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Definitions

• CRC Colorectal cancer
• mutated APC proteins lose the ability to activate glycogen synthase kinase 3b (GSK3P) which in turn phosphorylates N-terminal serine/threonine residues of b-catenin, mediating b-catenin degradation through ubiquitination.
• GSK3P glycogen synthase kinase 3b
• APC deficiency results in the accumulation of b-catenin which then moves to the nucleus to bind and de-repress the T-cell factor/lymphoid enhancer-binding factor (TCF/LEF) transcription factor complex, enabling activation of the canonical WNT signaling network.
• TCF/LEF T-cell factor/lymphoid enhancer-binding factor
• agents targeting the WNT pathway include inhibitors of WNT ligands, b-catenin degrading complex, TCF/LEF, and Notch and Sonic Hedgehog signaling that crosstalk with WNT.
• WNT targeting programs have yet to produce meaningful clinical results.
• orthogonal strategies to target APC-deficient colorectal cancer (CRC) and other APC-deficient tumor types.
• Various embodiments of the disclosure include methods for treating a subject with an APC-deficient cancer, methods for treating a subject with a cancer determined to have an APC mutation, methods for treating a subject with APC-deficient CRC, methods for identifying a cancer as being susceptible to TD02 inhibition, methods for identifying a cancer as being susceptible to inhibition of a cytokine activated by TD02 activity, methods for diagnosing a patient, methods for prognosing a patient, methods for detecting cancer cells, compositions for treating APC-deficient cancer, and methods for treating a subject with a cancer having constitutively active WNT signaling.
• Methods of the disclosure can include at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the following steps: providing a TD02 inhibitor, providing an inhibitor of a cytokine, identifying a cancer as having an APC deficiency, providing a pharmaceutical composition to a subject, sequencing a nucleic acid from cancer cells, identifying a mutation in a nucleic acid from cancer cells, comparing a nucleic acid expression level to a control or reference value, analyzing a methylation status of a nucleic acid from cancer cells, obtaining a biological sample, isolating cancer cells from a subject, treating a subject with a cancer therapy, treating a subject with immunotherapy, detecting an increased expression of a gene, determining an outcome of a treatment, identifying a cancer as being sensitive to TD02 inhibition, identifying a cancer as being sensitive to inhibition of a cytokine activated by TD02 activity, inhibiting TD02, inhibiting CXCL5, and inhibiting CXCLl/2.
• a method for treating a subject with a cancer determined to have an adenomatous polyposis coli (APC) mutation comprising providing to the subject a pharmaceutical composition comprising an effective amount of an inhibitor of (a) tryptophan 2,3 -dioxygenase (TD02) or (b) a cytokine activated by TD02 activity.
• TD02 tryptophan 2,3 -dioxygenase
• a cytokine activated by TD02 activity a method for treating a subject for an APC-deficient cancer, the method comprising providing to the subject a pharmaceutical composition comprising an effective amount of an inhibitor of (a) TD02 or (b) a cytokine activated by TD02 activity.
• a method for treating a subject for cancer comprising (a) identifying the cancer as having an APC deficiency and (b) providing to the subject a pharmaceutical composition comprising an effective amount of an inhibitor of (i) TD02 or (ii) a cytokine activated by TD02 activity.
• a method for treating cancer in a subject comprising determining whether the cancer has an APC mutation and (a) if the cancer has an APC mutation, providing to the subject an effective amount of an inhibitor of (ii) TD02 or (ii) a cytokine activated by TD02 activity and (b) if the cancer does not have an APC mutation, providing to the subject an effective amount of an alternate therapy.
• An alternate therapy may be, for example, radiotherapy, chemotherapy, or surgery.
• an inhibitor is an inhibitor of TD02. In some embodiments, the inhibitor inhibits the expression of TD02 in the cancer. In some embodiments, the inhibitor inhibits the activity of TD02 in the cancer. In some embodiments, the inhibitor is an siRNA, an shRNA, an antisense oligonucleotide, a small molecule inhibitor, an antibody, or an antibody-like molecule. In some embodiments, the inhibitor is an siRNA, shRNA, or antisense oligonucleotide targeting TD02.
• the inhibitor is PF06845102/EOS200809, 680C91, LM10, HTI-1090, DN1406131, RG70099, EPL-1410, CB548, CMG017, or a derivative thereof. In some embodiments, the inhibitor is PF06845102/EOS200809. In some embodiments, the inhibitor is 680C91.
• the pharmaceutical composition is administered intravenously, intramuscularly, intraperitoneally, intracerobrospinally, subcutaneously, intra-articularly, intrasynovially, intrathecally, orally, topically, through inhalation, or through a combination of two or more routes of administration.
• the inhibitor is an inhibitor of a cytokine activated by TD02 activity.
• the cytokine is CXCL5, CXCL7, CSF3, CXCR2, CXCL2, CXCL10, CCL2, or CXCL1.
• the cytokine is CXCL5, CXCL7, or CSF3.
• the cytokine is CXCL5.
• the inhibitor is a CXCLl/2 inhibitor.
• the inhibitor is a CXCL5 inhibitor.
• the inhibitor is an antibody or antibody-like molecule targeting CXCR5.
• the inhibitor is an siRNA, shRNA, or an antisense oligonucleotide targeting CXCL5.
• a method for identifying a cancer as being sensitive to TD02 inhibition comprising (a) obtaining cancer cells from a biological sample from a subject; (b) detecting a deficiency in an APC gene in the cancer cells; and (c) identifying the cancer as being sensitive to TD02 inhibition based on (b).
• a method for determining whether a biological sample comprises cancer cells sensitive to TD02 inhibition comprising (a) measuring a presence or absence of an APC deficiency in the biological sample; (b) determining that the biological sample comprises cancer cells sensitive to TD02 inhibition if the biological sample comprises an APC deficiency; and (c) determining that the biological sample does not comprise cancer cells sensitive to TD02 inhibition if the biological sample does not comprise an APC deficiency.
• the method further comprises detecting an increased expression or activity of TD02 in the cancer cells relative to cells from a non-cancerous biological sample. In some embodiments, the method further comprises measuring an expression or activity level of TD02 in the biological sample. In some embodiments, the method further comprises determining that the biological sample does not comprise cancer cells sensitive to TD02 inhibition if the TD02 expression or activity level in the biological sample is not significantly different from the expression or activity level in a non-cancerous biological sample.
• an APC deficiency is an APC mutation. In some embodiments, the APC deficiency is a repression of APC expression. In some embodiments, the repression is an epigenetic repression.
