFP, and zRFP.

[0102] The anti-GAG motif antibodies and antigen-binding fragments thereof disclosed herein may also be fluorescently labeled using a fluorescent dye, including, but not limited to, (E)-Stilbene, (Z)-Stilbene, 1-Chloro-9,10-bis(phenylethynyl)anthracene, 2-Chloro-9,10- bis(phenylethynyl)anthracene, 2-Chloro-9,10-diphenylanthracene, 5,12- Bis(phenylethynyl)naphthacene, 7-Aminoactinomycin D, 8-Anilinonaphthalene-1-sulfonic acid, 9,10-Bis(phenylethynyl)anthracene, Abberior® dyes (including CAGE 500, CAGE 532, CAGE 552, CAGE 590, CAGE 635, FLIP 565, STAR 440SXP, STAR 470SXP, STAR 488, STAR 520SXP, STAR 580, STAR 600, STAR 635, STAR 635P, STAR RED), Alexa Fluor® (AF) dyes (including 350, 405, 430, 488, 514, 532, 546, 555, 568, 594, 610-X, 633, 647, 660, 680, 700, 750, 790), Atto dyes (including Atto® 390, Atto® 425, Atto® 430 LS, Atto® 465, Atto® 488, Atto® 490 LS, Atto® 495, Atto® 514, Atto® 520, Atto® 532, Atto® 540Q, Atto® 542, Atto® 550, Atto® 565, Atto® 580Q, Atto® 590, Atto® 594, Atto® 610, Atto® 612Q, Atto® 620, Atto® 633, Atto® 647, Atto® 647-N, Atto® 655, Atto® 665, Atto® 680, Atto® 700, Atto® 725, Atto® 740, Atto® MB2, Atto® Oxa12, Atto® Rho101, Atto® Rho11, Atto® Rho12, Atto® Rho13, Atto® Rho14, Atto® Rho3B, Atto® Rho6G , Atto® Thio12), Auramine–rhodamine stain, Benzanthrone, BHQ-1, BHQ-2, BHQ-3, Bimane, Bisbenzimide, BODIPY, Carboxy-rhodamine 6G, 5-isomer, Carboxy-X-rhodamine (ROX), 5-isomer, Carboxy-X-rhodamine (ROX), 6-isomer, Chromeo™ 488, Chromeo™ 494, Chromeo™ 546, Chromeo™ 642, Coumarin, Cyanine 3, Cyanine 3.5, Cyanine 3.5 NHS, Cyanine 5, Cyanine 5 NHS, Cyanine 5.5 Amidite, Cyanine 5.5 NHS, Cyanine 7 NHS, DAPI, Dark quencher, Diphenylhexatriene, Dy® 350, Dy® 350 XL, Dy® 360 XL, Dy® 370 XL, Dy® 375 XL, Dy® 380 XL, Dy® 395 XL, Dy® 405, Dy® 415, Dy® 430, Dy® 431, Dy® 478, Dy® 480 XL, Dy® 481 XL, Dy® 485 XL, Dy® 490, Dy® 495, Dy® 505, Dy® 505-X, Dy® 510 XL, Dy® 511 XL, Dy® 520 XL, Dy® 521 XL, Dy® 530, Dy® 547, Dy® 547P1, Dy® 548, Dy® 549P1, Dy® 550, Dy® 554, Dy® 555, Dy® 556, Dy® 560, Dy® 590, Dy® 591, Dy® 594, Dy® 601 XL, Dy® 605, Dy® 610, Dy® 615, Dy® 630, Dy® 631, Dy® 632, Dy® 633, Dy® 634, Dy® 635, Dy® 636, Dy® 647, Dy® 647P1, Dy® 648, Dy® 648P1, Dy® 649, Dy® 649P1, Dy® 650, Dy® 651, Dy® 652, Dy® 654, Dy® 675, Dy® 676, Dy® 677, Dy® 678, Dy® 679P1, Dy® 680, Dy® 681, Dy® 682, Dy® 700, Dy® 701, Dy® 703, Dy® 704, Dy® 730, Dy® 731, Dy® 732, Dy® 734, Dy® 749P1, Dy® 750, Dy® 751, Dy® 752, Dy® 754, Dy® 776, Dy® 777, Dy® 778, Dy® 780, Dy® 781, Dy® 782 (infrared!), Dy® 800, Dy® 831, Dy®Q 1, Dy®Q 2, Dy®Q 3, Dy®Q 4, Dy®Q 660, Dy®Q 661, DyLight Fluor, EDANS, Epicocconone, Eterneon™ 350/430, Eterneon™ 350/455, Eterneon™ 384/480, Eterneon™ 393/523, Eterneon™ 394/507, Eterneon™ 480/635, Eterneon™ Far Red 680 Azide, Eterneon™ Green 515 Azide, Eterneon™ Orange 570 Azide, Eterneon™ Orange 580 Azide, Eterneon™ Red 600 Azide, Eterneon™ Red 630 Azide, Eterneon™ Red 645 Azide, Eterneon™ Yellow 530 Azide, Eterneon™ Yellow 550 Azide, Eterneon™ Yellow 555 Azide, FAM, 5-isomer, FAM, 6-isomer, FlAsH-EDT2, FluoProbes, Fluorescein-5-EX, , Fluorescein Isothiocyanate (FITC), Fluorescence image-guided surgery, Fluoro-Jade stain, Fura-2, Fura-2-acetoxymethyl ester, HEX, Hoechst stain, IAEDANS, IBApy 493/503, IBApy FL, Iminocoumarin, Indo-1, JOE, 6-isomer, Laurdan, Lucifer yellow, Luciferin, Methylene Blue (on request), NBD-TMA, Optical brightener, Oyster® 488, Oyster® 550, Oyster® 555, Oyster® 647, Oyster® 650, Oyster® 680, Perylene, Phycobilin, Phycoerythrobilin, Pyranine, Pyrene, Reichardt's dye, Rhodamine 110X, RiboGreen,

Rubrene, Squaraine dye, Sulforhodamine 101, TAMRA, 6-isomer, TET, Tetraphenyl butadiene, Tetrasodium tris(bathophenanthroline disulfonate)ruthenium(II), Titan yellow, TSQ, Umbelliferone, and Violanthrone. Fluorescent dyes can be chemically linked to proteins, including antibodies and antigen-binding fragments thereof, through various mechanisms. For instance, amine-reactive organic fluorophores include acylating reagents that form carboxamides, sulfonamides or thioureas upon reaction with amines. Amine- reactive organic fluorophores include, but are not limited to isothiocyanates, active esters and carboxylic acids, or sulfonyl chlorides. Thiol-reactive fluorescent dyes such as

iodoacetamides or maleimides primarily target cysteine residues.

