Method for treating squamous cell carcinoma with farnesyl transferase inhibitor

Abstract

To provide a method for treating squamous cell carcinoma with a farnesyl transferase inhibitor.SOLUTION: The invention relates to the field of cancer therapies. Specifically, there is provided a method for treating squamous cell carcinoma in a subject with a farnesyl transferase inhibitor (FTI), the method including determining whether the subject is likely to be responsive to an FTI therapy on the basis of the H-Ras expression level. Provided herein is a method for treating SCC in a subject having SCC overexpressing H-Ras by administering a therapeutically effective amount of a farnesyl transferase inhibitor (FTI) to the subject.SELECTED DRAWING: None

Description

[Technical field]

[0001] cross reference This application claims the benefit of priority from U.S. Provisional Patent Application No. 62 / 992,749, filed March 20, 2020, and further claims the benefit of priority from U.S. Provisional Patent Application No. 62 / 826,771, filed March 29, 2019. Each of the aforementioned related applications is incorporated herein by reference in its entirety.

[0002] The present invention relates to the field of cancer therapy. Specifically, provided herein is a method for treating squamous cell carcinoma with a farnesyltransferase inhibitor. [Background technology]

[0003] Stratification of patient populations to improve treatment response rates has become increasingly important in the clinical management of cancer patients. Farnesyltransferase inhibitors (FTIs) are useful therapeutic agents for the treatment of cancers, such as squamous cell carcinoma ("SCC"). However, patients respond variably to FTI treatment. Thus, methods for predicting the responsiveness of subjects with cancer to FTI treatment or for selecting cancer patients for FTI treatment represent an unmet need. The methods and compositions provided herein meet these needs and provide other related advantages. Summary of the Invention [Means for solving the problem]

[0004] Provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of a farnesyltransferase inhibitor (FTI) to the subject with SCC that overexpresses H-Ras.In some embodiments, the subject has H-Ras expression that is at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 15-fold, or at least 20-fold higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a population of healthy subjects.In some embodiments, the reference level is the median expression level of H-Ras in a population of subjects with SCC.

[0005] In some embodiments, provided herein is a method of treating SCC in a subject by administering a therapeutically effective amount of an FTI to the subject, the subject having a ratio of H-Ras expression to K-Ras expression that is higher than a reference ratio. In some embodiments, provided herein is a method of treating SCC in a subject by administering a therapeutically effective amount of an FTI to the subject, the subject having a ratio of H-Ras expression to N-Ras expression that is higher than a reference ratio. In some embodiments, provided herein is a method of treating SCC in a subject by administering a therapeutically effective amount of an FTI to the subject, the subject having a ratio of H-Ras expression to combined expression of K-Ras and N-Ras that is higher than a reference ratio. In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the reference ratio is the median ratio in a healthy subject population. In some embodiments, the reference ratio is the median ratio in a population of subjects with SCC.

[0006] In some embodiments, the SCC also has an H-Ras mutation, hi some embodiments, the H-Ras mutation comprises an amino acid substitution at a codon selected from the group consisting of G12, G13, Q61, Q22, K117, A146, and any combination thereof.

[0007] In some embodiments, the mutant HRAS gene encodes a mutant H-Ras protein, and the HRAS gene mutation is or comprises a modification in a codon that encodes an amino acid substitution at a specific position selected from the group consisting of G12, G13, Q61, Q22, K117, A146, and any combination thereof, of the corresponding mutant H-Ras protein.

[0008] In some embodiments, the SCC is head and neck SCC (HNSCC), lung SCC (LSCC), thyroid SCC (TSCC), esophageal SCC (ESCC), bladder SCC (BSCC), or urothelial carcinoma (UC).

[0009] In some embodiments, the SCC is an HNSCC. The HNSCC can be an HNSCC of the trachea. The HNSCC can be an HNSCC of the maxilla. The HNSCC can be an HNSCC of the oral cavity.

[0010] In some embodiments, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is advanced or metastatic. In some embodiments, the SCC is recurrent. In some embodiments, the SCC is refractory.

[0011] In some embodiments, the methods provided herein include analyzing H-Ras expression levels in a sample from a subject. In some embodiments, the methods provided herein further include analyzing K-Ras expression, N-Ras expression, or both in the sample.

[0012] In some embodiments, the methods provided herein include measuring protein levels of H-Ras, K-Ras, N-Ras, or any combination thereof. Protein levels can be determined using immunohistochemistry (IHC) approaches, immunoblotting assays, flow cytometry (FACS), or ELISA.

[0013] In some embodiments, the methods provided herein include measuring the mRNA levels of H-Ras, K-Ras, N-Ras, or any combination thereof. The mRNA levels can be measured using qPCR, RT-PCR, RNA-seq, microarray analysis, SAGE, MassARRAY techniques, or FISH.

[0014] In some embodiments, the methods provided herein include determining the mutation status of H-Ras in the sample.

[0015] In some embodiments, the sample is a tissue biopsy, in some embodiments, the sample is a tumor biopsy, in some embodiments, the sample is an isolated cell.

[0016] In some embodiments, the FTI used in the methods provided herein is selected from the group consisting of tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, and BMS-214662.

[0017] In some embodiments, the FTI is tipifarnib. In some embodiments, the FTI is lonafarnib. In some embodiments, the FTI is BMS-214662.

[0018] In some embodiments, tipifarnib is administered at a dose of 0.05 to 500 mg / kg body weight. In some embodiments, tipifarnib is administered twice daily.

[0019] In some embodiments, tipifarnib is administered at a dose of 100-1200 mg twice daily. In some embodiments, tipifarnib is administered at a dose of 100 mg, 200 mg, 300 mg, 400 mg, 600 mg, 900 mg, or 1200 mg twice daily.

[0020] In some embodiments, tipifarnib is administered on days 1-7 and days 15-21 of a 28 day treatment cycle. In some embodiments, tipifarnib is administered on days 1-21 of a 28 day treatment cycle. In some embodiments, tipifarnib is administered on days 1-7 of a 28 day treatment cycle.

[0021] In some embodiments, tipifarnib is administered for at least 1 cycle. In some embodiments, tipifarnib is administered for at least 3 cycles, 6 cycles, 9 cycles, or 12 cycles.

[0022] In some embodiments, tipifarnib is administered before, during, or after radiation.

[0023] In some embodiments, the method provided herein further comprises administering a therapeutically effective amount of a second active agent.Tipifarnib can be administered before, during, or after the administration of the second active agent.In some embodiments, the amount of tipifarnib administered in combination with the second active agent is less than the amount of tipifarnib administered in monotherapy treatment.

[0024] In some embodiments, the second active agent is selected from the group consisting of DNA hypomethylating agents, alkylating agents, topoisomerase inhibitors, therapeutic antibodies that specifically bind to cancer antigens, hematopoietic growth factors, cytokines, antibiotics, cox-2 inhibitors, CDK inhibitors, PI3K-α inhibitors, AKT inhibitors, MTOR1 / 2 inhibitors, immunomodulatory agents, antithymocyte globulin, immunosuppressants, and corticosteroids or pharmacological derivatives thereof.

[0025] In some embodiments, the second active agent is an EGFR inhibitor. In some embodiments, the EGFR inhibitor is cetuximab. In some embodiments, the second active agent is an alkylating agent. In some embodiments, the alkylating agent is cisplatin. In some embodiments, the second active agent is a CDK inhibitor. In some embodiments, the CDK inhibitor is palbociclib. In some embodiments, the second active agent is an anti-PD1 antibody, an anti-PDL1 antibody, or an anti-CTLA-4 antibody. In some embodiments, the second active agent is a PI3K-α inhibitor. In some embodiments, the PI3K-α inhibitor is BYL719. In some embodiments, the second active agent is an AKT inhibitor. In some embodiments, the AKT inhibitor is GSK2141795. In some embodiments, the second active agent is an MTOR1 / 2 inhibitor. In some embodiments, the MTOR1 / 2 inhibitor is INK-128.

[0026] In some embodiments, the methods provided herein further comprise administering a supportive care therapy. [Brief description of the drawings]

[0027] [Figure 1A] Increased efficacy of tipifarnib in HNSCC PDX models with high H-Ras expression levels or high H-Ras / K-Ras+N-Ras ("H / K+N") ratio. Tumor growth curves of mice inoculated with primary human HNSCC tissue and treated with either tipifarnib or vehicle are shown. Four HNSCC PDX models with various H-Ras expression levels and H / K+N ratios were tested. Tipifarnib treatment resulted in tumor regression in HNSCC PDX model HN2576 (H / K+N=4.6; H-Ras=3.0×median). [Figure 1B]Increased efficacy of tipifarnib in HNSCC PDX models with high H-Ras expression levels or high H-Ras / K-Ras+N-Ras ("H / K+N") ratio. Tumor growth curves of mice inoculated with primary human HNSCC tissue and treated with either tipifarnib or vehicle are shown. Four HNSCC PDX models with various H-Ras expression levels and H / K+N ratios were tested. Tipifarnib treatment inhibited tumor growth in HNSCC PDX model HN2594 (H / K+N=3.6; H-Ras=2.8×median). [Figure 1C] Increased efficacy of tipifarnib in HNSCC PDX models with high H-Ras expression levels or high H-Ras / K-Ras+N-Ras ("H / K+N") ratio. Tumor growth curves of mice inoculated with primary human HNSCC tissue and treated with either tipifarnib or vehicle are shown. Four HNSCC PDX models with various H-Ras expression levels and H / K+N ratios were tested. Tipifarnib treatment resulted in a slight inhibition of tumor growth in the HNSCC PDX model HN5111 (H / K+N=2.2; H-Ras=1.3×median). [Figure 1D] Increased efficacy of tipifarnib in HNSCC PDX models with high H-Ras expression levels or high H-Ras / K-Ras+N-Ras ("H / K+N") ratio. Tumor growth curves of mice inoculated with primary human HNSCC tissue and treated with either tipifarnib or vehicle are shown. Four HNSCC PDX models with various H-Ras expression levels and H / K+N ratios were tested. Tipifarnib treatment resulted in a slight inhibition of tumor growth in the HNSCC PDX model HN5123 (H / K+N=2.1; H-Ras=1.6×median). [Figure 2A] Increased efficacy of tipifarnib in ESCC but not in breast cancer PDX models with high H-Ras / K-Ras+N-Ras ratio. Tumor growth curves of mice inoculated with primary human ESCC tissue and treated with either tipifarnib or vehicle. Tipifarnib treatment resulted in tumor regression in ESCC PDX model ES0204 (H / K+N=6.3). [Figure 2B] Increased efficacy of tipifarnib in ESCC but not in breast cancer PDX models with high H-Ras / K-Ras+N-Ras ratio. Tumor growth curves of mice inoculated with primary human ESCC tissue and treated with either tipifarnib or vehicle. Tipifarnib treatment inhibited tumor growth in ESCC PDX model ES0172 (H / K+N=6.3). [Figure 2C] Increased efficacy of tipifarnib in ESCC but not in breast cancer PDX models with high H-Ras / K-Ras+N-Ras ratio. Tumor growth curves of mice inoculated with primary human breast cancer tissue and treated with either tipifarnib or vehicle. Tipifarnib treatment did not inhibit tumor growth in breast cancer PDX model BR1282 (H / K+N=22.6). [Figure 2D] Increased efficacy of tipifarnib in ESCC but not in breast cancer PDX models with high H-Ras / K-Ras+N-Ras ratio. Tumor growth curves of mice inoculated with primary human breast cancer tissue and treated with either tipifarnib or vehicle. Tipifarnib treatment resulted in a slight inhibition of tumor growth in breast cancer PDX model BR1458 (H / K+N=10.4). [Figure 3A] Combination treatment with tipifarnib and a second agent synergistically inhibited tumor growth in the HNSCC PDX model HN3411 (H-Ras=4.1×median; H / K+N=2.7). Tumor growth curves for mice treated with vehicle, tipifarnib, cetuximab, or both agents. [Figure 3B] Combination treatment with tipifarnib and a second agent synergistically inhibited tumor growth in the HNSCC PDX model HN3411 (H-Ras=4.1×median; H / K+N=2.7). Tumor growth curves for mice treated with vehicle, tipifarnib, cisplatin, or both agents. [Figure 3C]Combination treatment with tipifarnib and a second agent synergistically inhibited tumor growth in the HNSCC PDX model HN3411 (H-Ras=4.1×median; H / K+N=2.7). Tumor growth curves for mice treated with vehicle, tipifarnib, palbociclib, or both agents. [Figure 4A] Combination treatment with tipifarnib and a second agent synergistically inhibited tumor growth in the HNSCC PDX model HN2594 (H-Ras=2.8×median; H / K+N=3.6). Tumor growth curves for mice treated with vehicle, tipifarnib, cetuximab, or both agents. [Figure 4B] Combination treatment with tipifarnib and a second agent synergistically inhibited tumor growth in the HNSCC PDX model HN2594 (H-Ras=2.8×median; H / K+N=3.6). Tumor growth curves for mice treated with vehicle, tipifarnib, cisplatin, or both agents. [Figure 4C] Combination treatment with tipifarnib and a second agent synergistically inhibited tumor growth in the HNSCC PDX model HN2594 (H-Ras=2.8×median; H / K+N=3.6). Tumor growth curves for mice treated with vehicle, tipifarnib, palbociclib, or both agents. [Diagram 5] Increased efficacy of tipifarnib in HNSCC PDX models with high H-Ras expression levels or high H-Ras / K-Ras+N-Ras ("H / K+N") ratio. A-D show tumor growth curves for mice inoculated with primary human HNSCC tissue and treated with either tipifarnib or vehicle. Four HNSCC PDX models with high H-Ras expression levels and / or H / K+N ratio were tested. A. Tipifarnib treatment resulted in tumor regression in HNSCC PDX model HN2576. B. Tipifarnib treatment inhibited tumor growth in HNSCC PDX model HN2594. C. Tipifarnib treatment inhibited tumor growth in HNSCC PDX model HN3461. D. Tipifarnib treatment inhibited tumor growth in HNSCC PDX model HN3679. [Figure 6] Modest efficacy of tipifarnib in HNSCC PDX models with low H-Ras expression levels or low H-Ras / K-Ras+N-Ras ("H / K+N") ratios. A-D show tumor growth curves for mice inoculated with primary human HNSCC tissue and treated with either tipifarnib or vehicle. Four HNSCC PDX models with low H-Ras expression levels and / or H / K+N ratios were tested. A. Tipifarnib treatment partially inhibited or did not inhibit tumor growth at all (inactive) in HNSCC PDX model HN2222. Tipifarnib treatment resulted in partial inhibition of tumor growth in HNSCC PDX model HN5111 (B), HNSCC PDX model HN5115 (C), and HNSCC PDX model HN5123 (D). [Figure 7] Combination treatment with tipifarnib and a second agent (cisplatin) synergistically inhibited tumor growth in mutant H-Ras HNSCC PDX models HN2579 (A), HN2581 (B), HN1420 (C), and HN3504 (D). Each figure shows tumor growth curves for mice treated with vehicle, tipifarnib, cisplatin, or combination therapy with both agents in the respective models. [Figure 8] Combination treatment with tipifarnib and a second agent (cisplatin) inhibits tumor growth in HNSCC PDX models HN3792 (A), HN0586 (B), HN2576 (C), and HN3067 (D), models with high H-Ras expression and / or high H / N+K ratios; the figures show tumor growth curves for mice treated with vehicle, tipifarnib, cisplatin, or combination therapy with both agents in each model. [Figure 9]Combination treatment with tipifarnib and a second agent (cisplatin) inhibits tumor growth in HNSCC PDX models HN2594 (A), HN3461 (B), HN3776 (C), and HN3474 (D), models with high H-Ras expression and / or high H / N+K ratios; the figures show tumor growth curves for mice treated with vehicle, tipifarnib, cisplatin, or combination therapy with both agents in each model. [Figure 10] Combination treatment with tipifarnib and a second agent (palbociclib) inhibits tumor growth in HNSCC PDX models HN2576 (A), HN3067 (B), HN2594 (C), and HN3679 (D), models with high H-Ras expression and / or high H / N+K ratios. The figures show tumor growth curves for mice treated with vehicle, tipifarnib, palbociclib, or combination therapy with both agents in each model. [Figure 11] Combination treatment with tipifarnib and a second agent (cetuximab) inhibits tumor growth in HNSCC PDX models HN2576 (A), HN3067 (B), HN2594 (C), and HN3679 (D), models with high H-Ras expression and / or high H / N+K ratios; the figures show tumor growth curves for mice treated with vehicle, tipifarnib, cetuximab, or combination therapy with both agents in each model. [Figure 12] Combination treatment with tipifarnib and a second agent (PI3K-α inhibitor BYL719) inhibits tumor growth in HNSCC PDX models HN2594 (A) and HN2576 (B) (both models with high H-Ras expression and / or high H / N+K ratio), as well as in the PDX HNSCC model HN1420 (C) with mutant H-Ras gene expression (at the HRAS A146P codon); A-C show tumor growth curves for mice treated with vehicle, tipifarnib, BYL719, or combination therapy with both agents in each model. [Figure 13]Combination treatment with tipifarnib and a second agent (AKT inhibitor GSK2141795) inhibits tumor growth in HNSCC PDX models HN2594 (A) and HN2576 (B) (both models have high H-Ras expression and / or high H / N+K ratio), as well as in the PDX HNSCC model HN1420 (C) which has mutant H-Ras gene expression (at the HRAS A146P codon); A-C show tumor growth curves for mice treated with vehicle, tipifarnib, GSK2141795, or combination therapy with both agents in each model. [Figure 14] Combination treatment with tipifarnib and a second agent (MTORC1 / 2 inhibitor INK-128) inhibits tumor growth in HNSCC PDX models HN2594 (A) and HN2576 (B) (both models have high H-Ras expression and / or high H / N+K ratio), as well as in the PDX HNSCC model HN1420 (C) which has mutant H-Ras gene expression (at the HRAS A146P codon); A-C show tumor growth curves for mice treated with vehicle, tipifarnib, INK-128, or combination therapy with both agents in each model. [Figure 15] Combination treatment with tipifarnib and a second agent (PI3K-α inhibitor BYL719) inhibits tumor growth in HNSCC PDX models HN1420 (A), HN2581 (B), HN2579 (C), and HN3504 (D) that harbor mutant H-Ras gene expression (at codons HRAS A146P, HRAS G13C, HRAS G12S, and HRAS K117L, respectively); A-D show tumor growth curves for mice treated with vehicle, tipifarnib, BYL719, or combination therapy with both agents in each model. [Figure 16]Combination treatment with tipifarnib and a second agent (PI3K-α inhibitor BYL719) inhibits tumor growth in HNSCC PDX models HN3067 (A) and HN3411 (C), which have high H-Ras expression levels and expression of wild-type PIK3CA, and in PDX HNSCC models HN2593 (B) and HN3690 (D), which have high H-Ras expression levels and expression of mutant PIK3CA (at codons PI3K-α G118D and PI3K-α E454K, respectively); A-D show tumor growth curves for mice treated with vehicle, tipifarnib, BYL719, or combination therapy with both agents in each model. [Figure 17] H-Ras expression levels in patients with squamous cell carcinoma (HNSCC, LSCC, and UC) and adenocarcinoma (CRC, PDAC, and LUAD) according to data available in the database TCGA PanCancer Atlas. [Figure 18] Correlation between H-Ras and PIK3CA gene expression levels in HNSCC patients according to data available within the database TCGA PanCancer Atlas. [Figure 19] Correlation between H-Ras and PIK3CA gene expression levels in UC (A) and LSCC (B) patients according to data available in the database TCGA PanCancer Atlas. [Figure 20] Distribution of H-Ras expression levels within UC patients with wild-type PIK3CA gene expression compared to the distribution with specific types of mutated forms of the expressed PIK3CA gene according to data available within the database TCGA PanCancer Atlas. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0028] As used herein, the articles "a," "an," and "the" refer to one or more of the grammatical object of the article. By way of example, a sample may refer to one sample or to more than one sample.