• the cancer has an increased expression of TD02 relative to a control or reference sample, which may be a biological sample from a healthy subject.
• the cancer comprises constitutively active WNT signaling.
• the cancer is colorectal cancer, breast cancer, prostate cancer, lung cancer, head and neck squamous cell carcinoma, or sarcoma.
• the cancer is colorectal cancer.
• the cancer is a cancer of a given diagnostic stage.
• the cancer is a stage I, stage Ila, stage lib, stage lie, stage Ilia, stage Mb, stage IIIc, stage IVa, or stage IVb cancer.
• the cancer is recurrant cancer.
• the subject was previously treated for the cancer.
• the subject was not previously treated for the cancer.
• the cancer was determined to be resistant to a previous treatment.
• the disclosed methods further comprise providing to the subject a cancer immunotherapy.
• a cancer immunotherapy may be, for example, an antibody therapy or a cellular therapy.
• the cancer immunotherapy is a checkpoint inhibitor therapy.
• the method further comprises providing to the subject an additional therapy wherein the additional therapy is chemotherapy, radiation therapy, surgery, or a combination thereof.
• the method does nor comprise any step of providing to the subject chemotherapy, radiation therapy, or surgery.
• the method comprises reducing a number of tumor associated macrophages in the subject.
• a biological sample is a blood or serum sample.
• cancer cells are colorectal cancer cells.
• a biological sample is a tissue sample adjacent to a surgical site of a colorectal cancer patient.
• a non-cancerous biological sample is normal mucosal tissue.
• aspects of the disclosure are directed to a method for treating a subject for a cancer determined to have constitutively active WNT signaling, the method comprising providing to the subject a pharmaceutical composition comprising an effective amount of an inhibitor of (a) TD02 or (b) a cytokine activated by TD02 activity.
• the constitutively active WNT signaling comprises an APC-deficiency.
• the constitutively active WNT signaling does not comprise an APC-deficiency.
• the cancer comprises a constitutively active b-catenin protein.
• Additional aspects are directed to use of (a) an inhibitor of (i) TD02 or (ii) a cytokine activated by TD02 activity and (b) a pharmaceutical acceptable carrier in the treatment of an APC-mutant cancer in a subject or in the manufacture of a medicament for treating an APC-mutant cancer in a subject.
• A, B, and/or C includes: A alone, B alone, C alone, a combination of A and B, a combination of A and C, a combination of B and C, or a combination of A, B, and C.
• “and/or” operates as an inclusive or. Is is specifically contemplated that A, B, or C may be specifically excluded from an embodiment.
• the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.
• FIG. IF shows IHC analysis of polyps from APCmin mice and tumors from iKAP mouse models, revealing increased nuclear b-catenin, Ki67, and TD02 compared to normal colon tissue. Representative images of triplicate studies are shown. Scale bar, IOOmhi.
• FIG. 2J shows Venn diagrams representative of analysis to identify SE genes for APC mutations in CRC. Two separate analyses using different cutoffs are shown. *Left P value - P value for genes that are essential for b-catenin active cancer cell lines.
• FIG. 3E shows that ChIP-seq in APC-WT and APC-KO MC38 cells showed binding peaks for TCF4 on the promoters of TD02 gene.
• FIG. 3F shows that CHIP-PCR using TCF4 antibody showed enriched binding to the promoter regions of TD02 gene in DLD-1 cells. GAPDH as a negative control and MYC and AXIN2 as positive controls.
• FIG. 3J shows immunoblotting of TD02 in MC38 cells supplemented with 0, 50 and lOOng of recombinant mouse WNT3a proteins for 36hrs.
• FIGs. 3K-3M show immunoblot for TD02 and b-catenin in DLD-1 cells (FIG. 3K), Caco-2 cells (FIG. 3L), and HCT-15 cells (FIG. 3M) treated with XAV-939 in a dose-dependent manner.
• FIGs. 4A-4P show results from studies demonstrating that TD02 is essential for survival in APC-mutated CRC cells.
• FIG. 4A-4P show results from studies demonstrating that TD02 is essential for survival in APC-mutated CRC cells.
• FIG. 4A shows RT-qPCR demonstrating TD02 shRNA knockdown efficiency in APC-WT and APC-KO MC38 cell lines.
• FIG. 4D shows immunofluorescence staining of RFP-caspase-3 in APCmin colonoids infected with ishTD02 after 96 h of dox treatment. Induction of shTD02 is indicated by GFP (highlighted with arrows). X63 magnification.
• FIG. 4E shows immunoblots for TD02 and cleaved Caspase-3 in APCmin ishTD02 organoid cell lysates after Dox treatment for 48h.
• FIG. 4G shows immunoblots of cleaved caspase-3 in APC-WT and APC-KO MC38 cell lines with ishTD02 after doxycycline (Dox) treatment.
• FIG. 41 shows total flux measurement of tumors from tumors in H. n.s.P>0.05, *P ⁇ 0.05.
• FIG. 4J shows weights of tumors harvested from mice in FIG.
• FIGs. 12A-12G show results from studies demonstrating that the TD02-AhR- CXCL5 axis regulates macrophage recruitment in APC-mutated CRC tumors.
• TD02-Kyn-AhR axis drives glycolysis and promotes cell proliferation and growth in APC-deficient CRC cells as well as upregulates CXCL5 which recruits tumor associated macrophages (TAMs). These TAMs promote an immunosuppressive tumor microenvironment (TME) as well as support cancer cell survival via their secretion of GAS6 which activates AXL in cancer cells.
• TAMs tumor associated macrophages
• TAMs immunosuppressive tumor microenvironment
• GAS6 tumor associated macrophages
• APC-deficiency creates a TD02-driven circuit that establishes a symbiotic relationship between cancer cells and infiltrating TAMs in the CRC TME.
• methods and compositions for targeting TD02 and downstream effectors e.g., cytokines
• Inhibitory oligonucleotides are well known in the art.
• siRNA and double-stranded RNA have been described in U.S. Patents 6,506,559 and 6,573,099, as well as in U.S. Patent Publications 2003/0051263, 2003/0055020, 2004/0265839, 2002/0168707, 2003/0159161, and 2004/0064842, all of which are herein incorporated by reference in their entirety.
• an inhibitory oligonucleotide may be capable of decreasing the expression of TD02 by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 90%, 95%, 99%, or 100% or any range or value in between the foregoing.
