Technical Field

The invention relates to methods for using biofluids, e.g. effluent, in cell culture assays to evaluate cellular response.

Background

A complete understanding of the mechanisms of cellular response is important in the diagnosis and treatment of disease. Diseases with complex and heterogeneous molecular etiologies, such as cancers, a one-size-fits-all treatment strategy result in unsatisfactory response and survival rates for many patients. However, to propose and sort patients according to their predicted response to a cure requires reliable tests to stratify and ultimately retain relevant groups of responsive patients.

Tools used to adapt treatments to the profile of the patient include diagnostic assays based on biomarkers relevant to targetable molecular pathways. Additionally, In vitro cell cultures are widely used in different key biomedical applications such as cellular and organismic biology, drug discovery, the study of cell responses to endogenous and exogenous perturbations, the mechanisms of cell development, and regenerative medicine. Cell-based assays, including predictive functional assays, may provide a personalized approach for systemic treatments, including chemotherapies, which have not yet been clinically associated with single or groups of biomarkers. However, cell-based assays have limitations, especially in the area of cancer research and treatment. For example, the main drawback of chemosensitivity and resistance assays is the lack of translatability of in vitro response into clinical response. In addition, functional assays are expensive per subject. If several samples must be tested for each patient, this significantly raises the costs and the complexity of the assay procedures.

The invention described below provides alternative methods of cell-based assays for greater precision in determining cellular response.

Summary

The survival, proliferation, and differentiation of cells in culture is determined not only by their intrinsic potential but also by the microenvironment in which the culture takes place. The present invention provides methods of using effluent biofluids in cell-based assays as all or part of the cell culture microenvironment. Specifically, the invention uses biofluids, such as drain fluid, effluent, or other bodily fluids to achieve novel assays that provide a rich source of information about cellular functional response. Methods of the invention contemplate that biofluids typically regarded as waste may be used in cell-based assays to achieve a cell culture microenvironment that provides a novel understanding of cellular response.

In understanding cellular function response, the robustness and reproducibility of cellbased assays and endpoints relies on the microenvironment in which the cells are cultured. Cellbased assays are performed in artificial two-dimensional or three-dimensional environments. While this allows one to study the correlation between cellular functions and some components of the microenvironment, this cellular environment in which these studies take place is unnatural. Consequently, the effect of the microenvironment may induce different cell behaviors than would occur in the in vivo microenvironment. Methods of the invention recognize that effluent biofluids, typically regarded as waste, actually comprise a rich source of biochemical constituents that are useful in creating an in vitro microenvironment that more closely mimics the in vivo microenvironment which leads to a more precise analysis of cellular functional response.

The cell culture microenvironment is a combination of biochemical, physical, and physiochemical factors that work in concert to regulate cell structure, function, and behavior. The biochemical microenvironment consists of cytokines, growth factors, hormones and other biomolecules, which combine to form complex signaling pathwaysthat contribute to deciding the fate of the cell. Soluble factor signaling occurs mainly via autocrine and paracrine processes, which rely heavily on diffusion of molecules to neighboring cells either of the same or of a different type. Endocrine signaling also plays a role, but relies more on convective transport of hormonal signals from distant locations in the body to the local microenvironment. Methods of the invention provide for using effluent obtained, for example, from medical procedures such as a surgery, biopsy, catheterization, dissection, or resection, as the microenvironment for cell-based assays.

A surgical intervention typically results in the expression of effluent, i.e. fluid, biofluids, or other bodily fluids, from and around the surgical wound site. The effluent is removed, either passively or actively, and is regarded as medical waste. Drains are also a common feature of post-operative care and serve to remove effluent build-up from a wound bed. Fluid build-up during or after surgery may result from damage to tissue that results in an inflammatory response. A common reason for removing fluid either during surgery or post-operatively is to reduce potentially painful swelling and to reduce the risk of painful fluid accumulation due to edema or other post- surgical complications. In addition, a surgeon may clear fluid during a procedure in order to increase access and visibility to tissue at the surgical site. Generally, these fluids are considered waste, and, other than assessing the effluent for evidence of infection, which usually involves pus and other detritus from bacterial cells, the effluent is not used for diagnostic purposes.