[0103] Detectable moieties or purification tags can also be conjugated to the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein using Sortase A, which allows post-translational modifications of proteins at the N- and/or C-terminus. Sortase A from S. aureus recognizes an exposed peptide motif LPXTG, which serves as the acceptor for small fluorescent probes that have a primary amino-group and a tri-glycine motif [35, 38]. Upon cleavage of the LPXTG motif, Sortase forms a thioester intermediate with the engineered molecule. This intermediate is then resolved by nucleophilic attack by the (Gly)n containing molecule to form a fusion between the two molecules with an intervening

LPXT(Gly)n motif. N and C-termini of proteins can be selectively labeled by using Sortases of different substrate specificity. For example, Sortase A from streptococcus pyogenes, recognizes and cleaves the LPXTA motif and accepts Ala-based nucleophiles. This SrtA also recognizes and cleaves the LPXTG motif with reduced efficiency. However, S. aureus.

Sortase A does not recognize LPXTA substrates and thus are orthogonal to the LPXTA sequence.

[0104] While the use of immunotags has the benefit of signal amplification through a secondary antibody, the fusion of antibodies or fragments thereof with fluorescing protein and the SORTase A-based approaches are advantageous because the antibodies or fragments thereof are stoichiometrically labeled and thus the signal is directly proportional to the amount of bound scFv.

[0105] In some embodiments, the anti-GAG motif antibodies or antigen-binding fragments thereof disclosed herein may be conjugated to affinity tags for detection and/or purification. Examples of affinity tags include, but are not limited to, Albumin-binding protein (ABP), Alkaline Phosphatase (AP), AU1 epitope, AU5 epitope, Bacteriophage T7 epitope (T7-tag), Bacteriophage V5 epitope (V5-tag), Biotin-carboxy carrier protein (BCCP), Bluetongue virus tag (B-tag), Calmodulin binding peptide (CBP), Chloramphenicol Acetyl Transferase (CAT), Cellulose binding domain (CBP), Chitin binding domain (CBD), Choline-binding domain (CBD), Dihydrofolate reductase (DHFR), E2 epitope, FLAG epitope, Galactose-binding protein (GBP), Green fluorescent protein (GFP), Glu-Glu (EE- tag), Glutathione S-transferase (GST), Human influenza hemagglutinin (HA), HaloTag®, Histidine affinity tag (HAT), Horseradish Peroxidase (HRP), HSV epitope, Ketosteroid isomerase (KSI), KT3 epitope, LacZ, Luciferase, Maltose-binding protein (MBP), Myc epitope, NusA, PDZ domain, PDZ ligand, Polyarginine (Arg-tag), Polyaspartate (Asp-tag), Polycysteine (Cys-tag), Polyhistidine (His-tag), Polyphenylalanine (Phe-tag), Profinity eXact, Protein C, S1-tag, S-tag, Streptavadin-binding peptide (SBP), Staphylococcal protein A (Protein A), Staphylococcal protein G (Protein G), Strep-tag, Streptavadin, Small Ubiquitin- like Modifier (SUMO), Tandem Affinity Purification (TAP), T7 epitope, Thioredoxin (Trx), TrpE, Ubiquitin, Universal, and VSV-G. [0106] Other conjugates of antibodies or antigen binding fragments thereof

[0107] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof disclosed herein are conjugated to a polymer to increase stability and/or half-life of the antibody or antigen binding fragment thereof. In one embodiment, the anti-GAG motif antibody or antigen binding fragment thereof is conjugated to a polyalkylene glycol moiety, for example, a PEG moiety and preferably a PEG-maleimide moiety. Preferred pegylation moieties (or related polymers) can be, for example, polyethylene glycol (“PEG”),

polypropylene glycol (“PPG”), polyoxyethylated glycerol (“POG”) and other

polyoxyethylated polyols, polyvinyl alcohol (“PVA”) and other polyalkylene oxides, polyoxyethylated sorbitol, or polyoxyethylated glucose. The polymer can be a homopolymer, a random or block copolymer, a terpolymer based on the monomers listed above, straight chain or branched, substituted or unsubstituted as long as it has at least one active sulfone moiety. The polymeric portion can be of any length or molecular weight but these

characteristics can affect the biological properties. Polymer average molecular weights particularly useful for decreasing clearance rates in pharmaceutical applications are in the range of 2,000 to 35,000 Daltons. In addition, if two groups are linked to the polymer, one at each end, the length of the polymer can impact upon the effective distance, and other spatial relationships, between the two groups. Thus, one skilled in the art can vary the length of the polymer to optimize or confer the desired biological activity. PEG is useful in biological applications for several reasons. PEG typically is clear, colorless, odorless, soluble in water, stable to heat, inert to many chemical agents, does not hydrolyze, and is nontoxic. Pegylation can improve pharmacokinetic performance of a molecule by increasing the molecule's apparent molecular weight. The increased apparent molecular weight reduces the rate of clearance from the body following subcutaneous or systemic administration. In many cases, pegylation can decrease antigenicity and immunogenicity. In addition, pegylation can increase the solubility of a biologically active molecule.

[0108] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof disclosed herein are attached to a salvage receptor binding epitope to increase the half-life of the anti-GAG motif antibodies or antigen binding fragments thereof. The term "salvage receptor binding epitope" may refer to an epitope of the Fc region of an IgG molecule (e.g., IgGl, IgG2, IgG3, or IgG4) that is responsible for increasing the in vivo serum half-life of the IgG molecule (e.g., Ghetie et al., 18 Ann. Rev. Immunol.739 (2000).