• an inhibitor may be between 17 to 25 nucleotides in length and comprises a 5’ to 3’ sequence that is at least 90% complementary to the 5’ to 3’ sequence of a mature TD02 mRNA.
• an inhibitor molecule is 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, or any range derivable therein.
• the cancer may specifically be of one or more of the following histological types, though it is not limited to these: undiffemeiated carcinoma, bladder, blood, bone, brain, breast, urinary, esophageal, thymomas, duodenum, colon, rectal, anal, gum, head, kidney, soft tissue, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testicular, tongue, uterine, thymic, cutaneous squamous-cell, noncolorectal gastrointestinal, colorectal, melanoma, Merkel-cell, renal-cell, cervical, hepatocellular, urothelial, non-small cell lung, head and neck, endometrial, esophagogastric, small-cell lung mesothelioma, ovarian, esophogogastric, glioblastoma, adrencorical, ceremoniesal, pancreatic, germ-cell, giant and spin
• methods of the present disclosure comprise treating cancer, where the cancer is colorectal cancer, breast cancer, prostate cancer, lung cancer, head and neck squamous cell carcinoma, or sarcoma.
• the cancer is colorectal cancer (CRC).
• the cancer is a cancer having constituitively active WNT signaling.
• the cancer is an APC-deficient cancer.
• the cancer is an APC-deficient CRC.
• an “APC-deficient cancer” describes a cancer which has reduced expression and/or activity of an adenomatous polyposis coli (APC) gene or protein relative to a normal or non-cancerous cell.
• an APC-deficient cancer is a cancer having a mutation in the APC gene or a regulatory region of the APC gene, where the mutation prevents expression of APC.
• an APC-deficient cancer is a cancer having a mutation in the APC gene, where the mutation prevents the APC protein from functioning normally (e.g., causes misfolding of the protein).
• an APC-deficient cancer is a cancer having epigenetic repression of APC gene expression.
• Certain aspects of the disclosure are directed to therapeutic methods for treating a subject with an APC-deficient cancer.
• the disclosed methods comprise detecting an APC deficiency (e.g., mutation, epigenetic repression, etc.) in cancer cells from a subject prior to treatment, for example via DNA sequencing, polymerase chain reaction, or other suitable molecular technique.
• the methods comprise treating a subject known to have a cancer with an APC deficiency.
• the methods comprise treating a subject presumed to have a cancer with an APC deficiency.
• the disclosed methods comprise administration of a cancer immunotherapy.
• Cancer immunotherapy (sometimes called immuno-oncology, abbreviated IO) is the use of the immune system to treat cancer.
• Immunotherapies can be categorized as active, passive or hybrid (active and passive). These approaches exploit the fact that cancer cells often have molecules on their surface that can be detected by the immune system, known as tumour-associated antigens (TAAs); they are often proteins or other macromolecules (e.g. carbohydrates).
• TAAs tumour-associated antigens
• Active immunotherapy directs the immune system to attack tumor cells by targeting TAAs.
• Passive immunotherapies enhance existing anti-tumor responses and include the use of monoclonal antibodies, lymphocytes and cytokines. Certain immumotherapies are known in the art, and some are described below.
• Embodiments of the disclosure may include administration of immune checkpoint inhibitors, which are further described below.
• PDL1 B7-H1, B7-4, CD274, and B7-H.
• Alternative names for “PDL2” include B7- DC, Btdc, and CD273.
• PD-1, PDL1, and PDL2 are human PD-1, PDL1 and PDL2.
• the PD-1 inhibitor is a molecule that inhibits the binding of PD-1 to its ligand binding partners.
• the PD-1 ligand binding partners are PDL1 and/or PDL2.
• a PDL1 inhibitor is a molecule that inhibits the binding of PDL1 to its binding partners.
• PDL1 binding partners are PD-1 and/or B7-1.
• the PDL2 inhibitor is a molecule that inhibits the binding of PDL2 to its binding partners.
• a PDL2 binding partner is PD-1.
• the PD-1 inhibitor is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody).
• the anti-PD- 1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and pidilizumab.
• the PD-1 inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDL1 or PDL2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence).
• the PDL1 inhibitor comprises AMP- 224.
• Nivolumab also known as MDX-1106-04, MDX- 1106, ONO-4538, BMS-936558, and OPDIVO®, is an anti-PD-1 antibody described in W 02006/121168.
• Pembrolizumab also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA®, and SCH-900475, is an anti-PD-1 antibody described in W02009/114335.
• Pidilizumab also known as CT-011, hBAT, or hBAT-1, is an anti-PD-1 antibody described in W02009/101611.
• the inhibitor comprises the heavy and light chain CDRs or VRs of nivolumab, pembrolizumab, or pidilizumab. Accordingly, in one embodiment, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of nivolumab, pembrolizumab, or pidilizumab, and the CDR1, CDR2 and CDR3 domains of the VL region of nivolumab, pembrolizumab, or pidilizumab.
• the antibody competes for binding with and/or binds to the same epitope on PD-1, PDL1, or PDL2 as the above- mentioned antibodies.
• the antibody has at least about 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies.
• CTLA-4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal.
• Intracellular CTLA- 4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.
• Inhibitors of the disclosure may block one or more functions of CTLA-4, B7-1, and/or B7-2 activity. In some embodiments, the inhibitor blocks the CTLA-4 and B7-1 interaction. In some embodiments, the inhibitor blocks the CTLA-4 and B7-2 interaction.
• the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• an anti-CTLA-4 antibody e.g., a human antibody, a humanized antibody, or a chimeric antibody
• an antigen binding fragment thereof e.g., an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.
• art recognized anti-CTLA-4 antibodies can be used.
• the anti- CTLA-4 antibodies disclosed in: US 8,119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab), U.S. Patent No. 6,207,156; Hurwitz et al., 1998; can be used in the methods disclosed herein.
• the teachings of each of the aforementioned publications are hereby incorporated by reference.
• Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used.
• a humanized CTLA-4 antibody is described in International Patent Application No. W 02001/014424, W02000/037504, and U.S. Patent No. 8,017,114; all incorporated herein by reference.
• a further anti-CTLA-4 antibody useful as a checkpoint inhibitor in the methods and compositions of the disclosure is ipilimumab (also known as 10D1, MDX- 010, MDX- 101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g., WOO 1/14424).
• the inhibitor comprises the heavy and light chain CDRs or VRs of tremelimumab or ipilimumab.
• Dendritic cell therapy provokes anti-tumor responses by causing dendritic cells to present tumor antigens to lymphocytes, which activates them, priming them to kill other cells that present the antigen.