[0029] As used herein, the term "subject" refers to a mammal. A subject may be a human or a non-human mammal, such as a dog, cat, cow, horse, mouse, rat, rabbit, or a transgenic species thereof. A subject may be a human.

[0030] As used herein, the term "sample" refers to a material or mixture of materials that contains one or more components of interest. A sample from a subject refers to a sample obtained from a subject, including samples from biological tissues or fluids obtained, arrived at, or harvested in vivo or in situ. A sample can be obtained from an area of ​​a subject that contains precancerous or cancerous cells or tissues. Such samples can be, but are not limited to, organs, tissues, fractions, and cells isolated from a mammal. Exemplary samples include lymph nodes, whole blood, partially purified blood, serum, plasma, bone marrow, and peripheral blood mononuclear cells ("PBMCs"). A sample can also be a tissue biopsy. Exemplary samples also include cell lysates, cell cultures, cell lines, tissues, oral tissues, gastrointestinal tissues, organs, organelles, biological fluids, blood samples, urine samples, skin samples, and the like.

[0031] As used herein, the term "analyzing" a sample refers to performing an art-recognized assay to make an assessment regarding a particular property or characteristic of the sample. The property or characteristic of the sample can be, for example, the type of cells in the sample, or the expression level of genes in the sample.

[0032] As used herein, the terms "treat", "treating" and "treatment", when used in reference to a cancer patient, can refer to the act of reducing the severity of the cancer or slowing or slowing the progression of the cancer, including (a) inhibiting the growth of the cancer or preventing the onset of the cancer, and (b) causing the regression of the cancer or delaying or minimizing one or more symptoms associated with the presence of the cancer. For example, "treating" a cancer, such as an SCC that overexpresses H-Ras in a subject, refers to the act of inhibiting the growth of the cancer in the subject.

[0033] As used herein, the terms "administer", "administering" or "administration" refer to the act of delivering or causing to be delivered a compound or pharmaceutical composition to the body of a subject, by methods described herein or otherwise known in the art. Administering a compound or pharmaceutical composition includes formulating the compound or pharmaceutical composition to be delivered to the patient's body. Exemplary dosage forms include oral dosage forms such as tablets, capsules, syrups, suspensions, etc.; injectable dosage forms such as intravenous (IV), intramuscular (IM), or intraperitoneal (IP); transdermal dosage forms including creams, jellies, powders, or patches; buccal dosage forms; inhalation powders, sprays, suspensions, and rectal suppositories.

[0034] As used herein, the terms "selecting" and "selected" with respect to a subject are used to mean that a particular subject is specifically selected from a relatively large group of subjects based on (or because) the particular subject meets a predetermined criterion or a set of predetermined criteria, e.g., has H-Ras expression higher than a reference level. Similarly, "selectively treating" a subject refers to providing a treatment to a subject who meets a predetermined criterion or a set of predetermined criteria. Similarly, "selectively administering" refers to administering a drug to a subject who meets a predetermined criterion or a set of predetermined criteria. Selecting, selectively treating, and selectively administering mean that a subject with SCC is provided with an individualized therapy based on the subject's biological status, rather than being provided with a standard treatment regimen based solely on having SCC.

[0035] As used herein, the term "therapeutically effective amount" of a compound, when used in relation to a disease or disorder, refers to an amount sufficient to provide a therapeutic benefit in the treatment of the disease or disorder, or to delay or minimize one or more symptoms associated with the disease or disorder. The disease or disorder referred to may be SCC. A therapeutically effective amount of a compound refers to an amount of a compound that, when used alone or in combination with other therapies, provides a therapeutic benefit in the treatment or management of a disease or disorder. The term encompasses an amount that improves overall therapy, reduces or avoids symptoms, or enhances the therapeutic effectiveness of another therapeutic agent. The term also refers to an amount of a compound that is sufficient to induce the biological or medical response of a biomolecule (e.g., protein, enzyme, RNA, or DNA), cell, tissue, system, animal, or human that a researcher, veterinarian, physician, or clinician is seeking.

[0036] As used herein, the term "express" or "expression", when used in reference to a gene, refers to the process by which the information carried by the gene becomes manifest as a phenotype, which includes the transcription of the gene into messenger RNA (mRNA), the subsequent translation of the mRNA molecule into a polypeptide chain, and its assembly into the final protein.

[0037] As used herein, the term "expression level" of a gene refers to the amount or accumulation of an expression product of the gene, such as, for example, the amount of the RNA product of the gene (the mRNA level of the gene) or the amount of the protein product of the gene (the protein level of the gene). When a gene has multiple alleles, the expression level of a gene refers to the total amount of accumulation of expression products for all present alleles of this gene, unless otherwise specified.

[0038] As used herein, the term "reference," when used in connection with a quantifiable value, refers to a predetermined value that can be used to determine the significance of a value measured in a sample.

[0039] As used herein, the term "reference expression level" refers to an expression level of a given gene that can be used to determine the significance of the expression level of the gene in a sample. The sample can be a cell, a group of cells, or a tissue. For example, the reference expression level of a gene can also be a cut-off value determined by a person skilled in the art through statistical analysis of the expression level of the gene in various sample cell populations. In some embodiments, the reference expression level of H-Ras can be the median expression level of H-Ras in a healthy subject population. In some embodiments, the reference expression level of H-Ras can be the median expression level of H-Ras in a subject population with the same type of tumor. For example, the reference expression level of HNSCC patients can be the median expression level of H-Ras in a HNSCC patient population. In another example, the reference expression level of LSCC patients can be the median expression level of H-Ras in a LSCC patient population. In another example, the reference expression level of BSCC patients can be the median expression level of H-Ras in a BSCC patient population. In another example, the reference expression level of UC patients can be the median expression level of H-Ras in a UC patient population. In some embodiments, the reference expression level of H-Ras may be a cutoff percentile of H-Ras expression in a population of subjects with the same type of tumor. The cutoff percentile may be the top 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% cutoff. The cutoff percentile may be the top 10% cutoff. The cutoff percentile may be the top 15% expression cutoff. The cutoff percentile may be the top 20% cutoff. The cutoff percentile may be the top 25% cutoff. The cutoff percentile may be the top 30% cutoff. The cutoff percentile may be the top 35% cutoff. The cutoff percentile may be the top 40% cutoff. The cutoff percentile may be the top 45% cutoff. The cutoff percentile may be the top 50% cutoff. For example, a reference expression level for HNSCC patients can be the cutoff for the top 30% of H-Ras expression in a population of HNSCC patients.For example, the reference expression level of LSCC patients can be the top 30% cutoff of H-Ras expression in LSCC patient population.For example, the reference expression level of BSCC patients can be the top 30% cutoff of H-Ras expression in BSCC patient population.For example, the reference expression level of UC patients can be the top 30% cutoff of H-Ras expression in UC patient population.The reference expression level can be determined by those skilled in the art, for example, through statistical analysis of H-Ras expression levels in samples from clinical cohorts.

[0040] As used herein, the term "overexpress" or "overexpression", when used in relation to a gene, means that the expression level of the gene in a tissue of a subject is higher than a reference level, the reference level being at least the median of the expression level of the gene in the same tissue in a healthy population. The tissue may also be a tumor. In some embodiments, a gene that is "overexpressed" in a subject may be expressed at a level at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 15-fold, or at least 20-fold higher than the reference level. A gene that is overexpressed in a particular tumor in a subject means that the expression level of the gene in the tumor in the subject is higher than a reference level, the reference level being at least the median of the expression level of the gene in the corresponding tissue in a healthy population.