Antibodies with substitutions in an Fc region thereof and increased serum half-lives are also described in WO 00/42072, WO 02/060919; Shields et al., 276 J. Biol. Chem.6591 (2001); Hinton, 279 J. Biol. Chem.6213-6216 (2004). For example, a nucleic acid molecule encoding the salvage receptor binding epitope can be linked in frame to a nucleic acid encoding a polypeptide sequence described herein so that the fusion protein expressed by the engineered nucleic acid molecule comprises the salvage receptor binding epitope and a polypeptide sequence described herein. In another embodiment, the serum half-life can also be increased, for example, by attaching other polypeptide sequences. For example, antibodies or antigen-binding fragments thereof useful in the methods of the invention can be attached to serum albumin or a portion of serum albumin. See also, Dennis et al., 277 J. Biol. Chem. 35035 (2002), for additional serum albumin binding peptide sequences. [0109] Kits

[0110] In some embodiments, provided are kits comprising one or more anti-GAG motif antibodies or antigen binding fragments thereof disclosed herein.

[0111] In some embodiments, the kit comprises one or more anti-GAG motif antibodies or antigen binding fragments thereof that are conjugated to a functional moiety that allows for the detection or purification of the one or more anti-GAG motif antibodies or antigen binding fragments thereof disclosed herein.

[0112] In some embodiments, the kit comprises one or more anti-GAG motif antibodies or antigen binding fragments thereof conjugated to a therapeutic or stabilizing moiety.

[0113] In some embodiments, the one or more anti-GAG motif antibodies or antigen binding fragments thereof may be present in the kit in a single composition. In other embodiments, the one or more anti-GAG motif antibodies or antigen binding fragments thereof may be present in separate compositions.

[0114] The kit may comprise additional therapeutic or non-therapeutic compositions. In certain embodiments, the kit comprise instructions in a tangible medium. [0115] Uses of anti-GAG motif antibodies or antigen binding fragments thereof

[0116] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are used for the identification, purification, or modulation of a cell or tissue based on a cellular glycotype.

[0117] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are provided in a partially or substantially purified form. In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are provided as supernatants of cells secreting the anti-GAG motif antibodies or antigen binding fragments thereof.

[0118] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are provided in form of cells expressing the anti-GAG motif antibodies or antigen binding fragments thereof. In some embodiment, the anti-GAG motif antibodies or antigen binding fragments thereof are fused to a transmembrane domain. In some embodiments, the cells expressing the anti-GAG motif antibodies or antigen binding fragments thereof are HEK293 cells or T cells.

[0119] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are provided in form of a chimeric antigen receptor, such as an artificial T cell receptor. [0120] Purification, and isolation methods

[0121] In one aspect, provided is a method of purifying or isolating cells, the method comprising contacting a mixture of cells comprising one or more target cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof, wherein the anti-GAG motif antibodies or antigen binding fragments thereof bind to the one or more target cells.

[0122] The methods disclosed herein are also useful for the isolation of tissues. As such, also provided is a method of purifying or isolating tissues, the method comprising contacting a mixture of tissues comprising one or more target tissues with one or more anti-GAG motif antibodies or antigen binding fragments thereof, wherein the anti-GAG motif antibodies or antigen binding fragments thereof bind to the one or more target tissues. The term “purification” or“isolating” refers to any process or method by which a specific compound and/or complex may be removed from a mixture or composition.

[0123] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof used for the purification of a cell or tissue are further conjugated to moiety that aids in purification. Non-limiting examples of such purification moieties include affinity tags (including, but not limited to, peptides and proteins) or magnetic moieties.

[0124] In some embodiments, the one or more target cells that are bound to the one or more anti-GAG motif antibodies or antigen binding fragments thereof are separated from cells that are not bound to the one or more anti-GAG motif antibodies or antigen binding fragments thereof by flow cytometry. In some embodiments, the flow cytometry is fluorescence-activated flow cytometry.

[0125] In some embodiments, the method comprises contacting the one or more target cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof comprising an affinity tag. In some embodiments, the method comprises

(a) contacting the one or more target cells with one or more anti-GAG motif

antibodies or antigen binding fragments thereof comprising an affinity tag;

(b) contacting the one or more target cells bound to the one or more anti-GAG motif antibodies or antigen binding fragments thereof comprising the affinity tag with a medium that has a higher affinity for the affinity tag than the remainder of the mixture or composition; and

(c) isolating the one or more target cells bound to the one or more anti-GAG motif antibodies or antigen fragments thereof carrying the affinity tag.

[0126] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof used for the purification of a cell or tissue is further conjugated to a magnetic moiety, allowing for magnetic separation of the one or more cells bound to the one or more anti-GAG motif antibodies or antigen fragments thereof.

[0127] Cell separating techniques utilizing antibodies or antigen binding fragments are known in the art and can be adapted by a person skilled in the person for the use in the methods disclosed herein.

[0128] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are used to differentiate between and isolate cell populations that cannot be separated using other surface markers, such as the CD system. For instance, hematopoietic cell populations stringently isolated based on the same cell surface CD markers display considerable heterogeneity, e.g. distinct transcriptional programs and defineable cellular subsets. [0129] Diagnostic methods

[0130] The anti-GAG motif antibodies and antigen binding fragments herein may be used to discriminate between healthy and diseased cells. As such, in one aspect, provided is a method for revealing a disease or disorder, the method comprising contacting one or more cells with one or more anti-GAG motif antibody or antigen binding fragment thereof.

[0131] In some embodiments, the presence of one or more GAG motifs is indicative of the disease or disorder. In one embodiment, provided is a method of detecting a disease or disorder, the method comprising:

(a) contacting one or more cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof;

(b) measuring binding of the one or more anti-GAG motif antibodies or antigen

binding fragments thereof to the one or more cells; and

(c) detecting the disease or disorder if binding of the one or more anti-GAG motif antibodies or antigen binding fragments thereof to the one or more cells was detected.

[0132] In some embodiments, the absence of one or more GAG motifs is indicative of the disease or disorder. In one embodiment, provided is a method of detecting a disease or disorder, the method comprising:

(a) contacting one or more cells with one or more anti-GAG motif antibodies or antigen binding fragments thereof;

(b) measuring binding of the one or more anti-GAG motif antibodies or antigen

binding fragments thereof to the one or more cells; and

(c) detecting the disease or disorder if binding of the one or more anti-GAG motif antibodies or antigen binding fragments thereof to the one or more cells was not detected.