• Dendritic cells are antigen presenting cells (APCs) in the mammalian immune system. In cancer treatment they aid cancer antigen targeting.
• APCs antigen presenting cells
• One example of cellular cancer therapy based on dendritic cells is sipuleucel-T.
• One method of inducing dendritic cells to present tumor antigens is by vaccination with autologous tumor lysates or short peptides (small parts of protein that correspond to the protein antigens on cancer cells). These peptides are often given in combination with adjuvants (highly immunogenic substances) to increase the immune and anti-tumor responses.
• adjuvants include proteins or other chemicals that attract and/or activate dendritic cells, such as granulocyte macrophage colony- stimulating factor (GM-CSF).
• Dendritic cells can also be activated in vivo by making tumor cells express GM- CSF. This can be achieved by either genetically engineering tumor cells to produce GM-CSF or by infecting tumor cells with an oncolytic virus that expresses GM-CSF.
• Another strategy is to remove dendritic cells from the blood of a patient and activate them outside the body.
• the dendritic cells are activated in the presence of tumor antigens, which may be a single tumor- specific peptide/protein or a tumor cell lysate (a solution of broken down tumor cells). These cells (with optional adjuvants) are infused and provoke an immune response.
• Dendritic cell therapies include the use of antibodies that bind to receptors on the surface of dendritic cells. Antigens can be added to the antibody and can induce the dendritic cells to mature and provide immunity to the tumor. Dendritic cell receptors such as TLR3, TLR7, TLR8 or CD40 have been used as antibody targets.
• Chimeric antigen receptors are engineered receptors that combine a new specificity with an immune cell to target cancer cells. Typically, these receptors graft the specificity of a monoclonal antibody onto a T cell. The receptors are called chimeric because they are fused of parts from different sources.
• CAR-T cell therapy refers to a treatment that uses such transformed cells for cancer therapy.
• CAR-T cell design involves recombinant receptors that combine antigen-binding and T-cell activating functions.
• the general premise of CAR-T cells is to artificially generate T-cells targeted to markers found on cancer cells.
• scientists can remove T-cells from a person, genetically alter them, and put them back into the patient for them to attack the cancer cells.
• CAR-T cells create a link between an extracellular ligand recognition domain to an intracellular signalling molecule which in turn activates T cells.
• the extracellular ligand recognition domain is usually a single-chain variable fragment (scFv).
• Example CAR-T therapies include Tisagenlecleucel (Kymriah) and Axicabtagene ciloleucel (Yescarta).
• the CAR-T therapy targets CD 19.
• Cytokines are proteins produced by many types of cells present within a tumor. They can modulate immune responses. The tumor often employs them to allow it to grow and reduce the immune response. These immune-modulating effects allow them to be used as drugs to provoke an immune response. Two commonly used cytokines are interferons and interleukins.
• Interferons are produced by the immune system. They are usually involved in anti viral response, but also have use for cancer. They fall in three groups: type I (IFNa and IFNP), type II (IFNy) and type III (IFN/,).
• Interleukins have an array of immune system effects.
• IF-2 is an exemplary interleukin cytokine therapy.
• Adoptive T cell therapy is a form of passive immunization by the transfusion of T- cells (adoptive cell transfer). They are found in blood and tissue and usually activate when they find foreign pathogens. Specifically they activate when the T-cell's surface receptors encounter cells that display parts of foreign proteins on their surface antigens. These can be either infected cells, or antigen presenting cells (APCs). They are found in normal tissue and in tumor tissue, where they are known as tumor infiltrating lymphocytes (TIFs). They are activated by the presence of APCs such as dendritic cells that present tumor antigens. Although these cells can attack the tumor, the environment within the tumor is highly immunosuppressive, preventing immune-mediated tumour death.
• APCs antigen presenting cells
• T-cells specific to a tumor antigen can be removed from a tumor sample (TIFs) or filtered from blood. Subsequent activation and culturing is performed ex vivo, with the results reinfused. Activation can take place through gene therapy, or by exposing the T cells to tumor antigens.
• a cancer treatment may exclude any of the cancer treatments described herein.
• embodiments of the disclosure include patients that have been previously treated for a therapy described herein, are currently being treated for a therapy described herein, or have not been treated for a therapy described herein.
• the patient is one that has been determined to be resistant to a therapy described herein.
• the patient is one that has been determined to be sensitive to a therapy described herein.
• methods involve obtaining a sample from a subject.
• the methods of obtaining provided herein may include methods of biopsy such as fine needle aspiration, core needle biopsy, vacuum assisted biopsy, incisional biopsy, excisional biopsy, punch biopsy, shave biopsy or skin biopsy.
• the sample is obtained from a biopsy from esophageal tissue by any of the biopsy methods previously mentioned.
• the sample may be obtained from any of the tissues provided herein that include but are not limited to non-cancerous or cancerous tissue and non-cancerous or cancerous tissue from the serum, gall bladder, mucosal, skin, heart, lung, breast, pancreas, blood, liver, muscle, kidney, smooth muscle, bladder, colon, intestine, brain, prostate, esophagus, or thyroid tissue.
• the sample may be obtained from any other source including but not limited to blood, sweat, hair follicle, buccal tissue, tears, menses, feces, or saliva.
• any medical professional such as a doctor, nurse or medical technician may obtain a biological sample for testing.
• the biological sample can be obtained without the assistance of a medical professional.
• a sample may include but is not limited to, tissue, cells, or biological material from cells or derived from cells of a subject.
• the biological sample may be a heterogeneous or homogeneous population of cells or tissues.
• the biological sample may be obtained using any method known to the art that can provide a sample suitable for the analytical methods described herein.
• the sample may be obtained by non-invasive methods including but not limited to: scraping of the skin or cervix, swabbing of the cheek, saliva collection, urine collection, feces collection, collection of menses, tears, or semen.
• the sample may be obtained by methods known in the art.
• the samples are obtained by biopsy.
• the sample is obtained by swabbing, endoscopy, scraping, phlebotomy, or any other methods known in the art.
• the sample may be obtained, stored, or transported using components of a kit of the present methods.
• multiple samples such as multiple esophageal samples may be obtained for diagnosis by the methods described herein.
• multiple samples such as one or more samples from one tissue type (for example esophagus) and one or more samples from another specimen (for example serum) may be obtained for diagnosis by the methods.
• multiple samples such as one or more samples from one tissue type (e.g.