[0041] In some embodiments, a gene that is overexpressed in a particular SCC in a subject may mean that the expression level of the gene in the SCC of the subject is higher than the median expression level of the gene in tumor samples in a population of subjects with the same tumor.For example, a subject with HNSCC that overexpresses H-Ras may mean that the H-Ras expression level in the HNSCC of the subject is at least higher than the median expression level of H-Ras in the corresponding head and neck tissue of a healthy population, or in some embodiments, higher than the median expression level of H-Ras in tumor samples from a population of HNSCC patients.The reference level may also be a cutoff percentile of the expression level of H-Ras in a population of subjects with the same type of tumor, and thus a subject with HNSCC that overexpresses H-Ras may mean that the H-Ras expression level in the HNSCC of the subject is higher than the cutoff percentile of H-Ras expression in a population of HNSCC patients. In another example, a subject with LSCC that overexpresses H-Ras may mean that the H-Ras expression level in the subject's LSCC is at least higher than the median expression level of H-Ras in the corresponding lung tissue of a healthy population, or in some embodiments, higher than the median expression level of H-Ras in tumor samples from a LSCC patient population. The reference level may also be a cutoff percentile of the expression level of H-Ras in a subject population with the same type of tumor, and thus a subject with LSCC that overexpresses H-Ras may mean that the H-Ras expression level in the subject's LSCC is higher than the cutoff percentile of H-Ras expression in a LSCC patient population. In another example, a subject with UC that overexpresses H-Ras may mean that the H-Ras expression level in the subject's UC is at least higher than the median expression level of H-Ras in the corresponding urothelial tissue of a healthy population, or in some embodiments, higher than the median expression level of H-Ras in tumor samples from a UC patient population.The reference level may also be a cutoff percentile of the expression level of H-Ras in a population of subjects having the same type of tumor, and thus a subject with UC that overexpresses H-Ras may mean that the H-Ras expression level in the subject's UC is higher than the cutoff percentile of H-Ras expression in a population of UC patients.

[0042] The cutoff percentile may be the top 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% cutoff. For example, the cutoff percentile may be the top 25% cutoff. In some embodiments, the subject with H-Ras overexpressing HNSCC may be the 25% of the HNSCC patient population with the highest H-Ras expression in the population. In some embodiments, the subject with H-Ras overexpressing LSCC may be the 25% of the LSCC patient population with the highest H-Ras expression in the population. In some embodiments, the subject with H-Ras overexpressing BSCC may be the 25% of the BSCC patient population with the highest H-Ras expression in the population. In some embodiments, the subject with H-Ras overexpressing UC may be the 25% of the UC patient population with the highest H-Ras expression in the population. In some embodiments, the expression level of a gene that is overexpressed in a subject's tumor may be at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 15-fold, or at least 20-fold higher than the reference level.

[0043] The term "reference ratio" as used herein in relation to the expression levels of two or more genes refers to a ratio predefined by a person skilled in the art that can be used to determine the significance of the ratio of the levels of these genes in a sample. The sample can be a cell, a group of cells, or a tissue. For example, the reference ratio of H-Ras expression to the combined expression of K-Ras and N-Ras can be a predefined ratio of H-Ras expression to the combined expression of K-Ras and N-Ras. The reference ratio of the expression levels of two or more genes can be the median of the ratio of the expression levels of these genes in a subject population. For example, the reference ratio of H-Ras expression to the combined expression of K-Ras and N-Ras can be the median of the ratio in a healthy population. In another example, the reference ratio of H-Ras expression to the combined expression of K-Ras and N-Ras can be the median of the ratio in a patient population with the same type of tumor. The reference ratio can also be the cutoff percentile of the expression ratio in a subject population with the same type of tumor. The cutoff percentile may be the top 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% cutoff. The cutoff percentile may be the top 10% cutoff. The cutoff percentile may be the top 15% expression cutoff. The cutoff percentile may be the top 20% cutoff. The cutoff percentile may be the top 25% cutoff. The cutoff percentile may be the top 30% cutoff. The cutoff percentile may be the top 35% cutoff. The cutoff percentile may be the top 40% cutoff. The cutoff percentile may be the top 45% cutoff. The cutoff percentile may be the top 50% cutoff. For example, the reference expression ratio of HNSCC patients can be the cut-off of the upper 30% of the ratio of H-Ras expression to the combined expression of K-Ras and N-Ras in HNSCC patient population.The reference ratio can also be the cut-off value determined by those skilled in the art, for example, through statistical analysis of the ratio of the expression levels of two genes in various sample cell populations.In certain embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20. In some embodiments, the reference ratio is 1 / 10. In some embodiments, the reference ratio is 1 / 9. In some embodiments, the reference ratio is 1 / 8. In some embodiments, the reference ratio is 1 / 7. In some embodiments, the reference ratio is 1 / 6. In some embodiments, the reference ratio is 1 / 5. In some embodiments, the reference ratio is 1 / 4. In some embodiments, the reference ratio is 1 / 3. In some embodiments, the reference ratio is 1 / 2. In some embodiments, the reference ratio is 1. In some embodiments, the reference ratio is 2. In some embodiments, the reference ratio is 3. In some embodiments, the reference ratio is 4. In some embodiments, the reference ratio is 5. In some embodiments, the reference ratio is 6. In some embodiments, the reference ratio is 7. In some embodiments, the reference ratio is 8. In some embodiments, the reference ratio is 9. In some embodiments, the reference ratio is 10. In some embodiments, the reference ratio is 15. In some embodiments, the reference ratio is 20.

[0044] As used herein, the term "responsive" or "responsive" when used in relation to a treatment refers to the effectiveness of the treatment in alleviating or reducing the symptoms of the disease being treated. In relation to a patient with SCC, the patient responds to an FTI treatment if the FTI treatment effectively inhibits the growth of SCC or prevents the development of SCC, causes regression of SCC, or delays or minimizes one or more symptoms associated with the presence of SCC in the patient.

[0045] As used herein, the term "likelihood" refers to the probability of an event. When a condition is met, a subject is "likely" to respond to a certain treatment, meaning that when the condition is met, the subject is more likely to respond to a certain treatment than when the condition is not met. The probability of responding to a certain treatment can be, for example, 5%, 10%, 25%, 50%, 100%, 200% or more higher in a subject who meets a certain condition compared to a subject who does not meet the condition. For example, if a subject has high H-Ras expression or a high H-Ras / N+K-Ras expression ratio, then a subject with SCC is "likely" to respond to FTI treatment means that the probability of the subject that will respond to FTI treatment is 5%, 10%, 25%, 50%, 100%, 200% or more higher among subjects who have H-Ras overexpression or an H-Ras / N+K-Ras expression ratio higher than the reference ratio compared to subjects who do not have H-Ras overexpression or an H-Ras / N+K-Ras expression ratio lower than the reference ratio.

[0046] A. Method Provided herein is a method for selecting subjects with SCC for FTI treatment.Provided herein is a method based in part on the discovery that SCC patients with different gene expression respond differently to FTI treatment, and the clinical benefit of FTI treatment is related to the expression level of certain genes.For example, provided herein is a method based on the discovery that patients with SCC that overexpress H-Ras may respond to FTI treatment, and selecting a patient population with SCC that overexpresses H-Ras for FTI treatment can improve the overall response rate of FTI treatment for SCC.

[0047] Furthermore, the methods provided herein are also based in part on the discovery that SCC patients with high H-Ras expression to K-Ras expression ratio ("H / K ratio"), high H-Ras expression to N-Ras expression ratio ("H / N ratio"), or high H-Ras expression to the combined expression ratio of K-Ras and N-Ras ("H / K+N ratio") may respond to FTI treatment, and selecting a population of SCC patients with a high H / K ratio, high H / N ratio, or high H / N+K ratio for FTI treatment may improve the overall response rate of FTI treatment for SCC.

[0048] Thus, provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of FTI to a subject with SCC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of FTI treatment to SCC by selectively treating SCC patients with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with SCC to FTI treatment based on the expression level of H-Ras, and predicting that the subject may respond when the subject has H-Ras overexpression.

[0049] In some embodiments, provided herein is a method for treating SCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, the subject having H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0050] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with SCC that overexpresses H-Ras. Also provided herein is a method for improving the response of tipifarnib treatment to SCC by selectively treating SCC patients with H-Ras overexpression. Also provided herein are methods for predicting the responsiveness of a subject with SCC to tipifarnib treatment based on the expression level of H-Ras, where the subject is predicted to be likely to respond if the subject has H-Ras overexpression.

[0051] In some embodiments, provided herein is a method of treating SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0052] In some embodiments, the subject has H-Ras expression at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 12-fold, at least 15-fold, or at least 20-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 2-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 2.5-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 3-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 3.5-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 4-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 4.5-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 5-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 6-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 7-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 8-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 9-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 10-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 12-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 15-fold higher than the reference level. In some embodiments, the subject has H-Ras expression at least 20-fold higher than the reference level. In some embodiments, the reference level is the median expression level of H-Ras in a population of healthy subjects. In some embodiments, the reference level is the median expression level of H-Ras in a population of subjects with SCC.

[0053] Squamous cell carcinoma (SCC) is the uncontrolled growth of abnormal cells arising from the squamous cells of the epidermis. Common types include head and neck SCC (HNSCC), lung SCC (LSCC), thyroid SCC, esophageal SCC, bladder SCC, or urothelial carcinoma (UC). Human papillomavirus infection (HPV) is associated with the development of SCC.

[0054] HNSCC is the sixth most common cancer worldwide, with approximately 650,000 cases and 200,000 deaths worldwide annually, and approximately 54,000 new cases annually in the United States. HNSCC is also the most common cancer in Central Asia. HNSCC has two distinct etiologies and corresponding tumor types. The first subtype is associated with smoking and alcohol consumption and is unrelated to human papillomavirus (HPV- or HPV-negative). The second subtype is associated with high-risk HPV infection (HPV+ or HPV-positive). The second subtype is mainly restricted to oropharyngeal cancer. HPV+ tumors are a separate entity with a better prognosis and may require different treatment. A significant proportion of HNSCC, especially oropharyngeal cancer, is caused by HPV infection. High-risk HPV subtype 16 accounts for 85% of all HPV+ tumors in HNSCC. P16 may be used as a surrogate marker for HPV infection in HNSCC, especially in the oropharynx. A more accurate HPV test is available that is based on E6 / E7 detection (Liang C, et al. Cancer Res. 2012;72:5004-5013).

[0055] HPV+ HNSCC shows significantly lower EGFR expression levels than HPV- HNSCC. EGFR amplification occurs only in HPV- HNSCC. High EGFR gene copy number and protein expression are associated with poor clinical outcome in advanced HNSCC.

[0056] Currently, first-line therapy for recurrent / metastatic HNSCC includes platinum-based doublets (e.g., cisplatin / 5-FU or carboplatin / paclitaxel), optionally combined with anti-EGFR antibody therapy (e.g., cetuximab, panitumumab, afatinib). Second-line therapy includes taxanes, methotrexate, and / or cetuximab. Anti-EGFR antibody therapy, such as cetuximab (chimeric IgG1) or panitumumab, may be used as a single agent, with chemotherapy (e.g., platinum / 5-FU, cisplatin), or with radiation therapy. Despite high EGFR expression levels in HNSCC, the single-agent response rate for cetuximab is only 13%, the SD rate is 33%, and there are currently no predictive biomarkers available.

[0057] Agents in development for HNSCC include those targeting the PI3K pathway: BKM120 (buparlisib) + cetuximab, BYL719 + cetuximab, temsirolimus + cetuximab, rigosertib + cetuximab; those targeting the MET pathway: tivantinib + cetuximab, ficlatuzumab + cetuximab; and those targeting the EGFR / HER3 pathway: afatinib + cetuximab ± paclitaxel, patritaxel. These include: FGFR pathway targeting: BGJ398; CDK4 / 6-cell cycle pathway targeting: palbociclib, LEE011, abemaciclib, and ribociclib; RTK inhibitors: anlotinib; PI3K-α inhibitors: BYL719; AKT inhibitors: MK2206, GSK2110183, and GSK2141795; MTOR1 / 2 inhibitors: INK-128; and chemotherapy: oral azacitidine. More recent treatment options for HNSCC include immunotherapy, such as anti-PD1 or anti-PDL1 antibodies. While high cure rates have been achieved for localized and locoregional disease using surgery, radiation, chemoradiotherapy, and induction chemotherapy, survival rates for recurrent / metastatic disease remain extremely poor and better treatment options are needed.

[0058] Lung SCC ("LSCC") accounts for approximately 30% of all lung cancers. This type of lung cancer tends to be found in the center of the lung. Approved treatment options for LSCC include surgery, radiation therapy, chemotherapy, angiogenesis inhibitors, and immunotherapy. Lung cancer that is only in one lung and has not spread to other organs is often treated with surgery, if the patient can tolerate it. If surgery is not possible, radiation therapy may be used as the primary treatment for early stage squamous cell lung cancer. In that case, radiation therapy may be given with or without chemotherapy. In some cases, radiation therapy is used before or after surgery.

[0059] Patients whose lung cancer has spread beyond the lungs to regional lymph nodes are often given chemotherapy and radiation therapy. Patients with LSCC are often given two chemotherapy drugs as first-line therapy. The platinum-based drugs cisplatin or carboplatin are combined with another chemotherapy drug. An example is cisplatin combined with gemcitabine. The drug necitumumab (Portrazza™) has also been approved by the FDA as a first-line treatment for patients with metastatic LSCC, used in combination with cisplatin and gemcitabine. If the LSCC has not been shown to have an EGFR mutation, necitumumab appears to work by blocking the expression of the EGFR protein. There are many other post-first-line options for LSCC, such as chemotherapy with or without angiogenesis inhibitors, or immunotherapy, such as nivolumab. The kinase inhibitor afatinib (Gilotrif®) has been approved by the FDA for the treatment of patients with metastatic LSCC who have progressed after platinum-based chemotherapy. Additional treatment options include ramucirumab (Cyramza®), nivolumab (Opdivo®), pembrolizumab (Keytruda), or atezolizumab (Tecentriq®).

[0060] SCC of the thyroid gland ("thyroid SCC" or "TSCC") can be either a primary or secondary disease, either due to direct extension of adjacent lesions or metastasis from other primary lesions; the latter is ten times more common. Primary SCC of the thyroid gland is a rare type of thyroid malignancy. It is more prevalent in women, with the average age of onset being in the 50s. Currently, surgical resection of the tumor with adjuvant radiation therapy and chemotherapy is the recommended option. The extent of surgical resection has not been well defined. However, in advanced stage disease, the widespread and invasive nature of thyroid SCC may be a major factor in surgical failure. Furthermore, primary thyroid SCC is also relatively resistant to radiation therapy, whereas standard chemotherapy has been shown to produce minimal to no response to the disease. The general prognosis of primary SCC of the thyroid gland is very unfavorable regardless of treatment modality due to its aggressive nature. Better treatment options are needed.