[0133] In some embodiments, the one or more cells contacted with the one or more anti- GAG motif antibodies or antigen binding fragments thereof are provided in a sample. In some embodiments, the sample is derived from a human, primate, hamster, rabbit, rodent, cow, pig, sheep, horse, goat, dog, guinea pig, ferret, or cat. In some embodiments, the sample is a blood, serum, plasma, urine, feces, tissue biopsy sample. [0134] In some embodiments, the methods disclosed herein are suitable for prognosing a disease or disorder. In some embodiments, the methods disclosed herein are suitable for monitoring progression of a disease. In some embodiments, the methods disclosed herein are suitable for determining the efficacy of treatment.

[0135] In some embodiments, the method of detecting a disease or disorder comprises determining the glycotype of a control. The“glycotype of a control” can refer to the glycotype of a cell derived from one or more individuals that do not have the disease or disorder to be detected. The control glycotype may be determined on an individual-by- individual basis, or on an aggregate basis such as an average. In some embodiments, the control glycotype is determined for the same individual whose condition is being monitored, but is obtained at a different time. In certain embodiments, the control glycoype can refer to a glycotype determined for the same patient at an earlier time, e.g., weeks, months, or years earlier. In some embodiment, the control glycotype is determined for a patient before the patient receives any treatment for a specific disease.

[0136] In some embodiments, the cells or tissues detected by the anti-GAG motif antibodies or antigen binding fragments thereof are cancer cells. In some embodiments, the cancer is basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and CNS cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer (including gastrointestinal cancer); glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer (e.g. , small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung); lymphoma including Hodgkin's and non-Hodgkin's lymphoma; melanoma; myeloma; neuroblastoma; oral cavity cancer (e.g., lip, tongue, mouth, and pharynx); ovarian cancer; pancreatic cancer; prostate cancer; retinoblastoma;

rhabdomyosarcoma; rectal cancer; cancer of the respiratory system; salivary gland carcinoma; sarcoma; skin cancer; squamous cell cancer; stomach cancer; testicular cancer; thyroid cancer; uterine or endometrial cancer; cancer of the urinary system; vulval cancer; as well as other carcinomas and sarcomas; as well as B-cell lymphoma (including low grade/follicular non-Hodgkin's lymphoma (NHL); small lymphocytic (SL) NHL;

intermediate grade/follicular NHL; intermediate grade diffuse NHL; high grade

immunoblastic NHL; high grade lymphoblastic NHL; high grade small non-cleaved cell NHL; bulky disease NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom's Macroglobulinemia); chronic lymphocytic leukemia (CLL); acute

lymphoblastic leukemia (ALL); Hairy cell leukemia; chronic myeloblastic leukemia; and post-transplant lymphoproliferative disorder (PTLD), as well as abnormal vascular proliferation associated with phakomatoses, edema (such as that associated with brain tumors), and Meigs’ syndrome.

[0137] In some embodiments, the methods disclosed herein are used to identify and/or isolate leukemic stem/progenitor and bulk cell populations.

[0138] It is noted that the methods disclosed herein can be used to diagnose any disease associated with a modified cellular glycotype as compared to the non-disease state. As such, diseases that can be diagnoses using the methods disclosed herein include, but are not limited to, metabolic diseases, infectious diseases, auto-immune diseases. [0139] Therapeutic methods

[0140] In one aspect, provided is a method of targeting a therapeutic agent to a target cell or a target tissue based on the glycotype of the target cell or target tissue. As such, provided herein are anti-GAG motif antibodies or antigen binding fragments thereof that are covalently or noncovalently conjugated to a therapeutic moiety and methods of using such anti-GAG motif antibodies or antigen binding fragments thereof.

[0141] In some embodiments, provided is a method of treating and/or preventing a disease, the method comprising administering to the subject in need thereof an effective amount of one or more anti-GAG motif antibodies or antigen binding fragments thereof that are conjugated to a therapeutic moiety, wherein the one or more anti-GAG motif antibodies or antigen binding fragments thereof bind to one or more GAG motifs on the surface of the target cell or target tissue.

[0142] To“treat” or to use for“therapy” refers to administering of a therapeutic agent to a subject already diagnosed as having or suffering from a disease or disorder with the goal of improving the subject’s condition. The object of the treatment is to prevent or slow down (lessen) an undesired physiological condition, disorder or disease, or to obtain beneficial or desired clinical results. Beneficial or desired clinical results include, but are not limited to, alleviation of symptoms; diminishment of the extent of the condition, disorder or disease; stabilization (i.e., not worsening) of the state of the condition, disorder or disease; delay in onset or slowing of the progression of the condition, disorder or disease; amelioration of the condition, disorder or disease state; and remission (whether partial or total), whether detectable or undetectable, or enhancement or improvement of the condition, disorder or disease. Treatment includes eliciting a clinically significant response without excessive levels of side effects. Treatment also includes prolonging survival as compared to expected survival if not receiving treatment.“Prevent” refers to prophylactic treatment of a subject who is not yet ill, but who is susceptible to, or otherwise at risk for, developing a disease or disorder.

[0143] Different formats of the anti-GAG motif antibodies may be used for the methods of treatment disclosed herein, including, but not limited to, whole IgG or scFv formats. The antigen binding portions of the anti-GAG motif antibodies and fragments disclosed herein may also be formatted in to a chimeric antigen receptor and may be used in CAR T-cell therapy.

[0144] Examples of therapeutic moieties which are useful in the methods and antibodies and antigen-binding fragments thereof contemplated by the invention include, for example, anti-inflammatory agents, anti-cancer agents, anti-neurodegenerative agents, anti-infective agents, or generally a therapeutic. The functional moiety may also have one or more of the above-mentioned functions.