• samples from another specimen may be obtained at the same or different times.
• Samples may be obtained at different times are stored and/or analyzed by different methods. For example, a sample may be obtained and analyzed by routine staining methods or any other cytological analysis methods.
• the biological sample may be obtained by a physician, nurse, or other medical professional such as a medical technician, endocrinologist, cytologist, phlebotomist, radiologist, or a pulmonologist.
• the medical professional may indicate the appropriate test or assay to perform on the sample.
• a molecular profiling business may consult on which assays or tests are most appropriately indicated.
• the patient or subject may obtain a biological sample for testing without the assistance of a medical professional, such as obtaining a whole blood sample, a urine sample, a fecal sample, a buccal sample, or a saliva sample.
• the sample is obtained by an invasive procedure including but not limited to: biopsy, needle aspiration, endoscopy, or phlebotomy.
• the method of needle aspiration may further include fine needle aspiration, core needle biopsy, vacuum assisted biopsy, or large core biopsy.
• multiple samples may be obtained by the methods herein to ensure a sufficient amount of biological material.
• the sample is a fine needle aspirate of a esophageal or a suspected esophageal tumor or neoplasm.
• the fine needle aspirate sampling procedure may be guided by the use of an ultrasound, X-ray, or other imaging device.
• the molecular profiling business may obtain the biological sample from a subject directly, from a medical professional, from a third party, or from a kit provided by a molecular profiling business or a third party.
• the biological sample may be obtained by the molecular profiling business after the subject, a medical professional, or a third party acquires and sends the biological sample to the molecular profiling business.
• the molecular profiling business may provide suitable containers, and excipients for storage and transport of the biological sample to the molecular profiling business.
• a medical professional need not be involved in the initial diagnosis or sample acquisition.
• An individual may alternatively obtain a sample through the use of an over the counter (OTC) kit.
• OTC kit may contain a means for obtaining said sample as described herein, a means for storing said sample for inspection, and instructions for proper use of the kit.
• molecular profiling services are included in the price for purchase of the kit. In other cases, the molecular profiling services are billed separately.
• a sample suitable for use by the molecular profiling business may be any material containing tissues, cells, nucleic acids, genes, gene fragments, expression products, gene expression products, or gene expression product fragments of an individual to be tested. Methods for determining sample suitability and/or adequacy are provided.
• the subject may be referred to a specialist such as an oncologist, surgeon, or endocrinologist.
• the specialist may likewise obtain a biological sample for testing or refer the individual to a testing center or laboratory for submission of the biological sample.
• the medical professional may refer the subject to a testing center or laboratory for submission of the biological sample.
• the subject may provide the sample.
• a molecular profiling business may obtain the sample.
• the therapy provided herein may comprise administration of a combination of therapeutic agents, such as a first cancer therapy (e.g., a TD02 inhibitor) and a second cancer therapy (e.g., an additional cancer therapy such as chemotherapy, radiation therapy, or immunotherapy).
• a first cancer therapy e.g., a TD02 inhibitor
• a second cancer therapy e.g., an additional cancer therapy such as chemotherapy, radiation therapy, or immunotherapy.
• the therapies may be administered in any suitable manner known in the art.
• the first and second cancer treatment may be administered sequentially (at different times) or concurrently (at the same time).
• the first and second cancer treatments are administered in a separate composition.
• the first and second cancer treatments are in the same composition.
• Embodiments of the disclosure relate to compositions and methods comprising therapeutic compositions.
• the different therapies may be administered in one composition or in more than one composition, such as 2 compositions, 3 compositions, or 4 compositions.
• Various combinations of the agents may be employed.
• the therapeutic agents of the disclosure may be administered by the same route of administration or by different routes of administration.
• the cancer therapy is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally.
• the antibiotic is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally.
• the appropriate dosage may be determined based on the type of disease to be treated, severity and course of the disease, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician.
• the treatments may include various “unit doses.”
• Unit dose is defined as containing a predetermined-quantity of the therapeutic composition.
• the quantity to be administered, and the particular route and formulation, is within the skill of determination of those in the clinical arts.
• a unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time.
• a unit dose comprises a single administrable dose.
• the quantity to be administered depends on the treatment effect desired.
• An effective dose is understood to refer to an amount necessary to achieve a particular effect.
• doses in the range from 10 mg/kg to 200 mg/kg can affect the protective capability of these agents.
• doses include doses of about 0.1, 0.5,
• Such doses can be administered at multiple times during a day, and/or on multiple days, weeks, or months.
• the effective dose of the pharmaceutical composition is one which can provide a blood level of about 1 mM to 150 mM.
• the effective dose provides a blood level of about 4 pM to 100 pM.; or about 1 pM to 100 pM; or about 1 pM to 50 pM; or about 1 pM to 40 pM; or about 1 pM to 30 pM; or about 1 pM to 20 pM; or about 1 pM to 10 pM; or about 10 pM to 150 pM; or about 10 pM to 100 pM; or about 10 pM to 50 pM; or about 25 pM to 150 pM; or about 25 pM to 100 pM; or about 25 pM to 50 pM; or about 50 pM to 150 pM; or about 50 pM to 100 pM (or any range derivable therein).
• the dose can provide the following blood level of the agent
• the therapeutic agent that is administered to a subject is metabolized in the body to a metabolized therapeutic agent, in which case the blood levels may refer to the amount of that agent.
• the blood levels discussed herein may refer to the unmetabolized therapeutic agent.
• Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance or other therapies a subject may be undergoing.
• dosage units of pg/kg or mg/kg of body weight can be converted and expressed in comparable concentration units of pg/ml or mM (blood levels), such as 4 pM to 100 pM. It is also understood that uptake is species and organ/tissue dependent. The applicable conversion factors and physiological assumptions to be made concerning uptake and concentration measurement are well-known and would permit those of skill in the art to convert one concentration measurement to another and make reasonable comparisons and conclusions regarding the doses, efficacies and results described herein.
• kits containing compositions of the disclosure or compositions to implement methods disclosed herein.
• kits can be used to evaluate one or more biomarkers.
• a kit contains, contains at least or contains at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
• kits for evaluating biomarker activity in a cell there are kits for evaluating biomarker activity in a cell.
• Kits may comprise components, which may be individually packaged or placed in a container, such as a tube, bottle, vial, syringe, or other suitable container means.
• Individual components may also be provided in a kit in concentrated amounts; in some embodiments, a component is provided individually in the same concentration as it would be in a solution with other components. Concentrations of components may be provided as lx, 2x, 5x, lOx, or 20x or more.