The present invention provides methods for using waste effluent and other bodily fluids as all or part of the microenvironment in which cells are cultured. The fluid may be obtained as effluent from a medical procedure such as a surgery, biopsy, catheterization, dissection, intubation, and the like. The fluid may also be obtained during treatment of a wound or interventional procedure. Importantly, the fluid may be any fluid removed from a person including, for example, effluent containing feces, mucus, urine, bile, blood, plasma, peritoneal fluid, aggregated tissue, irrigation fluid, lymphatic fluid, lymphovascular fluid, interstitial fluid, cells, cellular debris, bacteria, protein, and nucleic acid, or a combination thereof. The fluid may further comprise sweat, semen, vaginal secretions, cerebrospinal fluid, synovial fluid, pleural fluid, peritoneal fluid, pericardial fluid, amniotic fluid, or saliva depending on the location from which it is obtained.

Specifically, the fluid is combined with cells to achieve a novel cell culture microenvironment. For example, the waste effluent may be used as all or part of the substrate, the medium, and/or the extracellular matrix in a cell-based assay. However, the fluid may simply be combined with cells of interest in the cell culture microenvironment to evaluate the response of the cells in the fluid. Substrates, medium, and extracellular matrix influence cell functions such as attachment, proliferation, self-renewal, and induction of differentiation in cell culture. Thus, methods of the invention use the effluent as all or part of the microenvironment and/or the nutrients necessary for growth, metabolism, and activity of the cells.

For example, one aim of methods of the invention is to use the effluent to mimic, in vitro, the microenvironment present //? vivo, in order to determine cellular response. Use of the effluent as the microenvironment of cell-based assays provides a means of determining the mechanisms and constituents that influence the regulation of cell behavior, cell survival, shape, migration, proliferation, and differentiation which lead to the morphology and physiology that occur in vivo. By using waste effluents in the cell culture environment, methods of the invention can determine cellular response related to drug sensitivity or resistance, biocompatibility, responses to endogenous and exogenous perturbations, the mechanisms involved in cell development, and tissue morphogenesis.

Methods of the invention have wide applications across disciplines, particularly in cellbased therapies. The invention provides methods for improved accuracy in determining the mechanisms involved in disease progression and treatment. Cell growth and differentiation, both in vitro and in vivo, are strongly influenced by both mechanical andbiomolecular stimuli. Methods of the invention provide a means for evaluating cell response of cells cultured in biofluids that lead to improved understanding of interactions that influence cell organization and cell regulatory pathways. As such, methods of the invention may be used to determine chemosensitivity and/or resistance. Methods of the invention may also be used to advance drug discovery success by measuring the functional behavior of the cell of interest in response to a candidate compound. Further, methods of the invention may be used to determine disease recurrence or metastasis, or may be used for genomic analysis or functional pathway analysis.

Thus, methods of the invention find application in cell studies, personalized medicine, disease diagnosis, prognosis, and monitoring, regenerative medicine, and drug discovery. In this way, fluids typically regarded as waste, actually provide a rich source of information about the mechanisms of cellular response that more closely translate into clinical response. Methods of the invention allow for improved assessment of disease status as well as aiding in therapeutic selection and assessment of therapeutic efficacy.

In one aspect, the invention provides methods of determining a response of cells. The methods include the steps of obtaining a biofluid from a patient having a disease, obtaining a sample of biological cells, combining the cells with the biofluid such that the biofluid is used as all or part of the cell culture microenvironment, performing an assay on the cells, analyzing a result of the assay, and determining the response of the cells based on the result of the assay. The fluid may by any bodily fluid but may particularly comprise waste effluent from a medical intervention. For example, the waste effluent may be lymphatic fluid, lymphovascular fluid, interstitial fluid, or any combination of such fluids. The biofluid, for example, may be obtained from a patient having cancer.