[0145] Exemplary therapeutic moieties include radionuclides with high-energy ionizing radiation that are capable of causing multiple strand breaks in nuclear DNA, and therefore suitable for inducing cell death (e.g., of a cancer). Exemplary high-energy radionuclides include: ⁹⁰ Y, ¹²⁵ I, ¹³¹ I, ¹²³ I, ¹¹¹ In, ¹⁰⁵ Rh, ¹⁵³ Sm, ⁶⁷ Cu, ⁶⁷ Ga, ¹⁶⁶ Ho, ¹⁷⁷ Lu, ¹⁸⁶ Re and ¹⁸⁸ Re. These isotopes typically produce high-energy a- or b-particles which have a short path length. Such radionuclides kill cells to which they are in close proximity, for example neoplastic cells to which the conjugate has attached or has entered. They have little or no effect on non-localized cells and are essentially non-immunogenic.

[0146] Exemplary therapeutic moieties also include cytotoxic agents such as cytostatics (e.g. alkylating agents, DNA synthesis inhibitors, DNA-intercalators or cross-linkers, or DNA-RNA transcription regulators), enzyme inhibitors, gene regulators, cytotoxic nucleosides, tubulin binding agents, hormones and hormone antagonists, anti-angiogenesis agents, and the like.

[0147] Exemplary therapeutic moieties also include alkylating agents such as the anthracycline family of drugs (e.g., adriamycin, carminomycin, cyclosporin-A, chloroquine, methopterin, mithramycin, porfiromycin, streptonigrin, anthracenediones, and aziridines). In another embodiment, the chemotherapeutic moiety is a cytostatic agent such as a DNA synthesis inhibitor. Examples of DNA synthesis inhibitors include, but are not limited to, methotrexate and dichloromethotrexate, 3-amino-1,2,4-benzotriazine 1,4-dioxide, aminopterin, cytosine b-D-arabinofuranoside, 5-fluoro-5¢-deoxyuridine, 5-fluorouracil, ganciclovir, hydroxyurea, actinomycin-D, and mitomycin C. Exemplary DNA-intercalators or cross-linkers include, but are not limited to, bleomycin, carboplatin, carmustine, chlorambucil, cyclophosphamide, cis-diammineplatinum(II) dichloride (cisplatin), melphalan, mitoxantrone, and oxaliplatin.

[0148] Exemplary therapeutic moieties also include transcription regulators such as actinomycin D, daunorubicin, doxorubicin, homoharringtonine, and idarubicin. Other exemplary cytostatic agents that are compatible with the present invention include ansamycin benzoquinones, quinonoid derivatives (e.g. quinolones, genistein, bactacyclin), busulfan, ifosfamide, mechlorethamine, triaziquone, diaziquone, carbazilquinone, indoloquinone EO9, diaziridinyl-benzoquinone methyl DZQ, triethylenephosphoramide, and nitrosourea compounds (e.g. carmustine, lomustine, semustine).

[0149] Exemplary therapeutic moieties also include cytotoxic nucleosides such as, for example, adenosine arabinoside, cytarabine, cytosine arabinoside, 5-fluorouracil, fludarabine, floxuridine, ftorafur, and 6-mercaptopurine; tubulin binding agents such as taxoids (e.g. paclitaxel, docetaxel, taxane), nocodazole, rhizoxin, dolastatins (e.g. Dolastatin-10, -11, or - 15), colchicine and colchicinoids (e.g. ZD6126), combretastatins (e.g. Combretastatin A-4, AVE-6032), and vinca alkaloids (e.g. vinblastine, vincristine, vindesine, and vinorelbine (navelbine)); anti-angiogenesis compounds such as Angiostatin K1-3, DL-a-difluoromethyl- ornithine, endostatin, fumagillin, genistein, minocycline, staurosporine, and (±)-thalidomide.

[0150] Exemplary therapeutic moieties also include hormones and hormone antagonists, such as corticosteroids (e.g. prednisone), progestins (e.g. hydroxyprogesterone or

medroprogesterone), estrogens, (e.g. diethylstilbestrol), antiestrogens (e.g. tamoxifen), androgens (e.g. testosterone), aromatase inhibitors (e.g. aminogluthetimide), 17-(allylamino)- 17-demethoxygeldanamycin, 4-amino-1,8-naphthalimide, apigenin, brefeldin A, cimetidine, dichloromethylene-diphosphonic acid, leuprolide (leuprorelin), luteinizing hormone-releasing hormone, pifithrin-a, rapamycin, sex hormone-binding globulin, and thapsigargin.

[0151] Exemplary therapeutic moieties also include enzyme inhibitors such as, S(+)- camptothecin, curcumin, (-)-deguelin, 5,6-dichlorobenz-imidazole 1-b-D-ribofuranoside, etoposide, formestane, fostriecin, hispidin, 2-imino-1-imidazolidineacetic acid (cyclocreatine), mevinolin, trichostatin A, tyrphostin AG 34, and tyrphostin AG 879.

[0152] Exemplary therapeutic moieties also include gene regulators such as 5-aza-2¢- deoxycytidine, 5-azacytidine, cholecalciferol (vitamin D3), 4-hydroxytamoxifen, melatonin, mifepristone, raloxifene, trans-retinal (vitamin A aldehydes), retinoic acid, vitamin A acid, 9- cis-retinoic acid, 13-cis-retinoic acid, retinol (vitamin A), tamoxifen, and troglitazone.

[0153] Exemplary therapeutic moieties also include cytotoxic agents such as, for example, the pteridine family of drugs, diynenes, and the podophyllotoxins. Particularly useful members of those classes include, for example, methopterin, podophyllotoxin, or

podophyllotoxin derivatives such as etoposide or etoposide phosphate, leurosidine, vindesine, leurosine and the like.

[0154] Still other cytotoxins that are compatible with the teachings herein include auristatins (e.g. auristatin E and monomethylauristan E), calicheamicin, gramicidin D, maytansanoids (e.g. maytansine), neocarzinostatin, topotecan, taxanes, cytochalasin B, ethidium bromide, emetine, tenoposide, colchicin, dihydroxy anthracindione, mitoxantrone, procaine, tetracaine, lidocaine, propranolol, puromycin, and analogs or homologs thereof.

[0155] Exemplary therapeutic moieties also include immunomodulatory agents. In some embodiments, the immunomodulatory agent enhances the immune response and may, for example, be used in the treatment of cancer. In another embodiment, the immunomodulatory agent decrease the immune response and/or blocks immunostimulatory interactions and may, for example, be used for the treatment of auto-immune or inflammatory diseases.