• Kits for using probes, synthetic nucleic acids, nonsynthetic nucleic acids, and/or inhibitors of the disclosure for prognostic or diagnostic applications are included as part of the disclosure.
• any such molecules corresponding to any biomarker identified herein which includes nucleic acid primers/primer sets and probes that are identical to or complementary to all or part of a biomarker, which may include noncoding sequences of the biomarker, as well as coding sequences of the biomarker.
• kits may include a sample that is a negative or positive control for methylation of one or more bio markers.
• a control includes a nucleic acid that contains at least one CpG or is capable of identifying a CpG methylation site.
• any method or composition described herein can be implemented with respect to any other method or composition described herein and that different embodiments may be combined.
• the claims originally filed are contemplated to cover claims that are multiply dependent on any filed claim or combination of filed claims.
• Any embodiment of the disclosure involving specific biomarker by name is contemplated also to cover embodiments involving biomarkers whose sequences are at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% identical to the mature sequence of the specified nucleic acid.
• kits for analysis of a pathological sample by assessing biomarker profile for a sample comprising, in suitable container means, two or more biomarker probes, wherein the biomarker probes detect one or more of the biomarkers identified herein.
• the kit can further comprise reagents for labeling nucleic acids in the sample.
• the kit may also include labeling reagents, including at least one of amine-modified nucleotide, poly(A) polymerase, and poly(A) polymerase buffer. Labeling reagents can include an amine- reactive dye. VIII. Cancer Therapy
• the disclosed methods comprise administering a cancer therapy to the patient.
• the cancer therapy may be chosen based on the expression level measurements, alone or in combination with the clinical risk score calculated for the patient.
• the cancer therapy comprises a local cancer therapy.
• the cancer therapy excludes a systemic cancer therapy.
• the cancer therapy excludes a local therapy.
• the cancer therapy comprises a local cancer therapy without the administration of a system cancer therapy.
• the cancer therapy comprises an immunotherapy, which may be an immune checkpoint therapy.
• the cancer therapy comprises treatment with an ID02 inhibitor.
• the cancer therapy comprises treatment with an inhibitor of a cytokine activated by ID02 activity. Any of these cancer therapies may also be excluded. Combinations of these therapies may also be administered.
• the gene or miRNA expression measurement and analysis may indicate that one or more cancer therapies would be likely to be effective or ineffective.
• cells may be cultured for at least between about 10 days and about 40 days, for at least between about 15 days and about 35 days, for at least between about 15 days and 21 days, such as for at least about 15, 16, 17, 18, 19 or 21 days.
• the cells of the disclosure may be cultured for no longer than 60 days, or no longer than 50 days, or no longer than 45 days.
• the cells may be cultured for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
• the cells may be cultured in the presence of a liquid culture medium.
• the medium may comprise a basal medium formulation as known in the art.
• basal media formulations can be used to culture cells herein, including but not limited to Eagle's Minimum Essential Medium (MEM), Dulbecco's Modified Eagle's Medium (DMEM), alpha modified Minimum Essential Medium (alpha-MEM), Basal Medium Essential (BME), Iscove's Modified Dulbecco's Medium (IMDM), BGJb medium, F-12 Nutrient Mixture (Ham), Liebovitz L-15, DMEM/F-12, Essential Modified Eagle's Medium (EMEM), RPMI-1640, and modifications and/or combinations thereof.
• MEM Eagle's Minimum Essential Medium
• DMEM Dulbecco's Modified Eagle's Medium
• alpha-MEM alpha modified Minimum Essential Medium
• BME Basal Medium Essential
• BGJb medium F-12 Nutri
• compositions of the above basal media are generally known in the art, and it is within the skill of one in the art to modify or modulate concentrations of media and/or media supplements as necessary for the cells cultured.
• a culture medium formulation may be explants medium (CEM) which is composed of IMDM supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, 100 pg/ml streptomycin and 2 mmol/L L-glutamine.
• CEM explants medium
• FBS fetal bovine serum
• Other embodiments may employ further basal media formulations, such as chosen from the ones above.
• Any medium capable of supporting cells in vitro may be used to culture the cells.
• Media formulations that can support the growth of cells include, but are not limited to, Dulbecco's Modified Eagle's Medium (DMEM), alpha modified Minimal Essential Medium (aMEM), and Roswell Park Memorial Institute Media 1640 (RPMI Media 1640) and the like.
• DMEM Dulbecco's Modified Eagle's Medium
• aMEM alpha modified Minimal Essential Medium
• RPMI Media 1640 Roswell Park Memorial Institute Media 1640
• FBS fetal bovine serum
• a defined medium also can be used if the growth factors, cytokines, and hormones necessary for culturing cells are provided at appropriate concentrations in the medium.
• Media useful in the methods of the disclosure may comprise one or more compounds of interest, including, but not limited to, antibiotics, mitogenic compounds, or differentiation compounds useful for the culturing of cells.
• the cells may be grown at temperatures between 27° C to 40° C, such as 31° C to 37° C, and may be in a humidified incubator.
• the carbon dioxide content may be maintained between 2% to 10% and the oxygen content may be maintained between 1% and 22%.
• the disclosure should in no way be construed to be limited to any one method of isolating and culturing cells. Rather, any method of isolating and culturing cells should be construed to be included in the present disclosure.
• media can be supplied with one or more further components.
• additional supplements can be used to supply the cells with the necessary trace elements and substances for optimal growth and expansion.
• Such supplements include insulin, transferrin, selenium salts, and combinations thereof.
• These components can be included in a salt solution such as, but not limited to, Hanks' Balanced Salt Solution (HBSS), Earle's Salt Solution.
• Further antioxidant supplements may be added, e.g., b-mercaptoethanol. While many media already contain amino acids, some amino acids may be supplemented later, e.g., L-glutamine, which is known to be less stable when in solution.
• a medium may be further supplied with antibiotic and/or antimycotic compounds, such as, typically, mixtures of penicillin and streptomycin, and/or other compounds, exemplified but not limited to, amphotericin, ampicillin, gentamicin, bleomycin, hygromycin, kanamycin, mitomycin, mycophenolic acid, nalidixic acid, neomycin, nystatin, paromomycin, polymyxin, puromycin, rifampicin, spectinomycin, tetracycline, tylosin, and zeocin.