[0061] Esophageal squamous cell carcinoma ("esophageal SCC" or "ESCC") is one of the most aggressive squamous cell carcinomas and is highly prevalent in Asia. Patients with ESCC are treated endoscopically or surgically, with chemotherapy, or with radiation therapy based on the stage of the tumor. Minimally invasive treatments help improve the quality of life of patients undergoing such treatment. Early stage ESCC, which has a negligible risk of metastasis to lymph nodes, can be cured by endoscopic local treatments such as ER and / or ablation techniques (e.g., radiofrequency ablation or photodynamic therapy). Surgery is also widely used to obtain locoregional control and has an important role in the treatment of esophageal cancer. Neoadjuvant or neoadjuvant chemoradiotherapy is performed as the standard treatment for locally advanced ESCC. The combination of cisplatin and 5-FU is commonly used in chemotherapy for patients with unresectable locally advanced or metastatic ESCC and is considered superior to best supportive care. Targeted therapies such as anti-EGFR antibodies (e.g., cetuximab) and anti-PD1 / PD-L1 antibodies are also under investigation.

[0062] Bladder squamous cell carcinoma ("bladder SCC" or "BSCC") usually appears at a late stage and portends a poor prognosis. Bladder SCC accounts for 2-5% of bladder malignancies in the United States. BSCC is divided into two subtypes: BSCC associated with bilharzoma infection (schistosomiasis), i.e., bilharzoma-associated BSCC (B-BSCC), and BSCC not associated with bilharzoma infection, i.e., non-bilharzoma-associated SCC (NB-BSCC). B-BSCC and NB-BSCC have different epidemiological, natural history, and clinicopathological characteristics. B-BSCC is primarily found in areas where schistosomiasis is endemic, such as the Middle East, Southeast Asia, and South America. NB-BSCC has been reported in patients with spinal cord injury (SCI) in the United States, especially after prolonged use of indwelling catheters. Patients with NB-BSCC are generally diagnosed at a late stage and show a poor prognosis. Both B-BSCC and NB-BSCC are treated with radical cystectomy (RC). The use of other treatments, including neoadjuvant and adjuvant therapies in combination with RC, is less well established. Further research incorporating multimodal approaches, modern radiation techniques, immunotherapy, and systemic therapies is also needed.

[0063] Urothelial carcinoma (UC) is an indication with a 5-year survival rate of 77%. Cells in UC generally display squamous epithelial differentiation and characteristics defined by the presence of intercellular bridges, keratinization, or both. Liu et al.,Cancer Control 24(1):78-82(2017).

[0064] In some embodiments of the methods provided herein, the SCC is a human papillomavirus (HPV) negative SCC. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is a metastatic SCC. In some embodiments, the SCC is a recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC. For example, the SCC can be a head and neck SCC (HNSCC), a lung SCC (LSCC), a thyroid SCC, an esophageal SCC, a bladder SCC, or a urothelial carcinoma (UC).

[0065] In some embodiments, SCC is HNSCC, and provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of FTI to a subject with HNSCC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of HNSCC to FTI treatment by selectively treating HNSCC subjects with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with HNSCC to FTI treatment based on the expression level of H-Ras, and predicting that the subject may respond if the subject has H-Ras overexpression.

[0066] In some embodiments, provided herein is a method for treating HNSCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has HNSCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0067] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with HNSCC that overexpresses H-Ras. Also provided herein is a method for improving the response of tipifarnib treatment to HNSCC by selectively treating HNSCC subjects with H-Ras overexpression. Also provided herein is a method for predicting the responsiveness of a subject with HNSCC to tipifarnib treatment based on the expression level of H-Ras, where the subject is predicted to be likely to respond if the subject has H-Ras overexpression.

[0068] In some embodiments, provided herein is a method of treating HNSCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, the subject having H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has HNSCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0069] In some embodiments, the subject has H-Ras expression that is at least 2 times, at least 2.5 times, at least 3 times, at least 3.5 times, at least 4 times, at least 4.5 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 12 times, at least 15 times, or at least 20 times higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a healthy subject population.In some embodiments, the reference level is the median expression level of H-Ras in a subject population with HNSCC.

[0070] In some embodiments, the HNSCC is a tracheal HNSCC. In some embodiments, the HNSCC is a maxillary HNSCC. In some embodiments, the HNSCC is an oral HNSCC. In some embodiments, the HNSCC is a human papillomavirus (HPV) negative HNSCC. In some embodiments, the HNSCC is at an advanced stage. In some embodiments, the HNSCC is a metastatic HNSCC. In some embodiments, the HNSCC is a recurrent HNSCC. In some embodiments, the HNSCC is a refractory HNSCC.

[0071] In some embodiments, SCC is LSCC, and provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of FTI to a subject with LSCC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of LSCC to FTI treatment by selectively treating LSCC patients with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with LSCC to FTI treatment based on the expression level of H-Ras, and predicting that the subject may respond if the subject has H-Ras overexpression.

[0072] In some embodiments, provided herein is a method for treating LSCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has LSCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0073] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with LSCC that overexpresses H-Ras. Also provided herein is a method for improving the response of tipifarnib treatment to LSCC by selectively treating LSCC patients with H-Ras overexpression. Also provided herein is a method for predicting the responsiveness of a subject with LSCC to tipifarnib treatment based on the expression level of H-Ras, where the subject is predicted to be likely to respond if the subject has H-Ras overexpression.

[0074] In some embodiments, provided herein is a method for treating LSCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has LSCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0075] In some embodiments, the subject has H-Ras expression that is at least 2 times, at least 2.5 times, at least 3 times, at least 3.5 times, at least 4 times, at least 4.5 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 12 times, at least 15 times, or at least 20 times higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a population of healthy subjects.In some embodiments, the reference level is the median expression level of H-Ras in a population of subjects with LSCC.

[0076] In some embodiments, the LSCC is a human papillomavirus (HPV) negative LSCC. In some embodiments, the LSCC is at an advanced stage. In some embodiments, the LSCC is a metastatic LSCC. In some embodiments, the LSCC is a recurrent LSCC. In some embodiments, the LSCC is a refractory LSCC.

[0077] In some embodiments, SCC is thyroid SCC, and provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of FTI to a subject with thyroid SCC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of thyroid SCC to FTI treatment by selectively treating thyroid SCC patients with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with thyroid SCC to FTI treatment based on the expression level of H-Ras, and predicting that the subject is likely to respond if the subject has H-Ras overexpression.

[0078] In some embodiments, provided herein is a method for treating thyroid SCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, the subject having H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has a thyroid SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0079] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having thyroid SCC that overexpresses H-Ras. Also provided herein is a method for selectively treating thyroid SCC patients with H-Ras overexpression, thereby improving the response of tipifarnib treatment to thyroid SCC. Also provided herein is a method of predicting the responsiveness of a subject with thyroid SCC to tipifarnib treatment based on the expression level of H-Ras, where the subject is predicted to be likely to respond if the subject has H-Ras overexpression.

[0080] In some embodiments, provided herein is a method of treating thyroid SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, the subject having H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure an expression level of H-Ras in the sample, and determining that the subject has a thyroid SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0081] In some embodiments, the subject has H-Ras expression that is at least 2 times, at least 2.5 times, at least 3 times, at least 3.5 times, at least 4 times, at least 4.5 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 12 times, at least 15 times, or at least 20 times higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a population of healthy subjects.In some embodiments, the reference level is the median expression level of H-Ras in a population of subjects with thyroid SCC.

[0082] In some embodiments, the thyroid SCC is human papillomavirus (HPV) negative thyroid SCC. In some embodiments, the thyroid SCC is at an advanced stage. In some embodiments, the thyroid SCC is metastatic thyroid SCC. In some embodiments, the thyroid SCC is recurrent thyroid SCC. In some embodiments, the thyroid SCC is refractory thyroid SCC.

[0083] In some embodiments, SCC is esophageal SCC, and provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of FTI to a subject with esophageal SCC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of esophageal SCC to FTI treatment by selectively treating esophageal SCC patients with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with esophageal SCC to FTI treatment based on the expression level of H-Ras, and predicting that the subject is likely to respond if the subject has H-Ras overexpression.

[0084] In some embodiments, provided herein is a method for treating esophageal SCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, the subject having H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has esophageal SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0085] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having esophageal SCC that overexpresses H-Ras. Also provided herein is a method for improving the response of tipifarnib treatment to esophageal SCC by selectively treating esophageal SCC patients with H-Ras overexpression. Also provided herein is a method of predicting the responsiveness of a subject with esophageal SCC to tipifarnib treatment based on the expression level of H-Ras, where the subject is predicted to be likely to respond if the subject has H-Ras overexpression.

[0086] In some embodiments, provided herein is a method of treating esophageal SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, the subject having H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has esophageal SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0087] In some embodiments, the subject has H-Ras expression that is at least 2 times, at least 2.5 times, at least 3 times, at least 3.5 times, at least 4 times, at least 4.5 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 12 times, at least 15 times, or at least 20 times higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a population of healthy subjects.In some embodiments, the reference level is the median expression level of H-Ras in a population of subjects with esophageal SCC.

[0088] In some embodiments, the esophageal SCC is a human papillomavirus (HPV) negative esophageal SCC. In some embodiments, the esophageal SCC is at an advanced stage. In some embodiments, the esophageal SCC is a metastatic esophageal SCC. In some embodiments, the esophageal SCC is a recurrent esophageal SCC. In some embodiments, the esophageal SCC is a refractory esophageal SCC.

[0089] In some embodiments, SCC is bladder SCC, and provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of FTI to a subject with bladder SCC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of bladder SCC to FTI treatment by selectively treating bladder SCC patients with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with bladder SCC to FTI treatment based on the expression level of H-Ras, and predicting that the subject may respond if the subject has H-Ras overexpression.

[0090] In some embodiments, provided herein is a method for treating bladder SCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has bladder SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0091] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with bladder SCC that overexpresses H-Ras. Also provided herein is a method for improving the response of tipifarnib treatment to bladder SCC by selectively treating bladder SCC patients with H-Ras overexpression. Also provided herein is a method of predicting the responsiveness of a subject with bladder SCC to tipifarnib treatment based on the expression level of H-Ras, where the subject is predicted to be likely to respond if the subject has H-Ras overexpression.

[0092] In some embodiments, provided herein is a method for treating bladder SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has bladder SCC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0093] In some embodiments, the subject has H-Ras expression that is at least 2 times, at least 2.5 times, at least 3 times, at least 3.5 times, at least 4 times, at least 4.5 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 12 times, at least 15 times, or at least 20 times higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a healthy subject population.In some embodiments, the reference level is the median expression level of H-Ras in a subject population with bladder SCC.

[0094] In some embodiments, the bladder SCC is human papillomavirus (HPV) negative bladder SCC. In some embodiments, the bladder SCC is at an advanced stage. In some embodiments, the bladder SCC is metastatic bladder SCC. In some embodiments, the bladder SCC is recurrent bladder SCC. In some embodiments, the bladder SCC is refractory bladder SCC.

[0095] In some embodiments, SCC is UC, and provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of FTI to a subject with UC that overexpresses H-Ras.Also provided herein is a method for improving the responsiveness of FTI treatment for UC by selectively treating UC patients with H-Ras overexpression.Also provided herein is a method for predicting the responsiveness of a subject with UC to FTI treatment based on the expression level of H-Ras, and predicting that the subject may respond if the subject has H-Ras overexpression.

[0096] In some embodiments, provided herein is a method for treating UC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has UC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0097] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with UC that overexpresses H-Ras. Also provided herein is a method for improving the responsiveness of tipifarnib treatment for UC by selectively treating UC patients with H-Ras overexpression. Also provided herein is a method for predicting the responsiveness of a subject with UC to tipifarnib treatment based on the expression level of H-Ras, and predicting that the subject is likely to respond if the subject has H-Ras overexpression.

[0098] In some embodiments, provided herein is a method for treating UC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, wherein the subject has H-Ras expression higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the expression level of H-Ras in the sample, and determining that the subject has UC that overexpresses H-Ras if the expression level of H-Ras in the sample is higher than the reference level.

[0099] In some embodiments, the subject has H-Ras expression that is at least 2 times, at least 2.5 times, at least 3 times, at least 3.5 times, at least 4 times, at least 4.5 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, at least 10 times, at least 12 times, at least 15 times, or at least 20 times higher than the reference level.In some embodiments, the reference level is the median expression level of H-Ras in a healthy subject population.In some embodiments, the reference level is the median expression level of H-Ras in a subject population with UC.

[0100] In some embodiments, the UC is human papillomavirus (HPV) negative UC. In some embodiments, the UC is in an advanced stage. In some embodiments, the UC is metastatic UC. In some embodiments, the UC is recurrent UC. In some embodiments, the UC is refractory UC.

[0101] Also provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of SCC to FTI treatment by selectively treating SCC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having SCC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects having SCC.

[0102] Also provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of SCC to FTI treatment by selectively treating SCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having SCC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having SCC.

[0103] Also provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of SCC to FTI treatment by selectively treating SCC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having SCC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects having SCC.

[0104] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10. In some embodiments, the reference ratio is 1 / 10. In some embodiments, the reference ratio is 1 / 9. In some embodiments, the reference ratio is 1 / 8. In some embodiments, the reference ratio is 1 / 7. In some embodiments, the reference ratio is 1 / 6. In some embodiments, the reference ratio is 1 / 5. In some embodiments, the reference ratio is 1 / 4. In some embodiments, the reference ratio is 1 / 3. In some embodiments, the reference ratio is 1 / 2. In some embodiments, the reference ratio is 1. In some embodiments, the reference ratio is 2. In some embodiments, the reference ratio is 3. In some embodiments, the reference ratio is 4. In some embodiments, the reference ratio is 5. In some embodiments, the reference ratio is 6. In some embodiments, the reference ratio is 7. In some embodiments, the reference ratio is 8. In some embodiments, the reference ratio is 9. In some embodiments, the reference ratio is 10.