[0156] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof disclosed herein are provided in form of a bispecific antibody. In one embodiment, the second binding site of the bispecific antibody is derived from an immunomodulatory antibody and antigen binding fragment thereof.

[0157] In one embodiments, the therapeutic moiety is an immune cell engager, including but not limited to a T cell, NK cell, and/or macrophage engager. In one embodiment, the therapeutic moiety is bi-specific T-cell engagers (BiTEs), which forms a bridge between a cytotoxic T cell and a tumor cell. In some embodiments, the therapeutic moiety is a cytokine, a chemokine, an interleukin, or an immunomodulatory imide drug.

[0158] In one embodiment, the therapeutic moiety is a checkpoint inhibitor. Checkpoint proteins interact with specific ligands that send a signal into the T cell and switch off or inhibit T cell function. By expressing high levels of checkpoint proteins on their surface, cancer cells can control the function of T cells that enter the tumor microenvironment, thus suppressing the anticancer immune response. The immune checkpoint protein Programmed Death-1 (PD-1) is a key immune checkpoint receptor expressed by activated T and B cells and mediates immunosuppression. PD-1 is a member of the CD28 family of receptors, which includes CD28, CTLA-4, ICOS, PD-1, and BTLA. Two cell surface glycoprotein ligands for PD-1 have been identified, Programmed Death Ligand-1 (PD-L1) and Programmed Death Ligand-2 (PD-L2), that are expressed on antigen-presenting cells as well as many human cancers and have been shown to downregulate T cell activation and cytokine secretion upon binding to PD-1 (Freeman et al., 2000; Latchman et al., 2001). Inhibition of the PD-1/PD-L1 interaction can promote potent antitumor activity. Examples of PD-1 inhibitors include, but are not limited to, Pembrolizumab (MK-3475), Nivolumab (MDX-1106), Cemiplimab-rwlc (REGN2810), Pidilizumab (CT-011), Spartalizumab (PDR001), tislelizumab (BGB-A317), PF-06801591, AK105, BCD-100, BI 754091, JS001, LZM009, MEDI0680, MGA012, Sym021, TSR-042. Examples of PD-L1 inhibitors include, but are not limited to,

Atezolizumab (MPDL3280A), Durvalumab (MEDI4736), Avelumab (MSB0010718C), BGB-A333, CK-301, CS1001, FAZ053, KN035, MDX-1105, MSB2311, SHR-1316.

[0159] In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are fused to or expressed on the surface of an immune cell, including, but not limited to a T cells NK cell, macrophage, or another immune effector cell. In some embodiments, the anti-GAG motif antibodies or antigen binding fragments thereof are provided in form of a chimeric antigen receptor, such as an artificial T cell receptor, which is expressed on a T cell.

[0160] Techniques for conjugating such therapeutic moiety to antibodies are well known, see, e.g., Amon et al., "Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy", in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.), pp.243-56 (Alan R. Liss, Inc.1985); Hellstrom et al., "Antibodies For Drug Delivery", in Controlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp.623-53 (Marcel Dekker, Inc.1987); Thorpe, "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review", in

Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); "Analysis, Results, And Future Prospective Of The Therapeutic Use Of Radiolabeled Antibody In Cancer Therapy", in Monoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.), pp.303-16 (Academic Press 1985), and Thorpe et al., "The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates", Immunol. Rev., 62:119-58 (1982). [0161] It is to be understood that this invention is not limited to the particular molecules, compositions, methodologies, or protocols described, as these may vary. Any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present invention. It is further to be understood that the disclosure of the invention in this specification includes all possible combinations of such particular features. For example, where a particular feature is disclosed in the context of a particular aspect or embodiment of the invention, or a particular claim, that feature can also be used, to the extent possible, in combination with and/or in the context of other particular aspects and embodiments of the invention, and in the invention generally.

[0162] Where reference is made herein to a method comprising two or more defined steps, the defined steps can be carried out in any order or simultaneously (except where the context excludes that possibility), and the method can include one or more other steps which are carried out before any of the defined steps, between two of the defined steps, or after all the defined steps (except where the context excludes those possibilities).

[0163] All other referenced patents and applications are incorporated herein by reference in their entirety. Furthermore, where a definition or use of a term in a reference, which is incorporated by reference herein is inconsistent or contrary to the definition of that term provided herein, the definition of that term provided herein applies and the definition of that term in the reference does not apply.

[0164] To facilitate a better understanding of the present invention, the following examples of specific embodiments are given. The following examples should not be read to limit or define the entire scope of the invention.

EXAMPLES

[0165] Example 1: Glycotype-based discrimination of different cell types using cell- cell interaction assays or purified anti-GAG motif antibody fragments

[0166] First, it was determined whether anti-GAG motif antibodies or antigen binding fragments expressed on the surface of reporter cells can be used to discriminate between different cell types based on the cell’s glycotype. The expression of anti-GAG motif antibodies on the surface of reporter cells circumvents the cost of large-scale expression and purification of anti-GAG motif antibodies or antigen binding fragments, as the anti-GAG motif antibodies or antigen binding fragments are made by and presented on the surface of transfected reporter cells.

[0167] A library of cDNA clones was synthesized encoding 36 anti-HS motif scFvs. The scFcs were engineered to contain both a secretion signal at the N-terminus and a

transmembrane domain fused to a fluorescent protein tag (e.g., GFP, YFP, RFP) at the C- terminus. The scFvs were then transgenically expressed in living animals or tissues to visualize HS. For this, the scFv cDNA was cloned into a mammalian expression vector that allows expression of the scFv on the surface of reporter cells as transmembrane proteins. These fluorescently labeled scFvs were then used to detect glycan-scFv interaction in cell-cell interactions assays. Cells transiently expressing an anti-HS motif-scFv/GFP fusion were mixed with cyto-tracker labeled fluorescent sample cells and the interaction between the two cells populations quantified using flow cytometry (see Figure 2A).