• antibiotic and/or antimycotic compounds such as, typically, mixtures of penicillin and streptomycin, and/or other compounds, exemplified but not limited to, amphotericin, ampicillin, gentamicin, bleomycin, hygromycin, kanamycin, mitomycin, mycophenolic acid, nalidixic acid, neo
• cells are cultured in a cell culture system comprising a cell culture medium, preferably in a culture vessel, in particular a cell culture medium supplemented with a substance suitable and determined for protecting the cells from in vitro aging and/or inducing in an unspecific or specific reprogramming.
• Certain methods of the disclosure concern culturing the cells obtained from human tissue samples.
• cells are plated onto a substrate that allows for adherence of cells thereto. This may be carried out, for example, by plating the cells in a culture plate that displays one or more substrate surfaces compatible with cell adhesion. When the one or more substrate surfaces contact the suspension of cells (e.g ., suspension in a medium) introduced into the culture system, cell adhesion between the cells and the substrate surfaces may ensue.
• suspension of cells e.g ., suspension in a medium
• cells are introduced into a culture system that features at least one substrate surface that is generally compatible with adherence of cells thereto, such that the plated cells can contact the said substrate surface, such embodiments encompass plating onto a substrate, which allows adherence of cells thereto.
• Cells of the present disclosure may be identified and characterized by their expression of specific marker proteins, such as cell-surface markers. Detection and isolation of these cells can be achieved, for example, through flow cytometry, ELISA, and/or magnetic beads. Reverse-transcription polymerase chain reaction (RT-PCR) may be used to quantify cell-specific genes and/or to monitor changes in gene expression in response to differentiation.
• RT-PCR Reverse-transcription polymerase chain reaction
• the marker proteins used to identify and characterize the cells are selected from the list consisting of c-Kit, Nanog, Sox2, Heyl, SMA, Vimentin, Cyclin D2, Snail, E-cadherin, Nkx2.5, GATA4, CD105, CD90, CD29, CD73, Wtl, CD34, CD45, and a combination thereof.
• the method for detecting the genetic signature may include selective oligonucleotide probes, arrays, allele- specific hybridization, molecular beacons, restriction fragment length polymorphism analysis, enzymatic chain reaction, flap endonuclease analysis, primer extension, 5’-nuclease analysis, oligonucleotide ligation assay, single strand conformation polymorphism analysis, temperature gradient gel electrophoresis, denaturing high performance liquid chromatography, high-resolution melting, DNA mismatch binding protein analysis, surveyor nuclease assay, sequencing, or a combination thereof, for example.
• the method for detecting the genetic signature may include fluorescent in situ hybridization, comparative genomic hybridization, arrays, polymerase chain reaction, sequencing, or a combination thereof, for example.
• the detection of the genetic signature may involve using a particular method to detect one feature of the genetic signature and additionally use the same method or a different method to detect a different feature of the genetic signature. Multiple different methods independently or in combination may be used to detect the same feature or a plurality of features.
• SNP Single Nucleotide Polymorphism
• Particular embodiments of the disclosure concern methods of detecting a SNP in an individual.
• One may employ any of the known general methods for detecting SNPs for detecting the particular SNP in this disclosure, for example.
• Such methods include, but are not limited to, selective oligonucleotide probes, arrays, allele- specific hybridization, molecular beacons, restriction fragment length polymorphism analysis, enzymatic chain reaction, flap endonuclease analysis, primer extension, 5’-nuclease analysis, oligonucleotide ligation assay, single strand conformation polymorphism analysis, temperature gradient gel electrophoresis, denaturing high performance liquid chromatography, high-resolution melting, DNA mismatch binding protein analysis, surveyor nuclease assay, sequencing, or a combination thereof.
• the method used to detect the SNP comprises sequencing nucleic acid material from the individual and/or using selective oligonucleotide probes.
• Sequencing the nucleic acid material from the individual may involve obtaining the nucleic acid material from the individual in the form of genomic DNA, complementary DNA that is reverse transcribed from RNA, or RNA, for example. Any standard sequencing technique may be employed, including Sanger sequencing, chain extension sequencing, Maxam-Gilbert sequencing, shotgun sequencing, bridge PCR sequencing, high-throughput methods for sequencing, next generation sequencing, RNA sequencing, or a combination thereof.
• Any standard sequencing technique may be employed, including Sanger sequencing, chain extension sequencing, Maxam-Gilbert sequencing, shotgun sequencing, bridge PCR sequencing, high-throughput methods for sequencing, next generation sequencing, RNA sequencing, or a combination thereof.
• After sequencing the nucleic acid from the individual one may utilize any data processing software or technique to determine which particular nucleotide is present in the individual at the particular SNP.
• the nucleotide at the particular SNP is detected by selective oligonucleotide probes.
• the probes may be used on nucleic acid material from the individual, including genomic DNA, complementary DNA that is reverse transcribed from RNA, or RNA, for example.
• Selective oligonucleotide probes preferentially bind to a complementary strand based on the particular nucleotide present at the SNP.
• one selective oligonucleotide probe binds to a complementary strand that has an A nucleotide at the SNP on the coding strand but not a G nucleotide at the SNP on the coding strand
• a different selective oligonucleotide probe binds to a complementary strand that has a G nucleotide at the SNP on the coding strand but not an A nucleotide at the SNP on the coding strand.
• Similar methods could be used to design a probe that selectively binds to the coding strand that has a C or a T nucleotide, but not both, at the SNP.
• any method to determine binding of one selective oligonucleotide probe over another selective oligonucleotide probe could be used to determine the nucleotide present at the SNP.
• One method for detecting SNPs using oligonucleotide probes comprises the steps of analyzing the quality and measuring quantity of the nucleic acid material by a spectrophotometer and/or a gel electrophoresis assay; processing the nucleic acid material into a reaction mixture with at least one selective oligonucleotide probe, PCR primers, and a mixture with components needed to perform a quantitative PCR (qPCR), which could comprise a polymerase, deoxynucleotides, and a suitable buffer for the reaction; and cycling the processed reaction mixture while monitoring the reaction.
• qPCR quantitative PCR
• the polymerase used for the qPCR will encounter the selective oligonucleotide probe binding to the strand being amplified and, using endonuclease activity, degrade the selective oligonucleotide probe. The detection of the degraded probe determines if the probe was binding to the amplified strand.
• Another method for determining binding of the selective oligonucleotide probe to a particular nucleotide comprises using the selective oligonucleotide probe as a PCR primer, wherein the selective oligonucleotide probe binds preferentially to a particular nucleotide at the SNP position.