[0105] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, also provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K ratio higher than a reference ratio. Also provided herein is a method for improving the responsiveness of tipifarnib treatment for SCC by selectively treating SCC patients having a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with SCC to tipifarnib treatment based on the H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than a reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and K-Ras in the sample, and if the subject has a H / K ratio higher than the reference ratio, the subject is selected for tipifarnib treatment. The reference ratio can be determined by a person skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with SCC.

[0106] Also provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of SCC to tipifarnib treatment by selectively treating SCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having SCC to tipifarnib treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having SCC.

[0107] Also provided herein is a method for treating SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for improving the response of SCC to tipifarnib treatment by selectively treating SCC patients having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for predicting the response of a subject having SCC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras, K-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with SCC.

[0108] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0109] In some embodiments, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC. For example, the SCC can be head and neck SCC (HNSCC), lung SCC (LSCC), thyroid SCC, esophageal SCC, bladder SCC, or urothelial carcinoma (UC).

[0110] Also provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of HNSCC to FTI treatment by selectively treating HNSCC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having HNSCC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects having HNSCC.

[0111] Also provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of HNSCC to FTI treatment by selectively treating HNSCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having HNSCC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having HNSCC.

[0112] Also provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of HNSCC to FTI treatment by selectively treating HNSCC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having HNSCC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects having HNSCC.

[0113] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10. In some embodiments, the reference ratio is 1 / 10.

[0114] The FTI can be any FTI, including those described herein.For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662.In some embodiments, the FTI is tipifarnib.Therefore, also provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with a H / K ratio higher than a reference ratio.Also provided herein is a method for improving the response of tipifarnib treatment to HNSCC by selectively treating HNSCC patients with a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with HNSCC to tipifarnib treatment based on H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than the reference ratio.In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K ratio higher than the reference ratio.In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects.In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with HNSCC.

[0115] Also provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of HNSCC to tipifarnib treatment by selectively treating HNSCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having HNSCC to tipifarnib treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having HNSCC.

[0116] Also provided herein is a method for treating HNSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the response of HNSCC to tipifarnib treatment by selectively treating HNSCC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the response of a subject having HNSCC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with HNSCC.

[0117] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0118] In some embodiments, the HNSCC is a tracheal HNSCC. In some embodiments, the HNSCC is a maxillary HNSCC. In some embodiments, the HNSCC is an oral HNSCC. In some embodiments, the HNSCC is a human papillomavirus (HPV) negative HNSCC. In some embodiments, the HNSCC is at an advanced stage. In some embodiments, the HNSCC is a metastatic HNSCC. In some embodiments, the HNSCC is a recurrent HNSCC. In some embodiments, the HNSCC is a refractory HNSCC.

[0119] Also provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of LSCC to FTI treatment by selectively treating LSCC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having LSCC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects having LSCC.

[0120] Also provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of LSCC to FTI treatment by selectively treating LSCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having LSCC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having LSCC.

[0121] Also provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of LSCC to FTI treatment by selectively treating LSCC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having LSCC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects having LSCC.

[0122] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0123] In some embodiments, the LSCC is a human papillomavirus (HPV) negative LSCC. In some embodiments, the LSCC is at an advanced stage. In some embodiments, the LSCC is a metastatic LSCC. In some embodiments, the LSCC is a recurrent LSCC. In some embodiments, the LSCC is a refractory LSCC.

[0124] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, also provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with a H / K ratio higher than a reference ratio. Also provided herein is a method for improving the responsiveness of tipifarnib treatment for LSCC by selectively treating LSCC patients with a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with LSCC to tipifarnib treatment based on the H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than a reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and K-Ras in the sample, and if the subject has a H / K ratio higher than a reference ratio, the subject is selected for tipifarnib treatment. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with LSCC.

[0125] Also provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of LSCC to tipifarnib treatment by selectively treating LSCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having LSCC to tipifarnib treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having LSCC.

[0126] Also provided herein is a method for treating LSCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of LSCC to tipifarnib treatment by selectively treating LSCC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having LSCC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras, K-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with LSCC.

[0127] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0128] In some embodiments, the LSCC is a human papillomavirus (HPV) negative LSCC. In some embodiments, the LSCC is at an advanced stage. In some embodiments, the LSCC is a metastatic LSCC. In some embodiments, the LSCC is a recurrent LSCC. In some embodiments, the LSCC is a refractory LSCC.

[0129] Also provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving responsiveness of thyroid SCC to FTI treatment by selectively treating thyroid SCC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting responsiveness of a subject having thyroid SCC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects having thyroid SCC.

[0130] Also provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving responsiveness of thyroid SCC to FTI treatment by selectively treating thyroid SCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting responsiveness of a subject having thyroid SCC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having thyroid SCC.

[0131] Also provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving responsiveness of thyroid SCC to FTI treatment by selectively treating thyroid SCC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting responsiveness of a subject having thyroid SCC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects having thyroid SCC.

[0132] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0133] In some embodiments, the thyroid SCC is human papillomavirus (HPV) negative thyroid SCC. In some embodiments, the thyroid SCC is at an advanced stage. In some embodiments, the thyroid SCC is metastatic thyroid SCC. In some embodiments, the thyroid SCC is recurrent thyroid SCC. In some embodiments, the thyroid SCC is refractory thyroid SCC.

[0134] The FTI can be any FTI, including those described herein.For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662.In some embodiments, the FTI is tipifarnib.Therefore, also provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with a H / K ratio higher than a reference ratio.Also provided herein is a method for improving the response of tipifarnib treatment to thyroid SCC by selectively treating thyroid SCC patients with a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with thyroid SCC to tipifarnib treatment based on H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with thyroid SCC.

[0135] Also provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than a reference ratio. Also provided herein is a method for improving the response of thyroid SCC to tipifarnib treatment by selectively treating thyroid SCC patients having a H / N ratio higher than a reference ratio. Also provided herein is a method for predicting the response of a subject having thyroid SCC to tipifarnib treatment based on an H / N ratio, where the subject is predicted to be likely to respond if the subject has an H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has an H / N ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having thyroid SCC.

[0136] Also provided herein is a method for treating thyroid SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for improving the response of thyroid SCC to tipifarnib treatment by selectively treating thyroid SCC patients having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for predicting the response of a subject having thyroid SCC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with thyroid SCC.

[0137] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0138] In some embodiments, the thyroid SCC is human papillomavirus (HPV) negative thyroid SCC. In some embodiments, the thyroid SCC is at an advanced stage. In some embodiments, the thyroid SCC is metastatic thyroid SCC. In some embodiments, the thyroid SCC is recurrent thyroid SCC. In some embodiments, the thyroid SCC is refractory thyroid SCC.

[0139] Also provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of esophageal SCC to FTI treatment by selectively treating esophageal SCC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having esophageal SCC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects having esophageal SCC.

[0140] Also provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of esophageal SCC to FTI treatment by selectively treating esophageal SCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having esophageal SCC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having esophageal SCC.

[0141] Also provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for improving the responsiveness of esophageal SCC to FTI treatment by selectively treating esophageal SCC patients having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having esophageal SCC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with esophageal SCC.

[0142] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0143] In some embodiments, the esophageal SCC is a human papillomavirus (HPV) negative esophageal SCC. In some embodiments, the esophageal SCC is at an advanced stage. In some embodiments, the esophageal SCC is a metastatic esophageal SCC. In some embodiments, the esophageal SCC is a recurrent esophageal SCC. In some embodiments, the esophageal SCC is a refractory esophageal SCC.

[0144] The FTI can be any FTI, including those described herein.For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662.In some embodiments, the FTI is tipifarnib.Therefore, also provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with a H / K ratio higher than a reference ratio.Also provided herein is a method for improving the response of tipifarnib treatment to esophageal SCC by selectively treating esophageal SCC patients with a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with esophageal SCC to tipifarnib treatment based on H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than the reference ratio.In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K ratio higher than the reference ratio.In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects.In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with esophageal SCC.

[0145] Also provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than a reference ratio. Also provided herein is a method for improving the response of esophageal SCC to tipifarnib treatment by selectively treating esophageal SCC patients having a H / N ratio higher than a reference ratio. Also provided herein is a method for predicting the response of a subject having esophageal SCC to tipifarnib treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having esophageal SCC.

[0146] Also provided herein is a method for treating esophageal SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for improving the response of esophageal SCC to tipifarnib treatment by selectively treating esophageal SCC patients having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for predicting the response of a subject having esophageal SCC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with esophageal SCC.

[0147] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0148] In some embodiments, the esophageal SCC is a human papillomavirus (HPV) negative esophageal SCC. In some embodiments, the esophageal SCC is at an advanced stage. In some embodiments, the esophageal SCC is a metastatic esophageal SCC. In some embodiments, the esophageal SCC is a recurrent esophageal SCC. In some embodiments, the esophageal SCC is a refractory esophageal SCC.

[0149] Also provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of bladder SCC to FTI treatment by selectively treating bladder SCC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having bladder SCC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects having bladder SCC.

[0150] Also provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving bladder SCC responsiveness to FTI treatment by selectively treating bladder SCC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting responsiveness of a subject having bladder SCC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having bladder SCC.

[0151] Also provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for improving the responsiveness of bladder SCC to FTI treatment by selectively treating bladder SCC patients having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having bladder SCC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with bladder SCC.

[0152] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0153] In some embodiments, the bladder SCC is human papillomavirus (HPV) negative bladder SCC. In some embodiments, the bladder SCC is at an advanced stage. In some embodiments, the bladder SCC is metastatic bladder SCC. In some embodiments, the bladder SCC is recurrent bladder SCC. In some embodiments, the bladder SCC is refractory bladder SCC.

[0154] The FTI can be any FTI, including those described herein.For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662.In some embodiments, the FTI is tipifarnib.Therefore, also provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject with a H / K ratio higher than a reference ratio.Also provided herein is a method for improving the response of tipifarnib treatment to bladder SCC by selectively treating bladder SCC patients with a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with bladder SCC to tipifarnib treatment based on H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than the reference ratio.In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K ratio higher than the reference ratio.In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects.In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with bladder SCC.

[0155] Also provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than a reference ratio. Also provided herein is a method for improving the responsiveness of bladder SCC to tipifarnib treatment by selectively treating bladder SCC patients having a H / N ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject having bladder SCC to tipifarnib treatment based on an H / N ratio, where the subject is predicted to be likely to respond if the subject has an H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has an H / N ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects having bladder SCC.

[0156] Also provided herein is a method for treating bladder SCC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for improving the response of bladder SCC to tipifarnib treatment by selectively treating bladder SCC patients having a H / K+N ratio higher than a reference ratio. Also provided herein is a method for predicting the response of a subject having bladder SCC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with bladder SCC.

[0157] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0158] In some embodiments, the bladder SCC is human papillomavirus (HPV) negative bladder SCC. In some embodiments, the bladder SCC is at an advanced stage. In some embodiments, the bladder SCC is metastatic bladder SCC. In some embodiments, the bladder SCC is recurrent bladder SCC. In some embodiments, the bladder SCC is refractory bladder SCC.

[0159] Also provided herein is a method for treating urothelial carcinoma (UC) in a subject by administering a therapeutically effective amount of FTI to a subject having a H / K ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of UC to FTI treatment by selectively treating UC patients having a H / K ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with UC to FTI treatment based on the H / K ratio, where the subject is predicted to be likely to respond if the subject has a H / K ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and K-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with UC.

[0160] Also provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of an FTI to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of UC to FTI treatment by selectively treating UC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with UC to FTI treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / N ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects with UC.

[0161] Also provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of an FTI to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of UC to FTI treatment by selectively treating UC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with UC to FTI treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for FTI treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one of skill in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with UC.

[0162] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0163] In some embodiments, the UC is human papillomavirus (HPV) negative UC. In some embodiments, the UC is in an advanced stage. In some embodiments, the UC is metastatic UC. In some embodiments, the UC is recurrent UC. In some embodiments, the UC is refractory UC.

[0164] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib. Thus, also provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K ratio higher than a reference ratio. Also provided herein is a method for improving the responsiveness of tipifarnib treatment for UC by selectively treating UC patients having a H / K ratio higher than a reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with UC to tipifarnib treatment based on the H / K ratio, and predicting that the subject is likely to respond if the subject has a H / K ratio higher than a reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras and K-Ras in the sample, and if the subject has a H / K ratio higher than a reference ratio, the subject is selected for tipifarnib treatment. In some embodiments, the reference ratio is the median H / K ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / K ratio in a population of subjects with UC.

[0165] Also provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of UC to tipifarnib treatment by selectively treating UC patients having a H / N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with UC to tipifarnib treatment based on the H / N ratio, where the subject is predicted to be likely to respond if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from the subject to measure the expression levels of H-Ras and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / N ratio higher than the reference ratio. In some embodiments, the reference ratio is the median H / N ratio in a population of healthy subjects. In some embodiments, the reference ratio is the median H / N ratio in a population of subjects with UC.

[0166] Also provided herein is a method for treating UC in a subject by administering a therapeutically effective amount of tipifarnib to a subject having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for improving the responsiveness of UC to tipifarnib treatment by selectively treating UC patients having a H / K+N ratio higher than the reference ratio. Also provided herein is a method for predicting the responsiveness of a subject with UC to tipifarnib treatment based on the H / K+N ratio, where the subject is predicted to be likely to respond if the subject has a H / K+N ratio higher than the reference ratio. In some embodiments, the method includes analyzing a sample from a subject to measure the expression levels of H-Ras, K-Ras, and N-Ras in the sample, and selecting the subject for tipifarnib treatment if the subject has a H / K+N ratio higher than the reference ratio. The reference ratio can be determined by one skilled in the art through statistical analysis. In some embodiments, the reference ratio is the median H / K+N ratio in a healthy subject population. In some embodiments, the reference ratio is the median H / K+N ratio in a population of subjects with UC.

[0167] In some embodiments, the reference ratio is 1 / 10, 1 / 9, 1 / 8, 1 / 7, 1 / 6, 1 / 5, 1 / 4, 1 / 3, 1 / 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or any number between 1 / 10 and 10.