[0168] This cell-cell interaction assay was used to successfully glycotype two common laboratory cell lines: Suspension adapted human embryonic kidney cells (HEK 293) and Chinese hamster ovary cells (CHO). Figure 2B shows representative flow cytrometry data for HEK and CHO cells probed with reporter cells expressing anti-HS motif scFv HS4C3 on their surface. The reporter cells bind to HEK 293, but not to CHO cells.

[0169] scFv expressed on cells could further be used to differentiate cancer cells (adherent MIA PaCa-2 from control cells (immortalized primary pancreatic duct cells). Figure 2C shows representative flow cytrometry data for cancer and control cells probed with reporter cells expressing anti-HS motif scFv LKIV69 on their surface.

[0170] These results demonstrate that anti-GAG motif antibodies or antigen binding fragments expressed on the surface of reporter cells, as well as purified anti-GAG motif antibodies or antigen binding fragments can be used to discriminate between different cell types based on the cell’s glycotype. [0171] Example 2: Identification of cellular glycotypes

[0172] By measuring the binding of different anti-GAG motif antibodies or fragments thereof to a cell, a unique cellular glycotype can be defined. Such binding can be determined both qualitatively and quantitatively. Rather than analyzing the HS and/or CS structure of a given cell of interest, the HS/CS complement of a cell is defined by which anti-GAG motif antibodies or fragments thereof can bind to a cell, essentially creating a unique bar code for each cell. This concept is illustrated in Figure 3A and Figure 3B. [0173] Using the experimental setup and cell populations described in Example 1, cellular glycotypes were determined for CHO cells, HEK cells, MIA PaCa-2 cells, and control cells (see Figure 3C). For example, in regards to CHO vs HEK cells, it is noted that using only a subset of 23 of the 36 scFvs, including the MPB49 (which does not recognize any glycosaminoglycan) as a negative control, nine qualitative differences between both cell lines were identified.

[0174] This demonstrates the discriminatory power and utility of scFv-based glycotyping approach. [0175] Example 3: Anti-GAG motif antibodies and antigen binding fragments thereof are suitable for multiplexing

[0176] To provide a suite of anti-GAG motif antibodies suitable for high-throughput analysis of different cell types, a library of cDNA clones was synthesized encoding 36 anti- HS motif and 5 CS motif antibodies in scFv format. The scFvs were cloned into different mammalian expression vectors that allow expression of the scFvs as secreted forms, affinity tagged forms, and/or as Fc-fusions.

[0177] By using different immuno- and fluorescent tagging approaches, anti-GAG motif antibodies or antigen binding fragments thereof can be rendered amenable to multiplexing. For instance, the addition of an immunotag such as 6xHIS, FLAG, V5, VSVg, and Myc epitopes allows not only capture of labeled cells, but also signal amplification through a secondary antibody. scFvs can also be engineered to include a C-terminal signal that will allow for the enzymatic addition of fluorescent conjugates via the bacterial enzyme Sortase A. This method allows enzymatic labeling of the scFv with a single fluorescent or affinity molecule or of choice, providing great flexibility for multiplexing and customization purposes. Of note, the generation of anti-GAG motif antibody fusions with fluorescent proteins or the application of a Sortase A-based fluorescent labeling approach allows stoichiometrical labelling of anti-GAG motif antibodies or antigen binding fragments thereof and generating a signal that is directly proportional to the amount of bound anti-GAG motif antibody or antigen binding fragment thereof.

[0178] Secreted scFvs carrying affinity tags were produced in bacteria, or transgenically expressed in C. elegans as scFvs fused to fluorescent proteins including GFP, superfolder GFP, or tagRFP. scFvs containing a Sortase A substrate sequence were successfully fluorescently labeled using GGC::FITC, a tri-peptide conjugated to FITC, illustrating the flexibility of a Sortase A based labeling approach. [0179] Example 4: Glycotype-based discrimination of cancer cells using isolated anti- GAG motif antibody fragments

[0180] To assess whether purified anti-GAG motif antibodies or antigen binding fragments thereof could be used to differentiate between different cancer cell lines, a cell- based screening FACS assay was established that allows rapid quantification of fluorescent cells in a multi-well format. Using this platform, the differential binding of purified, His- tagged, anti-HS-motif antibodies in scFv format to a panel of five different hematopoietic cancer cell lines was determined: Murine erythroleukemia (cell line MEL), human erythroleukemia (cell line HEL), human acute monocytic leukemia (AML, cell lines MOLM- 14 and THP-1), and human chronic myelogenous leukemia (CML, cell line K-562). Two non-cancerous cell lines, which do not express HSPG, are shown as controls: Murine myeloblast (cell line 32D) and murine pro-B (cell line BAF3-EpoR). The signal was detected using an anti-His, phycoerythrin (PE)-labeled secondary antibody.

[0181] As shown in Figure 4, each cell line shows a distinct antibody binding profile. scFv MPB49, which shows no HS binding activity, served as a negative control.

[0182] No scFv binding was observed for MEL or MOLM-14 cells treated with

Heparinase, which digests heparan sulfate (but not chondroitin sulfate). Treatment of cells with chondroitinase ABC, which digests chondroitin sulfate (but not heparan sulfate), did not affect scFv binding to the cells, demonstrating that the binding of the scFvs in the FACS cell sorting experiments indeed rely on binding to heparan sulfate and not on some other, unknown potential epitope.

[0183] In summary, these data illustrate that anti-GAG motif antibodies and antigen binding fragments thereof are powerful tools to detect and discriminate between clinically relevant pathogenic and healthy cell types, both from human as well as murine origin. [0184] Example 5: Discrimination of murine primary hematopoietic stem and progenitor cells based on their glycotype using isolated anti-GAG motif antibody fragments

[0185] Next, purified, His-tagged, anti-HS motif antibodies in scFv format were used to determine the anti-HS motif antibody binding profiles for a well-characterized gating scheme of murine primary hematopoietic stem and progenitor cells of different lineage commitments. As shown in Figure 5, these cell populations show significant differences in anti-HS motif antibody binding.