In embodiments of the methods, the biofluid is used as all or part of the substrate, the medium, and/or the extracellular matrix of the cell culture microenvironment, or a combination thereof. Combining the cells with the biofluid may further mean that cells are cultured and grown in all or part of the biofluid. For example, the cells may be grown in the biofluid as part of the substrate or extracellular matrix, or the biofluid may be perfused as a cell culture medium.

The biological cells obtained are cells of interestupon which to perform the assay. The cells may be from the patient having the disease, or the cells may be obtained from a commercial cell line. The cells to be cultured in the biofluid may be contained in, or originate from, the biofluid itself. For example, the biofluid may contain immune cells, tumor cells or other cell types that are diagnostically relevant. In some embodiments, more than one type of cell or cell line may be used.

Once combined, and/or in contact with the biofluid, an assay may be performed on the cells. For example, the assay may be cell-based assay, such as a functional assay. In embodiments, the assay is a chemosensitivity assay that determines the chemosensitivity of the cells. The assay may also be a chemoresistance assay that identifies chemotherapeutic agents that may be ineffective against tumor growth. In other embodiments, methods of the invention may be used for drug discovery, wherein the functional assay determines a cellular response to a candidate drug compound. In still other embodiments, the functional assay is a diagnostic assay and/or one or more of a genomic analysis, phenotypic analysis, and functional pathway analysis. The invention contemplates that one or more assays may be performed on the cells in the cell-based assay at a given time.

In embodiments, the response of the cell is an indication of one or more of cell proliferation, programmed cell death, replicative immortality, induction of angiogenesis, metastasis, genome instability, and reprogramming of energy metabolism.

Methods of the invention may further comprise predicting the patient’s outcome to a systemic treatment based on the response of the cells. For example, the systemic treatment may be one or more of chemotherapy, a targeted drug, hormonal therapy, and immunotherapy Detailed Description

The invention provides novel methods of using effluent biofluids in cell-based assays. Methods of the invention contemplate thatbiofluids, such as effluent or other bodily fluids, typically regarded as waste, may be used in cell-based assaysto achieve a cell culture microenvironment that provides a novel understanding of cellular response. Specifically, the biofluids are used as all or part of the cell culture microenvironment.

For example, the biofluid may be used as all or part of any combination of the substrate, the cell culture medium, and/or the extracellular matrix. By doing so, a variety of functional parameters related to the behavior of the cell itself can be determined. Further, because the biofluids are used as an integral part of the cell culture microenvironment, the assays more closely mimic the in vivo microenvironment resulting in a more precise evaluation of cellular response and improved translation to clinical response. Thus, methods of the invention recognize thatbiofluids, conventionally regarded as waste, actually comprises a rich source of constituents useful in cell-based assays.

Aspects of the invention provide methods of determining a response of cells. The methods include the steps of obtaining a biofluid or biofluids from a patient having a disease, obtaining a sample of biological cells, and combining the biofluid and the cells such that the biofluid is used as all or part of the cell culture microenvironment. An assay is performed, the results analyzed, and the response of the cells is determined based on the results of the assay.

The invention contemplates that one or more biofluids maybe obtained and used in the methods. Biofluids are a biological fluid that may be excreted, such as urine or sweat, secreted, such as breast milk or bile, obtained with a needle, such as blood or cerebrospinal fluid, or develop as part of a pathological process, such as cyst fluid. The term biofluid, as used herein, is meant to include any biological fluid, including effluents typically regarded as waste, or other bodily fluids. For example, the biofluid may include blood, plasma, aggregated tissue, irrigation fluid, lymphatic fluid, lymph ovascular fluid, interstitial fluid or a combination these constituents. The biofluid may further comprise, for example, fecal matter, mucus, urine, bile, sweat, semen, vaginal secretions, cerebrospinal fluid, synovial fluid, pleural fluid, peritoneal fluid, pericardial fluid, amniotic fluid, saliva, cells, cellular debris, bacteria, proteins, nucleic acids, or a combination thereof depending on the location from which the fluid is obtained. The invention contemplates that one or more biofluids maybe collected and used in methods of the invention.