[0168] In some embodiments, the UC is human papillomavirus (HPV) negative UC. In some embodiments, the UC is in an advanced stage. In some embodiments, the UC is metastatic UC. In some embodiments, the UC is recurrent UC. In some embodiments, the UC is refractory UC.

[0169] As those skilled in the art will understand, the reference expression level of a gene or the reference ratio between the expression levels of two genes can also be determined based on the statistical analysis of data from previous clinical trials, including the outcome of a patient group, i.e., the responsiveness of the patient to FTI treatment, and the expression level of a gene or the ratio of the expression levels between genes of a patient group.Many statistical methods are well known in the art for determining the reference level (or referred to as "cut-off value") of one or more genes, when used to predict the responsiveness of a patient to a particular treatment or to stratify patients for a particular treatment.

[0170] One method of the present invention includes the analysis of expression profiles of genes identified herein to distinguish between responders and non-responders and determine reference expression levels of one or more genes. Comparison between responders and non-responders can be performed using the Mann-Whitney U test, chi-square test, or Fisher's exact test. Analysis and comparison of descriptive statistics can be performed using SigmaStat Software (Systat Software, Inc., San Jose, CA, USA).

[0171] In some embodiments, classification and regression tree (CART) analysis can be employed to determine the reference level. CART analysis is based on a two-way recursive partitioning algorithm, which allows for the discovery of complex predictor variable interactions that may not be evident using more conventional methods such as multiple linear regression. Two-way recursive partitioning refers to an analysis that is 1) two-way, i.e., there are two possible outcome variables, i.e., "responders" and "non-responders," that act to divide patients into two groups; 2) recursive, i.e., the analysis can be performed multiple times; and 3) partitioned, i.e., the entire data set can be divided into parts. This analysis also has the ability to eliminate poorly performing predictor variables. Classification trees can be constructed using Salford Predictive Modeler v6.6 (Salford Systems, San Diego, CA, USA).

[0172] Receiver operating characteristic (ROC) analysis can be used to determine a reference expression level, or a reference expression ratio, or to test the overall predictive value of individual genes and / or multiple genes. A review of ROC analysis can be found in Soreide, J Clin Pathol 10.1136 (2008), which is incorporated herein by reference in its entirety.

[0173] To ensure both high sensitivity and specificity, a reference level can be determined from the ROC curve of the training set. The performance of predictors, including differences in gene numbers, can be evaluated based on the misclassification error rate, sensitivity, specificity, and p-value, which measures the separation of the Kaplan-Meier curves of the two predicted groups.

[0174] The Top Scoring Pair (TSP) algorithm, first introduced by Geman et al. (2004), can be used. Essentially, this algorithm ranks all gene pairs (genes i and j) based on the absolute difference (Dij) in the frequency of events in which gene i has a higher expression value than gene j in samples between classes C1 and C2. If there are multiple top-scoring pairs (all sharing the same Dij), the top pair is selected by a secondary rank score, which measures the degree to which reversal of gene expression levels occurs from one class to the other within a gene pair. The top pair with the highest absolute Dij frequency over 2-fold across all samples will be selected as the candidate pair. The candidate pairs can then be evaluated on an independent test dataset. Leave-one-out cross-validation (LOOCV) can be performed on the training dataset to evaluate how the algorithm works. The performance of the predictors can be evaluated based on the maximum misclassification error rate. All statistical analyses can be performed using R (R Development Core Team, 2006).

[0175] The clinically reportable range (CRR) is the range of values ​​of an analyte that a method can measure, taking into account specimen dilutions, concentrations, or other pretreatments used to extend the direct analytical measurement range. As provided in Basic Methods Validation by Dr. Westgard, the experiment to be performed is often called a "linearity experiment," although technically it is not necessary for a method to provide a linear response unless a two-point calibration is used. This range may also be referred to as the "linear range," "analytical range," or "working range" of the method.

[0176] The reportable range is assessed by inspection of the linearity graph. The inspection may involve manually drawing the straightest line through the linear portion of the points, drawing a line from point to point through all the points and then comparing it to the straightest line, or fitting a regression line through the points in the linear range. There are more complex statistical calculations recommended in some guidelines, such as the Clinical Laboratory Standards Committee (CLSI) EP-6 protocol for evaluating the linearity of an analytical method. However, it is generally accepted that the reportable range can be adequately determined from a "visual" evaluation, i.e., by manually drawing the straightest line that fits the lowest points in the series. The Clinical Laboratory Standards Committee (CLSI) recommends a minimum of at least four, and preferably five, different concentration levels. More than five can be used, especially if the upper end of the reportable range needs to be maximized, but five levels are convenient and sufficient in most cases.

[0177] Reference intervals are usually established by assaying specimens obtained from individuals (reference sample groups) that meet carefully defined criteria. Protocols such as the International Federation of Clinical Chemistry (IFCC) Expert Panel on the Theory of Reference Values ​​and the CLSI protocol detail comprehensive systematic processes for establishing reference intervals using carefully selected reference sample groups. These protocols usually require a minimum of 120 reference individuals for each group (or subgroup) that needs to be characterized.

[0178] CLSI Recognition Guideline C28-A2 describes various methods by which laboratories can verify the transfer of established reference intervals to individual laboratories, including: 1. divine judgment, where the laboratory simply reviews the submitted information and subjectively verifies that the reference interval can be applied to the laboratory's patient population and test methodology employed; 2. 20-sample verification, where experimental verification is performed by collecting and analyzing specimens from 20 individuals representative of the reference sample population; 3. 60-sample estimation, where experimental verification is performed by collecting and analyzing specimens from 60 individuals representative of the reference sample population and using a statistical formula comparing the means and standard deviations of the two populations to estimate the actual reference interval and compare it to the claimed or reported interval; and 4. calculation from comparison method, where the claimed or reported reference interval can be adjusted or corrected based on observed methodological biases and a demonstrated mathematical relationship between the analytical methods used.

[0179] Those skilled in the art will understand that the reference expression levels of genes disclosed herein and the reference ratios between two or more genes can be determined by one or more methods provided herein or other methods known in the art.

[0180] In some embodiments, the methods provided herein also include obtaining a sample from the subject. Samples used in the methods provided herein include bodily fluids from the subject or tumor biopsies from the subject.

[0181] In some embodiments, the sample used in the method comprises a biopsy (e.g., a tumor biopsy). The biopsy may be from any organ or tissue, such as skin, liver, lung, heart, colon, kidney, bone marrow, teeth, lymph node, hair, spleen, brain, breast, or other organ. Any biopsy technique known to those skilled in the art, such as open biopsy, closed biopsy, core biopsy, incisional biopsy, excision biopsy, or fine needle aspiration biopsy, may be used to isolate a sample from a subject. In some embodiments, the sample used in the method comprises an aspirate (e.g., a bone marrow aspirate). In some embodiments, the sample is a lymph node biopsy. In some embodiments, the sample may be a frozen tissue sample. In some embodiments, the sample may be a formalin-fixed paraffin-embedded ("FFPE") tissue sample. In some embodiments, the sample may be a deparaffinized tissue section. In some embodiments, the sample may be a liver sample. In some embodiments, the sample may be a testis sample. In some embodiments, the sample may be a spleen sample. In some embodiments, the sample may be a lymph node sample.

[0182] In some embodiments, the sample is a bodily fluid sample. Non-limiting examples of bodily fluids include blood (e.g., peripheral whole blood, peripheral blood), plasma, bone marrow, amniotic fluid, aqueous humor, bile, lymph, menstrual blood, serum, urine, cerebrospinal fluid around the brain and spinal cord, and synovial fluid around bone joints. In some embodiments, the sample can be a cerebrospinal fluid sample.

[0183] In some embodiments, the sample is a blood sample. The blood sample can be a whole blood sample, a partially purified blood sample, or a peripheral blood sample. The blood sample can be obtained using conventional techniques, such as those described in Innis et al, editors, PCR Protocols (Academic Press, 1990). White blood cells can be separated from the blood sample using conventional techniques or commercially available kits, such as the RosetteSep kit (Stein Cell Technologies, Vancouver, Canada). Subpopulations of white blood cells, such as mononuclear cells, NK cells, B cells, T cells, monocytes, granulocytes, or lymphocytes, can be further isolated using conventional techniques, such as magnetic activated cell sorting (MACS) (Miltenyi Biotec, Auburn, California), or fluorescence activated cell sorting (FACS) (Becton Dickinson, San Jose, California). In some embodiments, the sample is serum. In some embodiments, the sample is plasma. In one embodiment, the sample is a bone marrow sample.

[0184] In certain embodiments, the sample used in the methods provided herein comprises a plurality of cells. Such cells can include any type of cell, such as stem cells, blood cells (e.g., PBMCs), lymphocytes, NK cells, B cells, T cells, monocytes, granulocytes, immune cells, or tumor or cancer cells. Specific cell populations can be obtained using a combination of commercially available antibodies (e.g., Quest Diagnostic (San Juan Capistrano, Calif.), Dako (Denmark)). In some embodiments, the sample is an isolated cell.

[0185] In certain embodiments, the sample used in the methods provided herein comprises a plurality of cells from a diseased tissue, e.g., a tumor sample from a subject with SCC. In some embodiments, the cells can be obtained from tumor tissue, such as a tumor biopsy or tumor explant. In certain embodiments, the number of cells used in the methods provided herein ranges from a single cell to about 109 In some embodiments, the number of cells used in the methods provided herein can range from about 1×10 4 , 5×10 4 , 1×10 5 , 5×10 5 , 1×10 6 , 5×10 6 , 1×10 7 , 5×10 7 , 1×10 8 , or 5 × 10 8 Various types of procedures are available to obtain a tumor biopsy from a patient, including skin biopsy, shave (tangential) biopsy, punch biopsy, incisional biopsy (removing a portion of the tumor) and excision biopsy (removing the entire tumor). Lymph node biopsy is usually performed to find out if the cancer has spread. Both fine needle aspiration (FNA) biopsy and surgical (excision) lymph node biopsy are available options. An FNA biopsy involves the use of a thin needle on the patient to obtain a small piece of lymph node, which is less invasive than surgical options but may not always yield a sample large enough to find cancer cells.

[0186] The number and type of cells harvested from a subject can be monitored by measuring changes in morphology and cell surface markers using standard cell detection techniques such as, for example, flow cytometry, cell sorting, immunocytochemistry (e.g., staining with tissue-specific or cell marker-specific antibodies), fluorescence-activated cell sorting (FACS), magnetic activated cell sorting (MACS), by examining cell morphology using optical or confocal microscopy, and / or by measuring changes in gene expression using techniques well known in the art such as PCR and gene expression profiling. These techniques can also be used to identify cells that are positive for one or more specific markers. Fluorescence-activated cell sorting (FACS) is a well-known method for separating particles, including cells, based on the fluorescent properties of the particles (Kamarch, 1987, Methods Enzymol, 151:150-165). Laser excitation of the fluorescent moieties of individual particles creates a small charge, allowing electromagnetic separation of positive and negative particles from a mixture. In one embodiment, the cell surface marker-specific antibodies or ligands are labeled with distinct fluorescent labels. The cells are processed through a cell sorter to separate cells based on their ability to bind to the antibody used. FACS-sorted particles can be directly deposited into individual wells of 96- or 384-well plates to facilitate separation and cloning.

[0187] In certain embodiments, a subset of cells is used in the methods provided herein. Methods for sorting and isolating specific cell populations are well known in the art and can be based on cell size, morphology, or intracellular or extracellular markers. Such methods include, but are not limited to, flow cytometry, flow sorting, FACS, bead-based separation (such as magnetic cell sorting), size-based separation (e.g., sieves, obstacle arrays, or filters), sorting on microfluidic devices, antibody-based separation, precipitation, affinity adsorption, affinity extraction, density gradient centrifugation, laser capture microdissection, and the like.

[0188] The expression level of a gene may refer to the protein level or the mRNA level of the gene. In some embodiments, the expression level of a gene refers to the mRNA level of the gene, and the methods provided herein comprise determining the mRNA level of the gene. In some embodiments, the expression level of a gene refers to the protein level of the gene, and the methods provided herein comprise determining the protein level of the gene.

[0189] In some embodiments, the expression level of a gene may refer to the mRNA level of the gene. Thus, the H-Ras expression level may refer to the mRNA level of H-Ras in a sample. The N-Ras expression level or the K-Ras expression level may refer to the respective mRNA levels. The PIK3CA expression level may refer to the mRNA level of PIK3CA in a sample. The H / K ratio may refer to the ratio of the H-Ras mRNA level to the K-Ras mRNA level. The H / N ratio may refer to the ratio of the H-Ras mRNA level to the N-Ras mRNA level. The H / K+N ratio may refer to the ratio of the H-Ras mRNA level to the combined mRNA level of K-Ras and N-Ras.

[0190] Thus, in some embodiments, provided herein is a method for treating SCC in a subject comprising administering a therapeutically effective amount of an FTI to the subject, the subject having an H-Ras mRNA level higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure an H-Ras mRNA level in the sample, and determining that the subject has an SCC that overexpresses H-Ras if the H-Ras mRNA level in the sample is higher than the reference level.

[0191] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib, and provided herein is a method of treating SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, wherein the subject has a H-Ras mRNA level higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the mRNA level of H-Ras in the sample, and determining that the subject has SCC that overexpresses H-Ras if the H-Ras mRNA level in the sample is higher than the reference level.

[0192] In some embodiments, the subject has an H-Ras mRNA level that is at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 12-fold, at least 15-fold, or at least 20-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 2-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 2.5-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 3-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 3.5-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 4-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 4.5-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level that is at least 5-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 6-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 7-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 8-fold higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 9 times higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 10 times higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 12 times higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 15 times higher than the reference level. In some embodiments, the subject has an H-Ras mRNA level at least 20 times higher than the reference level. In some embodiments, the reference level is the median H-Ras mRNA level in a population of healthy subjects. In some embodiments, the reference level is the median H-Ras mRNA level in a population of subjects with SCC.