[0186] These data indicate that even with a limited set of anti-HS motif antibodies, binding patterns could be identified that differ both quantitatively and qualitatively among the different cell types that could not be discriminated using existing proteinacious cell surface makers (e.g. CD system). [0187] Example 6: Sorting of cell populations based on their glycotype

[0188] To demonstrate that anti-GAG motif antibodies and antigen binding fragments thereof can be used to sort cell populations and assign functional characteristics to these populations, murine megakaryocyte precursors were isolated based on their anti-HS motif antibody binding profile. As shown in Figure 6, megakaryocytes and erythrocytes and their precursors display differential binding to purified, His-tagged anti-HS motif scFvs.

[0189] Total c-kit+ bone marrow cells were sorted by FACS using anti-HS scFvs EW5F5, HS3A8, and EW4E9, which bind to erythrocyte precursors, but not to megakaryocyte precursors (see Figure 6 and Figure 7A). Megakaryocyte colonies were detected using MegaCult™-C, a collagen-based culture system for colony-forming unit (CFU) assays of megakaryocyte progenitors (STEMCELL Technologies) following the manufacturer’s instructions.

[0190] Representative results are shown for scFv EW4E9. Acetylcholinesterase-positive megakaryocyte-forming colonies (Figure 7B, left, upper panel) reside exclusively in cells negative/low for EW4E9 (quantified in (Figure 7B, lower panel), whereas cells with high EW4E9 binding form no colonies (Figure 7B, right, upper panel).

[0191] These experiments demonstrate that the anti-GAG motif antibodies and antigen binding fragments can be used to effectively differentiate between blood cell types of different provenance, even for cells that could not previously be further differentiated using the CD system. The data also underscores the utility of the anti-GAG motif antibodies and antigen binding fragments for the isolation of populations of live cells for further phenotypic and functional studies. [0192] Example 7: Anti-GAG motif antibody fragments can be used to identify conserved HS modification patterning in mice and humans with regards to

megakaryocyte and erythroid lineage commitment

[0193] Next, the utility of using anti-GAG motif antibodies and antigen binding fragments to interrogate HS modification patterns within human progenitors and their subsequent differentiation into megakaryocyte and erythroid lineages was demonstrated. Glycotyping of human CD34 ⁺ HSPCs showed binding of the HS scFv panel was very similar to the binding previously observed in mouse HSPCs (Figures 5 and 8 and Examples 5 and 6). Additionally, analysis of publicly available gene expression data from sorted human progenitors revealed the same HS gene targets that were identified in mice as enriched within megakaryocyte- erythrocyte progenitors (MEPs) compared to multipotent common myeloid progenitor cell (CMP) and granulocyte-monocyte progenitor (GMP) populations (Figure 9), showing a conserved HS modification patterning in mice and humans with regards to megakaryocyte and erythroid lineage commitment. To further corroborate this finding, in vitro

megakaryocytic or erythroid differentiation experiments with human CD34 ⁺ cells were performed. A temporal and dynamic patterning of HS scFv binding during human erythroid commitment was observed. Also observed were low, minimally changing levels of HS scFv binding during megakaryocyte differentiation that resembled the prior observations in the murine system (data not shown).

[0194] Finally, a longitudinal differentiation assay utilizing the bi-potent

(erythroid/megakaryocytic) TF-1 cell line revealed diminished HS scFv binding during megakaryocyte differentiation as well as elevated binding upon erythroid commitment (Figure 10).

[0195] Taken together, these data demonstrate conserved HS modification patterning within hematopoietic progenitors and specifically during megakaryocyte and erythroid differentiation in humans and mice. [0196] Prophetic example 1: Determination of cellular glycotypes

[0197] To further validate that anti-GAG motif antibodies and antigen binding fragments thereof can be used to glycotype hematopoietic cell lineages, a panel of 18 hematopoietic cell lines are screened, including cell types of the different major lineages (T lymphoid, B lymphoid, myeloid, monocytic, megakaryocytic, eythroid).3 lines each are included for every major lineage, and cell lines of both sexes are included (T cell lines: JURKAT, LOUCY, MOLT-16; B cell lines: OCI-Ly1, REH, SU-DHL-16; myeloid cell lines: HL60, 32D, Kasumi-1; monocytic cell lines: MONO-MAC-6, MOLM14, THP-1; megakaryocytic cell lines: CMK, M-07e, MEG-01; erythroid cell lines: MEL, HEL, TF-1). These cell lines are used to establish multiplexing applications of selected HS-specific scFvs that uniquely label certain cell lines.

[0198] Additionally, several hematopoietic cell lines have the ability to differentiate upon treatment with differentiating agents and cytokines e.g.32D (model for granulocyte differentiation), K-562 (megakaryocyte and erythroid differentiation). After glycotyping the parental cells of these lines using anti-GAG motif antibodies or antigen binding fragments thereof, the HS landscape of these cells are characterized as they differentiate down their respective lineages.

[0199] Establishing a panel of fully-characterized hematopoietic cell lines using anti-GAG motif antibodies or antigen binding fragments thereof provides insight into the HS profile of hematopoietic cells in the setting of differentiation, and furthermore, attributes unique HS profiles to phenotypically distinct hematopoietic lineages and maturation stages. [0200] Prophetic example 2: Comparison of glycotype with established cellular classification systems

[0201] To compare the cellular glycotype as determined using anti-GAG motif antibodies or antigen binding fragments thereof with a validated cellular classification system, primary hematopoietic cells are glycotyped systematically and their glycotypes compared to existing CD markers.

[0202] Specifically, bone marrow cells from wild-type C57BL/6 mice (both sexes will be included) are used in combination with bona fide CD surface markers. The individual scFvs are screened against hematopoietic cell populations delineated by well-established and functionally validated CD marker-based gating schemas using flow cytometry. Leveraging the CD marker system, the HS-specific scFv binding of highly enriched stem and progenitor populations, as well as their terminally differentiated counterparts (including CD 3– T cells, B220– B cells, Gr-1– granulocytes, CD11b/Mac-1– monocytes, Ter119– erythrocytes, CD41/61– megakaryocytes, etc.) are queried. The glycotype approach allows to further sub- distinguish primary cells within a given CD marker gated population. The isolated subpopulations are characterized functionally using in vitro colony-forming assays in semisolid methylcellulose-based media as well as in vivo transplantation assays of isolated populations with different scFv binding profiles into congenic recipient mice.