In preferred embodiments, the biofluids may be obtained or collected from a medical procedure. For example, biofluids may be obtained from a surgical intervention as surgical waste effluent that would otherwise be discarded as medical waste. Because the lymph system is associated with many types of cancer and other pathologies, many surgical interventions involve the lymphatic system. These include direct interventions such as resection, dissection, or excision surgeries to remove a diseased portion of the lymphatic system or to obtain tissue samples. Additionally, given the lymphatic system’s role in the immune system, many surgical interventions, which do not directly target the lymphatic system, often require collecting and discarding lymphatic fluid, for example, during or after treatments to manage lymph fluid overload or to facilitate wound healing. Often, as part of a postoperative regime, patients receive an implanted surgical drain, such as a JP drain, which removes lymph fluid that collects at the site of a surgery.

The biofluid may essentially be from a single source, such as lymphatic fluid. Alternatively, the biofluid may be heterogenous in nature, having contributions from lymphatics, interstitial fluid, blood, and/or inflammatory fluids such as fluid resulting from histamine, bradykinin or prostaglandin release. The biofluid may be obtained from a liquid biopsy, for example from blood or plasma. It may be necessary to isolate a fraction of interest from the biofluid. However, the invention contemplates that samples of the raw biofluids, e g. effluent contain sufficient biochemical constituents for use as all or part of the microenvironment of cell-based assays without significant sample preparation.

The biofluid may be obtained during treatment of a wound or a medical/surgical or interventional procedure. The biofluid may be obtained from any surgical intervention such as an open surgical procedure or an endoscopic procedure. For example, the biofluid may be obtained from medical procedures resulting in stomas or percutaneous drains or ports such as a thoracenteses or anastomosis. The medical procedure or surgery from which the biofluid is obtained can be any form of bodily intervention, including an intervention that is wholly unrelated to disease. In some embodiments, the medical procedure is a resection surgery or anastomosis. However, these examples are meant to be non-limiting.

The biofluids may be obtained by collecting the biofluids using any known method. For example, waste effluent maybe collected passively or via a catheter, pump, tubing and the like from a surgical site or wound. The effluent may be collected by any suitable means, for instance by using a commercially available suction sampling apparatus, such as a Medline specimen sock, designed to attach to an accessory port of a suction canister and connected to suction tubing to safely and in a sterile manner collect a sample from the surgical drainage. Suction, for example using a vacuum, may also be used to obtain fluids during a surgical procedure. For example, surgical waste effluent may be collected by using a syringe, pipet, or catheter, such as by using a Jackson-Pratt (JP) drain. Surgical waste fluid may also be collected from biohazard waste containers, for example a suction canister, fdled during a procedure or diverted from a biohazard waste container during a surgical procedure. Alternatively, biofluids may be obtained by irrigating a surgical wound. Irrigating fluid may comprise water, saline, antibiotic solutions, antiseptic agents, or a combination thereof.

Surgical waste effluent is acceptable if aseptically collected by aspiration into a sterile container after disinfecting the collection tubing. Alternatively, the sample may be collected using a syringe, pipet, or catheter, and transferred to a container. The container may be any sample vessel, such as a vial, flask, or ampule, suitable for the sterile collection of medical specimens and known to the skilled artisan.

Further, the biofluid may be collected from a colostomy, ileostomy, or urostomy pouch or bag, a percutaneous catheter, peritoneal port, or intraperitoneal drain. The biofluid may be obtained using a catheter or a drain port and may be actively or passively collected. The biofluid may be collected in or transferred to a container, for example a sample vessel, such as a vial, flask, or ampule, suitable for the sterile collection of medical specimens.

Methods of the invention provide for obtaining the biofluid from a patient having a disease. The disease may be any disease, for example, an infectious disease, a deficiency disease, a hereditary disease such as a genetic or non-genetic disease, or a physiological disease. In non-limiting embodiments, the disease may be a type of cancer.