[0193] In some embodiments of the methods provided herein, where the expression level of a gene is determined by its mRNA level, the SCC is a human papillomavirus (HPV) negative SCC. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is a metastatic SCC. In some embodiments, the SCC is a recurrent SCC. In some embodiments, the SCC is refractory. The SCC may be a specific type of SCC. In some embodiments, the SCC is a head and neck SCC (HNSCC). In some embodiments, the SCC is a lung SCC (LSCC). In some embodiments, the SCC is a thyroid SCC. In some embodiments, the SCC is an esophageal SCC. In some embodiments, the SCC is a bladder SCC. In some embodiments, the SCC is a urothelial carcinoma (UC).

[0194] In some embodiments, the method provided herein comprises determining the mRNA level of a gene.The method of determining the mRNA level of a gene in a sample is well known in the art.For example, in some embodiments, the mRNA level can be determined by polymerase chain reaction (PCR), qPCR, qRT-PCR, RNA-seq, microarray analysis, SAGE, MassARRAY technology, next generation sequencing, or FISH.

[0195] Exemplary methods for detecting or quantifying mRNA levels include, but are not limited to, PCR-based methods, Northern blots, RNase protection assays, etc. The mRNA sequence can be used to prepare a probe that is at least partially complementary.The probe can then be used to detect the mRNA sequence in a sample using any suitable assay, such as PCR-based methods, Northern blots, dipstick assays, etc.

[0196] Commonly used methods known in the art for quantifying mRNA expression in a sample include Northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247-283(1999)), RNAse protection assay (Hod, Biotechniques 13:852-854(1992)), and polymerase chain reaction (PCR) (Weis et al., Trends in Genetics 8:263-264(1992)). Alternatively, antibodies can be used that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Representative methods of sequencing-based gene expression analysis include sequence analysis of gene expression (SAGE) and gene expression analysis by massively parallel signature sequencing (MPSS).

[0197] A highly sensitive and flexible quantitative method is PCR. Examples of PCR methods can be found in the literature. Examples of PCR assays can be found in U.S. Patent No. 6,927,024, which is incorporated herein by reference in its entirety. Examples of RT-PCR methods can be found in U.S. Patent No. 7,122,799, which is incorporated herein by reference in its entirety. The method of fluorescent in situ PCR is described in U.S. Patent No. 7,186,507, which is incorporated herein by reference in its entirety.

[0198] However, it should be noted that other nucleic acid amplification protocols (i.e., other than PCR) can also be used in the nucleic acid analysis methods described herein.For example, suitable amplification methods include ligase chain reaction (see, e.g., Wu & Wallace, Genomics 4:560-569, 1988); strand displacement assay (see, e.g., Walker et al., Proc. Natl. Acad. Sci. USA 89:392-396, 1992; U.S. Pat. No. 5,455,166); and several transcription-based amplification systems, including those described in U.S. Pat. Nos. 5,437,990, 5,409,818, and 5,399,491; transcription amplification system (TAS) (Kwoh et al., Proc. Natl. Acad. Sci. USA 86:1173-1177, 1989); and self-sustained sequence replication (3SR) (Guatelli et al. al., Proc. Natl. Acad. Sci. USA 87:1874-1878, 1990; WO 92 / 08800). Alternatively, a method of amplifying the probe to a detectable level can be used, such as Q-replicase amplification (Kramer & Lizardi, Nature 339:401-402, 1989; Lomeli et al., Clin. Chem. 35:1826-1831, 1989). A review of known amplification methods is provided, for example, by Abramson and Myers in Current Opinion in Biotechnology 4:41-47 (1993).

[0199] mRNA can be isolated from a sample. The sample can be a tissue sample. The tissue sample can be a tumor biopsy, such as a lymph node biopsy. General methods for mRNA extraction are well known in the art and are disclosed in standard texts on molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). In particular, RNA isolation can be performed using purification kits, buffer sets, and proteases from commercial manufacturers, such as Qiagen, according to the manufacturer's instructions. For example, total RNA from cultured cells can be isolated using Qiagen RNeasy mini-columns. Other commercially available RNA isolation kits include MASTERPURE® Complete DNA and RNA Purification Kit (EPICENTRE®, Madison, Wis.), and Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared from the tumor can be isolated, for example, by cesium chloride density gradient centrifugation.

[0200] In some embodiments, the first step of gene expression profiling by PCR is reverse transcription of the RNA template into cDNA, followed by its exponential amplification in a PCR reaction. In other embodiments, a multiplex reverse transcription polymerase chain reaction (RT-PCR) reaction can be used, for example, as described in U.S. Pat. Nos. 5,310,652, 5,322,770, 5,561,058, 5,641,864, and 5,693,517. Two commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is usually primed using specific primers, random hexamers, or oligo dT primers, depending on the situation and the purpose of expression profiling. For example, extracted RNA can be reverse transcribed using the GENEAMP™ RNA PCR kit (Perkin Elmer, Calif., USA) according to the manufacturer's instructions. The resulting cDNA is then used as a template for the subsequent PCR reaction.

[0201] In some embodiments, real-time reverse transcription PCR (qRT-PCR) can be used to both detect and quantify RNA targets (Bustin, et al., 2005, Clin. Sci., 109:365-379). Examples of qRT-PCR-based methods can be found, for example, in U.S. Patent No. 7,101,663, which is incorporated herein by reference in its entirety. Instruments for real-time PCR, such as the Applied Biosystems 7500, are commercially available, as are reagents such as TaqMan Sequence Detection chemistry.

[0202] For example, one can use TaqMan® Gene Expression Assays according to the manufacturer's instructions. These kits are pre-formulated gene expression assays for rapid and reliable detection and quantification of human, mouse and rat mRNA transcripts. One can use TaqMan® or the 5'-nuclease assay described in U.S. Patent Nos. 5,210,015, 5,487,972 and 5,804,375, and Holland et al., 1988, Proc. Natl. Acad. Sci. USA 88:7276-7280. TAQMAN® PCR typically utilizes the 5'-nuclease activity of Taq or Tth polymerase to hydrolyze hybridization probes bound to their target amplicons, although any enzyme with comparable 5' nuclease activity can be used. Two oligonucleotide primers are used to generate amplicons typical of a PCR reaction. A third oligonucleotide, the probe, is designed to detect the nucleotide sequence located between the two PCR primers. The probe is not extendable by Taq DNA polymerase enzyme and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye if the two dyes are located close to each other when on the probe. During the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resulting probe fragments dissociate in solution, and the signal from the released reporter dye is free of the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.

[0203] Any method suitable for detecting degradation products can be used in the 5' nuclease assay. Often, the detection probe is labeled with two fluorescent dyes, one of which can quench the fluorescence of the other dye. The dyes are attached to the probe (preferably one attached to the 5' end and the other attached to an internal site) so that quenching occurs when the probe is in an unhybridized state, and cleavage of the probe by the 5' to 3' exonuclease activity of DNA polymerase occurs between the two dyes.

[0204] Amplification results in cleavage of the probe between the dyes, which is accompanied by removal of quenching and an increase in observable fluorescence from the initially quenched dye. The accumulation of degradation products is monitored by measuring the increase in reaction fluorescence. U.S. Pat. Nos. 5,491,063 and 5,571,673, both of which are incorporated herein by reference, describe alternative methods for detecting probe degradation that occurs concomitantly with amplification. 5'-nuclease assay data can be expressed as the acronym Ct, or threshold cycle. As previously mentioned, fluorescence values ​​are recorded during every cycle and represent the amount of product amplified up to that point in the amplification reaction. The point at which the fluorescence signal is first recorded as being statistically significant is the threshold cycle (Ct).

[0205] To minimize errors and the effects of sample-to-sample variability, PCR is usually performed using an internal standard. An ideal internal standard is expressed at a consistent level among different tissues and is not affected by the experimental treatment. The RNAs most frequently used to normalize patterns of gene expression are the mRNAs of the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and P-actin.

[0206] PCR primers and probes are designed based on the intron sequences present in the gene to be amplified. In this embodiment, the first step of primer / probe design is the description of the intron sequences within the gene. This can be done by publicly available software, such as the DNA BLAST software developed by Kent, W., Genome Res. 12(4):656-64 (2002), or by the BLAST software (including its variations). Subsequent steps follow well-established methods of PCR primer and probe design.

[0207] To avoid non-specific signals, it may be important to mask repetitive sequences within introns when designing primers and probes. This can be easily accomplished by using the Repeat Masker program available online through Baylor College of Medicine, which screens DNA sequences against a library of repetitive elements and returns a query sequence with the repetitive elements masked. The masked intron sequences can then be used to design primers and probes using any commercially available or otherwise publicly available primer / probe design package, e.g., Primer Express (Applied Biosystems), MGB Assay by Design (Applied Biosystems), Primer3 (Rozen Biosystems), or other similar packages. Primer and probe sequences can be designed using Primer3 (Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386) on the WWW for general users and for biologist programmers.

[0208] RNA-Seq, also known as whole transcriptome shotgun sequencing (WTSS), refers to sequencing cDNA using high-throughput sequencing techniques to obtain information about the RNA content of a sample. Publications describing RNA-Seq include Wang et al., Nature Reviews, 2010. Genetics 10(1):57-63(January 2009), Ryan et al. BioTechniques 45(1):81-94 (2008), and Maher et al., Nature 458(7234):97-101 (January 2009), which are incorporated herein in their entireties.

[0209] Differential gene expression can also be identified or confirmed using microarray technology. In this method, polynucleotide sequences of interest (including cDNAs and oligonucleotides) are plated or arrayed on a microchip substrate. The arrayed sequences are then hybridized with specific DNA probes derived from cells or tissues of interest.

[0210] In one embodiment of the microarray technique, PCR-amplified inserts of cDNA clones are applied to a substrate in a high-density array. Preferably, at least 10,000 nucleotide sequences are applied to the substrate. The microarrayed genes immobilized on the microchip with 10,000 elements each are suitable for hybridization under stringent conditions. Fluorescently labeled cDNA probes can be made by incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. The labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array. After stringent washing to remove non-specifically bound probes, the chip is scanned by confocal laser microscopy or another detection method such as a CCD camera. Quantification of hybridization of each arrayed element allows evaluation of the corresponding mRNA abundance. In the case of dual-color fluorescence, separately labeled cDNA probes made from two RNA sources are paired and hybridized to the array. In this way, the relative abundance of the transcripts from the two sources corresponding to each specific gene is determined simultaneously. The miniaturization of hybridization scale allows easy and rapid evaluation of the expression patterns of a large number of genes.Such methods have been shown to have the required sensitivity to detect rare transcripts that are expressed at a few copies per cell, and to reproducibly detect at least about two-fold differences in expression levels (Schena et al., Proc. Natl. Acad. Sci. USA 93(2):106-149(1996)).Microarray analysis can be carried out by commercially available equipment, for example, by using Affymetrix GENCHIP™ technology, or Incyte's microarray technology, according to manufacturer's protocol.

[0211] Sequence analysis of gene expression (SAGE) is a method that allows for the simultaneous and quantitative analysis of many gene transcripts without the need to provide individual hybridization probes for each transcript. First, short sequence tags (approximately 10-14 bp) are generated that contain enough information to uniquely identify the transcripts, provided that the tags are derived from unique locations within each transcript. Many transcripts are then linked together to form long continuous molecules that can be sequenced to simultaneously reveal the identity of multiple tags. The expression pattern of any population of transcripts can be quantitatively assessed by determining the abundance of individual tags and identifying the genes that correspond to each tag. For further details, see, for example, Velculescu et al., Science 270:484-487 (1995), and Velculescu et al., Cell 88:243-51 (1997).

[0212] MassARRAY (Sequenom, San Diego, Calif.) technology is an automated high-throughput gene expression analysis method that uses mass spectrometry (MS) for detection. According to this method, after RNA isolation, reverse transcription, and PCR amplification, the cDNA is subjected to primer extension. The primer extension products obtained from the cDNA are purified and dispensed onto a chip array that is preloaded with the components required for the preparation of MALTI-TOF MS samples. The various cDNAs present in the reaction are quantified by analyzing the peak areas of the resulting mass spectrum.

[0213] mRNA levels can also be measured by hybridization-based assays. A typical mRNA assay method can include the steps of: 1) obtaining a surface-bound probe of interest; 2) hybridizing a population of mRNA to the surface-bound probe under conditions sufficient to provide specific binding; (3) performing post-hybridization washes to remove nucleic acids not bound during hybridization; and (4) detecting the hybridized mRNA. The reagents used in each of these steps and the conditions of their use can vary depending on the particular application.

[0214] Any suitable assay platform can be used to determine the mRNA level in a sample. For example, the assay can be in the form of a dipstick, a membrane, a chip, a disk, a test strip, a filter, a microsphere, a slide, a multi-well plate, or an optical fiber. The assay system can have a solid support to which the nucleic acid corresponding to the mRNA is attached. The solid support can have, for example, a plastic, a silicon, a metal, a resin, a glass, a membrane, a particle, a precipitate, a gel, a polymer, a sheet, a sphere, a polysaccharide, a capillary, a film, a plate, or a slide. The assay components can be prepared and packaged together as a kit for detecting mRNA.

[0215] Optionally, the nucleic acid can be labeled to generate a population of labeled mRNA. Generally, the sample is subjected to labeling using methods well known in the art (e.g., using DNA ligase, terminal transferase, or by labeling the RNA backbone (see, e.g., Ausubel, et al., Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons 1995). and Sambrook et al.,Molecular Cloning:A In some embodiments, the sample may be labeled with a fluorescent label. Exemplary fluorescent dyes include xanthene dyes, fluorescein dyes, rhodamine dyes, fluorescein isothiocyanate (FITC), 6 carboxyfluorescein (FAM), 6 carboxy-2',4',7',4,7-hexachlorofluorescein (HEX), 6 carboxy 4',5' dichloro 2',7' dimethoxyfluorescein (JOE or J), N,N,N',N' tetramethyl 6 carboxyrhodamine (TAMRA or T ... These include, but are not limited to, carboxy-X rhodamine (ROX or R), 5 carboxyrhodamine 6G (R6G5 or G5), 6 carboxyrhodamine 6G (R6G6 or G6) and rhodamine 110; cyanine dyes such as Cy3, Cy5 and Cy7 dyes; Alexa dyes such as Alexa-fluor-555; coumarin, diethylaminocoumarin, umbelliferone; benzimide dyes such as Hoechst 33258; phenanthridine dyes such as Texas Red; ethidium dyes; acridine dyes; carbazole dyes; phenoxazine dyes; porphyrin dyes; polymethine dyes, BODIPY dyes, quinoline dyes, pyrene, chlorotriazinyl fluorescein, R110, eosin, JOE, R6G, tetramethylrhodamine, Lissamine, ROX, naphthofluorescein and the like.