• the probe is generally designed so the 3’ end of the probe pairs with the SNP. Thus, if the probe has the correct complementary base to pair with the particular nucleotide at the SNP, the probe will be extended during the amplification step of the PCR.
• the probe will bind to the SNP and be extended during the amplification step of the PCR.
• the probe will not fully bind and will not be extended during the amplification step of the PCR.
• the SNP position is not at the terminal end of the PCR primer, but rather located within the PCR primer.
• the PCR primer should be of sufficient length and homology in that the PCR primer can selectively bind to one variant, for example the SNP having an A nucleotide, but not bind to another variant, for example the SNP having a G nucleotide.
• the PCR primer may also be designed to selectively bind particularly to the SNP having a G nucleotide but not bind to a variant with an A, C, or T nucleotide.
• PCR primers could be designed to bind to the SNP having a C or a T nucleotide, but not both, which then does not bind to a variant with a G, A, or T nucleotide or G, A, or C nucleotide respectively.
• the PCR primer is at least or no more than 10, 11, 12,
• the SNP can be determined to have the A nucleotide and not the G nucleotide.
• Particular embodiments of the disclosure concern methods of detecting a copy number variation (CNV) of a particular allele.
• CNV copy number variation
• Such methods include fluorescent in situ hybridization, comparative genomic hybridization, arrays, polymerase chain reaction, sequencing, or a combination thereof, for example.
• the CNV is detected using an array.
• Array platforms such as those from Agilent, Illumina, or Affymetrix may be used, or custom arrays could be designed.
• One example of how an array may be used includes methods that comprise one or more of the steps of isolating nucleic acid material in a suitable manner from an individual suspected of having the CNV and, at least in some cases from an individual or reference genome that does not have the CNV; processing the nucleic acid material by fragmentation, labelling the nucleic acid with, for example, fluorescent labels, and purifying the fragmented and labeled nucleic acid material; hybridizing the nucleic acid material to the array for a sufficient time, such as for at least 24 hours; washing the array after hybridization; scanning the array using an array scanner; and analyzing the array using suitable software.
• the software may be used to compare the nucleic acid material from the individual suspected of having the CNV to the nucleic acid material of an individual who is known not to have the CNV or a reference genome.
• PCR primers can be employed to amplify nucleic acid at or near the CNV wherein an individual with a CNV will result in measurable higher levels of PCR product when compared to a PCR product from a reference genome.
• the detection of PCR product amounts could be measured by quantitative PCR (qPCR) or could be measured by gel electrophoresis, as examples.
• Quantification using gel electrophoresis comprises subjecting the resulting PCR product, along with nucleic acid standards of known size, to an electrical current on an agarose gel and measuring the size and intensity of the resulting band.
• the size of the resulting band can be compared to the known standards to determine the size of the resulting band.
• the amplification of the CNV will result in a band that has a larger size than a band that is amplified, using the same primers as were used to detect the CNV, from a reference genome or an individual that does not have the CNV being detected.
• the resulting band from the CNV amplification may be nearly double, double, or more than double the resulting band from the reference genome or the resulting band from an individual that does not have the CNV being detected.
• the CNV can be detected using nucleic acid sequencing. Sequencing techniques that could be used include, but are not limited to, whole genome sequencing, whole exome sequencing, and/or targeted sequencing.
• DNA may be analyzed by sequencing.
• the DNA may be from an individual (e.g., from the germline of an individual).
• the DNA may be from a cancer cell.
• the DNA may be prepared for sequencing by any method known in the art, such as library preparation, hybrid capture, sample quality control, product-utilized ligation-based library preparation, or a combination thereof.
• the DNA may be prepared for any sequencing technique.
• a unique genetic readout for each sample may be generated by genotyping one or more highly polymorphic SNPs.
• sequencing such as 76 base pair, paired-end sequencing
• sequencing may be performed to cover approximately 70%, 75%, 80%, 85%, 90%, 95%, 99%, or greater percentage of targets at more than 20x, 25x, 30x, 35x, 40x, 45x, 50x, or greater than 50x coverage.
• mutations, SNPS, INDELS, copy number alterations (somatic and/or germline), or other genetic differences may be identified from the sequencing using at least one bioinformatics tool, including VarScan2, any R package (including CopywriteR) and/or Annovar.
• Sequencing may be used to determine a mutation in a gene. Sequencing may also be used to identify a methylation status of a gene (e.g., bisulfite sequencing or other methylation- sensitive sequencing).
• RNA may be analyzed by sequencing.
• the RNA may be prepared for sequencing by any method known in the art, such as poly-A selection, cDNA synthesis, stranded or nonstranded library preparation, or a combination thereof.
• the RNA may be prepared for any type of RNA sequencing technique, including stranded specific RNA sequencing. In some embodiments, sequencing may be performed to generate approximately 10M, 15M, 20M, 25M, 30M, 35M, 40M or more reads, including paired reads.
• the sequencing may be performed at a read length of approximately 50 bp, 55 bp, 60 bp, 65 bp, 70 bp, 75 bp, 80 bp, 85 bp, 90 bp, 95 bp, 100 bp, 105 bp, 110 bp, or longer.
• raw sequencing data may be converted to estimated read counts (RSEM), fragments per kilobase of transcript per million mapped reads (FPKM), and/or reads per kilobase of transcript per million mapped reads (RPKM).
• RSEM estimated read counts
• FPKM fragments per kilobase of transcript per million mapped reads
• RPKM reads per kilobase of transcript per million mapped reads
• one or more bioinformatics tools may be used to infer stroma content, immune infiltration, and/or tumor immune cell profiles, such as by using upper quartile normalized RSEM data.
• protein may be analyzed by mass spectrometry.
• the protein may be prepared for mass spectrometry using any method known in the art. Protein, including any isolated protein encompassed herein, may be treated with DTT followed by iodoacetamide.
• the protein may be incubated with at least one peptidase, including an endopeptidase, proteinase, protease, or any enzyme that cleaves proteins. In some embodiments, protein is incubated with the endopeptidase, LysC and/or trypsin.
• one or more fractions, including the combined fractions are subject to phosphopeptide enrichment, including phospho-enrichment by affinity chromatography and/or binding, ion exchange chromatography, chemical derivatization, immunoprecipitation, co-precipitation, or a combination thereof.
• the entirety or a portion of one or more fractions, including the combined fractions and/or phospho -enriched fractions, may be subject to mass spectrometry.
• the raw mass spectrometry data may be processed and normalized using at least one relevant bioinformatics tool.

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