In methods of the invention, cells of interest may be obtained and combined with the biofluid. The cells may be obtained from the same patient from which the biofluid is obtained. Alternatively, the cells may be obtained from a different patient source. The cells may be normal/healthy cells, or the cells may be indicative of disease such as from a tumor resection or biopsy. Tn certain embodiments, the cells of interest are obtained in the biofluid itself. For example, the biofluid may contain cells, such as immune or tumor cells or other cells indicative of disease, that are particularly relevant or of interest. The cells of interest may be normal or abnormal cells located in and/or originating from the biofluid itself. The cells obtained from the biofluid may be isolated from the biofluid and/or may originate from the biofluid. Thus, the biofluid may be used as all or part of the cell culture microenvironment, as well as the source of the cells of interest to be cultured. Cells in the biofluid may be cultured in situ or may be isolated and introduced into an external assay format.

Cells may be obtained from a patient by methods known to persons skilled in the art, such as from blood or tissue samples. For example, tumor material may be obtained during a medical procedure such as a diagnosis biopsy, resection fragment of primary lesion or metastasis, or effusion, ascites or blood containing circulating tumor cells. Alternatively, the cells may be obtained from a commercial cell line. As noted above, the cells may be located in or originate from the biofluid itself and thus may be obtained from the biofluid. The cells obtained from the biofluid may be cultured with or without first extracting or separating the cells from the biofluid. The cells obtained from the biofluid may be cultured with the same or different biofluid from which the cells originated, with the biofluid used as all or part of the cell culture microenvironment. In embodiments, the cells are combined with the biofluid such that the cells lines are grown in the biofluid to evaluate the functional outcomes of the cells.

Methods of the invention provide for using the biofluid as all or part of the cell culture microenvironment in assays. Thus, the cells obtained are cultured, all or in part, in the biofluid. For example, the biofluid may be used as all or part of the substrate, the cell culture medium, the extracellular matrix, and/or a combination of thereof. In other embodiments, the cells are simply cultured entirely in the biofluid obtained and the response of the cells is determined.

In vivo, cells are surrounded by their specific microenvironments, composed of, for example, cells, cytokines, and an extracellular matrix (ECM), which may dynamically change and affect cellular activities accordingly. According to methods of the invention, to mimic this microenvironment, cell culture substrates can be prepared by using biofluids obtained as described above. For example, the biofluids may be used as all or part of the cell culture substrate. Cell culture substrates are nutrients required for the growth, metabolism and activity of cells. The biofluids obtained contain a rich source of constituents that influence the microenvironment of the cell culture. Thus, the biofluids obtained maybe used as all or part of the substrate to influence attachment, proliferation, self-renewal, induction of differentiation, and cell metabolic activities.

Further, methods of the invention provide for using the obtained biofluids as all or part of the cell culture medium. The culture medium serves as the biochemical microenvironment of the culture, and typically consists of essential amino acids, vitamins, salts, carbohydrates, and other components in aqueous solution. For cells to proliferate in culture, basal media must be supplemented with factors that promote cell growth and division. Biofluids obtained as described above in methods of the invention, may provide all or part of the essential culture medium constituents necessary for cell culture.

In embodiments, methods of the invention use the biofluids obtained as all or part of the extracellular matrix (ECM) of the cell culture microenvironment. The synthetic ECM may be two-dimensional (2D) or three-dimensional (3D). Cell cultures have historically been performed on 2D flat surfaces such as polystyrene Petri dishes, flasks and well plates. Hydrophobic polystyrene surfaces are typically plasma-treated to render it hydrophilic, which facilitates cell adhesion. Most cells in the body are non-circulating, and therefore depend on attachmentto the surrounding ECM for survival. The ECM has both structural and fundamental functional roles, notably by producing dynamic signals that influence the cell fate. The biochemical and structural variability of the ECM, together with its dynamic and multifactorial nature, exert a functional role. The ECM structure and composition are not static. The ECM physical properties modulate several adhesion-related cell functions. Cells are anchored to the ECM via cell-surface integrins that are responsible not only for the physical attachment of cells to the matrix, but also for sensing and transducing mechanical signals from focal adhesion sites to the cytoskeletal machinery within the cell. These signals are known to drive various cellular processes that include migration, proliferation, differentiation, and apoptosis. Together, the forces exerted on the cell through mechanical attachments and external stimuli form a dynamic three-dimensional (3D) physical microenvironment that must be carefully considered when modeling cells and tissues in vitro. In embodiments, a combination of cell- and cell-formed ECM-derived substrates may be achieved using the obtained biofluids. Thus, methods of the invention may use the biofluids as all or part of the ECM of the cell culture microenvironment to more closely reproduce the in vivo behavior in cell microenvironments. Tn embodiments, the assay is a cell-based assay. Cell-based assays allow for the ability to manipulate the physico-chemical (i.e., temperature, pH, osmotic pressure, O ₂ and CO ₂ tension) and the physiological environment (i.e., hormone and nutrient concentrations) in which the cells propagate in orderto evaluate cell response. Cell-based assaysuse live cells grown in vitro and are used to assess the biochemistry and physiology of both healthy and diseased cells. Cell culture assays provide a means of quantitatively analyzing the presence, amount, or functional activity of a cell or tissue of interest.

Methods of invention provide for performing a cell-based assay on cells that are combined with the obtained biofluids. For example, the cell-based assay may be a functional assay. Functional assays elucidate key cellular processes including apoptosis, cell proliferation, cell cycle and viability, oxidative stress, internalization processes like phagocytosis andendocytosis as well as indicators for ion homeostasis. In embodiments, the functional assay may evaluate one or more of cell viability, oxidative metabolism, membrane potential, intracellular ionized calcium, intracellular pH, intracellular organelles, and/or maybe a gene reporter assay. Cell function assays can be performed on multiple instrument platforms as is known to persons skilled in the art, for example, by microscopy, flow cytometry, microplate readers, and high throughput screening.

In functional assays, the information of interest is the functional behavior of the cell itself. The information of interest and the cell behavior evaluated depends on both the type of disease and the purpose of the assay. For example, for cancer research and drug discovery, the assays may be tailored to evaluate cell capabilities for sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing/accessing vasculature, activating invasion and metastasis, reprogramming cellular metabolism, and/or avoiding immune destruction. Regardless of the purpose of the assay, methods of the invention provide functional assays that achieve a cell microenvironment that supports the cells of interest in a way that results in meaningful data about the cellular response. By using the obtained biofluids in which to culture the cells, methods of the invention provide a cell culture microenvironment that provides novel information about the functional response of the cells.

In embodiments, methods of the invention provide for using the biofluids as the cell culture microenvironment in a chemosensitivity and/or resistance assay. Chemosensitivity assays may measure the number of tumor cells that are killed by a cancer drug. Tumor chemosensitivity assays (TCAs), also known as drug response assays or individualized tumor response tests, are designed to select the most appropriate chemotherapy option for individual cancer patients by indicating resistance or sensitivity for drugs. For example, the TCA assay may be simple assay such as clonogenic assay, or technologically advanced assays such as luminescence-based assays like ATP-TCA or organoids. Methods of the invention may use any chemosensitivity assay as is known to persons skilled in the art, and for example as found in Ulukaya, 2021, Tumor chemosensitivity assays are helpful for personalized cytotoxic treatments in cancer patients, Medicina 57(6), 636: 1-16, incorporated by reference. Similarly, a chemoresistance assay identifies chemotherapeutic agents that may be ineffective against tumor growth. Any resistance assay may be usedin methods of the invention, for example as described in Bussmann, 2016, Perspectives in chemosensitivity and chemoresistance assays and their implementation in head and neck cancers, Eur Arch Oto 273(12):4073-4080, incorporated herein by reference.

Generally, the methods of the invention that determine chemosensitivity or resistance of cells involves obtaining biofluids as described above from a patient having cancer, and obtaining tumor cells. For example, a tumor specimen may be obtained during a medical procedure such as a diagnosis biopsy, or tumor resection. The cells may also be obtained from blood containing circulating tumor cells. Tumor cells may be obtained from the biofluid itself. If a tumor specimen is obtained, the tumor cells may be dissociated from the specimen and isolated. For example, the tumor material may be processed to two-dimension (2D)/three-dimension (3D) primary cultures retaining the tumor cells’ original characteristics as is known by persons skilled in the art. The methods further provide for combining the cells with the biofluid, and exposing the cells to primary cell culture in the presence of chemotherapies. Cell viability/mortality may then be analyzed and the result used to determine a cell response or chemosensitivity profde. The response of the cells may be determined by analyzing the biological response through a relevant endpoint to provide a functional profde such as chemosensitivity, chemoresistance, DNA repair, and the like.

In other embodiments, the assay may be one or more of assays to determine cellular response that evaluates one or more of the hallmarks of cancer. For example, the cellular response may evaluate cell capabilities for sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing/accessing vasculature, activating invasion and metastasis, reprogramming cellular metabolism, and avoiding immune destruction. The assays may also determine enabling processes such as genome instability and tumor-promoting inflammation. Importantly, by using biofluids obtained as described above, methods of the invention provide a cell culture microenvironment that better mimics the tumor microenvironment that is known to play an integral role in tumorigenesis and malignant progression. The assay may be any assay as is known to persons skilled in the art, for example, as found in Menyhart, et.al., 2016, Guidelines for the selection of functional assays to evaluate the hallmarks of cancer, Biochimica et Biophysica Acta 1866:300-319, incorporated by reference herein.

In embodiments, methods of the invention may be used for drug discovery. The cell-based assay enables high-throughput compound screening by measuring the functional behavior of the cell of interest in response to a candidate compound. For example, DNA repair capacities of cancer cells can be determined by combining cell extracts with the biofluid obtained and/or a drug candidate’s mode of action may be assessed. In other examples, The functional assay may be a predictive assay, such as an assay to predict radiosensitivity. For example, as known to persons skilled in the art, the radiosensitivity assay may be based on the quantification of clonogenic cell survival, micronuclei, p21 expression, apoptosis, chromosome and DNA repair, and signaling.

In non-limiting examples, the methods of the invention may be used for genomic analysis of a new cancer, drug resistance evaluation, disease recurrence, phenotypic analysis, biocomposite compatibility, drug preclinical evaluation, and/or functional pathway analysis. The examples of types of assays contained herein that may be used in methods of the invention are meant to be non-limiting. Methods of the invention provide for using the obtained biofluids in any cell-based assay to analyze and determine a cellular response of interest. Further, it is contemplated that more than one cell-based assay may be performed at a given time. Methods of the invention contemplate that biofluids, typically regarded as waste, may be used in cell-based assays to achieve a cell culture microenvironment that provides a novel understanding of cellular response.

The assay results or response characteristics may be analyzed by any method known to persons skilled in the art, for example, by immunoblot, RT-PCR, immunocytochemistry, immunoprecipitation, RNA microarray, RNA-seq, using flow cytometry fluorescence microscopy and/or multi-well readers.

In embodiments, methods of the invention further comprise predicting the patient’s outcome to a systemic treatment based on the response of the cells to the assay. For example the systemic treatment may be one or more of chemotherapy, a targeted drug therapy, hormonal therapy, and immunotherapy.

Incorporation by Reference

References and citations to other documents, such as patents, patent applications, patent publications, journals, books, papers, web contents, have been made throughout this disclosure. All such documents are hereby incorporated herein by reference in their entirety for all purposes.

Equivalents

Various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including references to the scientific and patent literature cited herein. The subject matter herein contains important information, exemplification and guidance that can be adapted to the practice of this invention in its various embodiments and equivalents thereof.