[0216] Hybridization can be carried out under suitable hybridization conditions, and these conditions can vary in terms of desired stringency.Normal conditions are sufficient to allow probe / target complex to form on solid surface between complementary binding elements, i.e., between the target probe bound to the surface and the complementary mRNA in sample.In certain embodiments, stringent hybridization conditions can be used.

[0217] Hybridization is usually carried out under stringent hybridization conditions. Standard hybridization techniques (e.g., under conditions sufficient to provide specific binding of target mRNA in a sample to a probe) are described in Kallioniemi et al., Science 258:818-821 (1992) and WO93 / 18186. Several guides to general techniques are available (e.g., Tijssen, Hybridization with Nucleic Acid Probes, Parts I and II (Elsevier, Amsterdam 1993)). For a description of techniques suitable for in situ hybridization, see Gall et al. Meth. Enzymol., 21:470-480 (1981), and Angerer et al. in Genetic Engineering: Principles and Methods (Setlow and Hollaender, Eds.) Vol 7, pgs 43-65 (Plenum Biol. 2000, 1999). Press, New York 1985). Selection of appropriate conditions, including temperature, salt concentration, polynucleotide concentration, hybridization time, stringency of washing conditions, and the like, will depend on the experimental design, including the source of the sample, the nature of the capture agent, the expected degree of complementation, and the like, and can be determined by one of skill in the art as a matter of routine experimentation. One of skill in the art will readily recognize that alternative, but comparable, hybridization and washing conditions can be used to provide conditions of similar stringency.

[0218] After the mRNA hybridization procedure, the polynucleotide bound to the surface is usually washed to remove unbound nucleic acid.Washing can be carried out using any convenient washing protocol, and the washing conditions are usually stringent as described above.Then, the hybridization of target mRNA to the probe is detected using standard techniques.

[0219] Any method described herein or otherwise known in the art can be used to determine the mRNA level of the gene in the sample from the subject described herein.For example, in some embodiments, provided herein is a method for treating AML in a subject, comprising: determining the FLT3LG mRNA level in the sample from the subject by using qRT-PCR; and when the FLT3LG mRNA level in the sample is higher than the reference expression level of FLT3LG, administering a therapeutically effective amount of FTI to the subject.

[0220] In some embodiments, the expression level of a gene may refer to the protein level of the gene. Thus, the H-Ras expression level may refer to the protein level of H-Ras in a sample. The N-Ras expression level or the K-Ras expression level may refer to the respective protein levels. The PIK3CA expression level may refer to the mRNA level of PIK3CA in a sample. The H / K ratio may refer to the ratio of the H-Ras protein level to the K-Ras protein level. The H / N ratio may refer to the ratio of the H-Ras protein level to the N-Ras protein level. The H / K+N ratio may refer to the ratio of the H-Ras protein level to the combined protein level of K-Ras and N-Ras.

[0221] Thus, in some embodiments, provided herein is a method for treating SCC in a subject, comprising administering a therapeutically effective amount of an FTI to the subject, the subject having an H-Ras protein level higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the protein level of H-Ras in the sample, and determining that the subject has an SCC that overexpresses H-Ras if the H-Ras protein level in the sample is higher than the reference level.

[0222] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib, and provided herein is a method of treating SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to the subject, wherein the subject has a H-Ras protein level higher than a reference level. In some embodiments, the method comprises analyzing a sample from the subject to measure the protein level of H-Ras in the sample, and determining that the subject has SCC that overexpresses H-Ras if the H-Ras protein level in the sample is higher than the reference level.

[0223] In some embodiments, the subject has an H-Ras protein level that is at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 12-fold, at least 15-fold, or at least 20-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 2-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 2.5-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 3-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 3.5-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 4-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 4.5-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level that is at least 5-fold higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 6 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 7 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 8 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 9 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 10 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 12 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 15 times higher than the reference level. In some embodiments, the subject has an H-Ras protein level at least 20 times higher than the reference level.In some embodiments, the reference level is the median protein level of H-Ras in a population of healthy subjects. In some embodiments, the reference level is the median protein level of H-Ras in a population of subjects with SCC.

[0224] In some embodiments of the methods provided herein, where the expression level of a gene is determined by its protein level, the SCC is a human papillomavirus (HPV) negative SCC. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is a metastatic SCC. In some embodiments, the SCC is a recurrent SCC. In some embodiments, the SCC is refractory. The SCC may be a specific type of SCC. In some embodiments, the SCC is a head and neck SCC (HNSCC). In some embodiments, the SCC is a lung SCC (LSCC). In some embodiments, the SCC is a thyroid SCC. In some embodiments, the SCC is an esophageal SCC. In some embodiments, the SCC is a bladder SCC. In some embodiments, the SCC is a urothelial carcinoma (UC).

[0225] Methods for determining the protein level of a gene in a sample are well known in the art. For example, in some embodiments, the protein level may be determined by immunohistochemistry (IHC) assay, immunoblotting (IB) assay, immunofluorescence (IF) assay, flow cytometry (FACS), or enzyme-linked immunosorbent assay (ELISA). In some embodiments, the protein level may be determined by hematoxylin and eosin staining ("H&E staining").

[0226] Protein levels of genes can be detected by various (IHC) approaches or other immunoassay methods. IHC staining of tissue sections has been shown to be a reliable method of assessing or detecting the presence of proteins in a sample. Immunohistochemistry techniques utilize antibodies to probe and visualize cellular antigens in situ, typically by chromogenic or fluorescent methods. Thus, expression is detected using, for example, antibodies or antisera, including polyclonal antisera, or monoclonal antibodies specific for each gene. As discussed in more detail below, antibodies can be detected by directly labeling the antibody itself, for example, with a radioactive label, a fluorescent label, a hapten label such as biotin, or an enzyme such as horseradish peroxidase or alkaline phosphatase. Alternatively, unlabeled primary antibodies are used in combination with labeled secondary antibodies, including antisera, polyclonal antisera, or monoclonal antibodies specific for the primary antibodies. Immunohistochemistry protocols and kits are well known in the art and are commercially available. Automated systems for slide preparation and IHC processing are commercially available. The Ventana® BenchMark XT system is an example of such an automated system.

[0227] Standard immunological and immunoassay procedures can be found in Basic and Clinical Immunology (Stites & Terr eds., 7th ed. 1991). In addition, immunoassays can be performed in any of several configurations, which are extensively reviewed in Enzyme Immunoassay (Maggio, ed., 1980), and Harlow & Lane, supra. For general immunoassay reviews, see also Methods in Cell Biology: Antibodies in Cell Biology, volume 37 (Asai, ed. 1993), Basic and Clinical Immunology (Stites & Ten, eds., 7th ed. 1991).

[0228] Commonly used assays for detecting the protein level of a gene include non-competitive assays, such as sandwich assays, and competitive assays. Typically, assays such as ELISA assays can be used. For example, ELISA assays are known in the art for assaying a wide variety of tissues and samples, including blood, plasma, serum, tumor biopsy, lymph node, or bone marrow. In some embodiments, the sample is a bone marrow biopsy. In some embodiments, the sample is a bone marrow aspirate. In some embodiments, the sample can be a cerebrospinal fluid sample, a liver sample, a testis sample, a spleen sample, or a lymph node sample. In some embodiments, the sample is an isolated cell.

[0229] A wide range of immunoassay techniques using such assay formats are available, see for example U.S. Patent Nos. 4,016,043, 4,424,279, and 4,018,653, which are incorporated herein by reference in their entirety. These include both non-competitive single-site and two-site or "sandwich" assays, as well as traditional competitive binding assays. These assays also include direct binding of labeled antibodies to target genes. Sandwich assays are commonly used assays. There are many variations of sandwich assay techniques. For example, in a typical forward assay, an unlabeled antibody is immobilized on a solid substrate and the sample to be tested is contacted with the bound molecule. After a suitable incubation period for a time sufficient to allow for the formation of an antibody-antigen complex, a second antibody specific for the antigen, labeled with a reporter molecule capable of generating a detectable signal, is then added and incubated for a time sufficient for the formation of another antibody-antigen-labeled antibody complex. Any unreacted material is washed away, and the presence of the antigen is determined by observing the signal generated by the reporter molecule. The results may be either qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control sample containing known amounts of gene.

[0230] Variations of the forward assay include simultaneous assays, in which both the sample and the labeled antibody are added simultaneously to the bound antibody. These techniques are well known to those of skill in the art, and include minor variations that will be readily apparent. In a typical forward sandwich assay, a first antibody with specificity for a gene is bound to a solid surface, either covalently or passively. The solid surface may be glass or polymeric, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride, or polypropylene. The solid support may be in the form of a tube, a bead, a disk of a microplate, or any other surface suitable for performing an immunoassay. The binding process is well known in the art and generally consists of cross-linking, covalent binding, or physical adsorption, and the polymer-antibody complex is washed in preparation for the test sample. An aliquot of the sample to be tested is then added to the solid phase complex and incubated for a period of time sufficient to allow binding of any subunits present in the antibody (e.g., 2-40 minutes, or more conveniently, overnight) and under suitable conditions (e.g., room temperature to 40°C, e.g., 25°C to 32°C, inclusive). After the incubation period, the antibody subunit solid phase is washed, dried, and incubated with a second antibody specific for a portion of the gene. The second antibody is linked to a reporter molecule that is used to indicate binding of the second antibody to the molecular marker.

[0231] An alternative method involves immobilizing the target gene in the sample and then exposing the immobilized target to a specific antibody, which may or may not be labeled with a reporter molecule. Depending on the amount of target and the strength of the reporter molecule signal, the bound target may be detectable by direct labeling with the antibody. Alternatively, a second labeled antibody specific to the first antibody is exposed to the target-first antibody complex, forming a ternary complex of target-first antibody-second antibody. This complex is detected by the signal emitted by the labeled reporter molecule.

[0232] In the case of enzyme immunoassays, the enzyme is generally conjugated to the second antibody by glutaraldehyde or periodate. However, as will be readily recognized, there are a wide variety of different conjugation techniques that are readily available to those skilled in the art. Commonly used enzymes include horseradish peroxidase, glucose oxidase, beta-galactosidase, and alkaline phosphatase, and others are discussed herein. Substrates used with a particular enzyme are generally selected for the production of a detectable color change upon hydrolysis by the corresponding enzyme. Examples of suitable enzymes include alkaline phosphatase and peroxidase. It is also possible to use fluorogenic substrates that yield fluorescent products rather than the chromogenic substrates mentioned above. In all cases, the enzyme-labeled antibody is added to the first antibody-molecular marker complex and allowed to bind, after which excess reagent is washed away. A solution containing the appropriate substrate is then added to the antibody-antigen-antibody complex. The substrate reacts with the enzyme bound to the second antibody to produce a qualitative visual signal that can be further quantified, usually spectrophotometrically, to indicate the amount of gene that was present in the sample. Alternatively, fluorescent compounds such as fluorescein and rhodamine can be chemically coupled to the antibody without altering its binding ability. When activated by irradiation with light of a particular wavelength, the fluorochrome-labeled antibody absorbs the light energy and induces an excitable state in the molecule, followed by the emission of light of a characteristic color that is visually detectable by light microscopy. As in EIA, the fluorescently labeled antibody is bound to the first antibody-molecular marker complex. After washing away the unbound reagent, the remaining ternary complex is then exposed to light of the appropriate wavelength, and the observed fluorescence indicates the presence of the molecular marker of interest. Both immunofluorescence and EIA techniques are very well established in the art and are discussed herein.

[0233] Any method described herein or otherwise known in the art can be used to determine the protein level of genes in a sample from a subject described herein.For example, in some embodiments, provided herein is a method for treating HNSCC in a subject, comprising: determining the protein level of H-Ras in a sample from a subject by using IF assay; and when the protein level of H-Ras in the sample is higher than the reference level of H-Ras protein, administering a therapeutically effective amount of tipifarnib to the subject.

[0234] Any method for analyzing expression levels (e.g., protein levels or mRNA levels) described herein or otherwise known in the art can be used to determine the levels of additional genes in the sample, such as an IHC assay, an IB assay, an IF assay, FACS, ELISA, protein microarray analysis, qPCR, qRT-PCR, RNA-seq, RNA microarray analysis, SAGE, MassARRAY technology, next generation sequencing, or FISH.

[0235] In some embodiments, provided herein is a method for treating SCC in a subject, comprising administering a therapeutically effective amount of FTI to the subject, the subject carrying an H-Ras gene mutation. In some embodiments, the H-Ras gene mutation leads to the activation of the corresponding H-Ras protein. In some embodiments, the H-Ras gene mutation leads to a change in the amino acid sequence of the H-Ras protein, which leads to the activation of the H-Ras protein. In some embodiments, the method comprises analyzing a sample from the subject to determine the H-Ras mutation status of the subject.

[0236] The FTI can be any FTI, including those described herein. For example, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. In some embodiments, the FTI is tipifarnib, and provided herein is a method of treating SCC in a subject, comprising administering a therapeutically effective amount of tipifarnib to a subject, the subject carrying an H-Ras gene mutation. In some embodiments, the H-Ras gene mutation results in activation of the corresponding H-Ras protein. In some embodiments, the H-Ras gene mutation results in a change in the amino acid sequence of the H-Ras protein, the change resulting in activation of the H-Ras protein. In some embodiments, the method includes analyzing a sample from the subject to determine the H-Ras mutation status of the subject.

[0237] In some embodiments of the methods provided herein, in which the subject harbors an H-Ras gene mutation, the SCC is a human papillomavirus (HPV) negative SCC. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is a metastatic SCC. In some embodiments, the SCC is a recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC. In some embodiments, the SCC is a head and neck SCC (HNSCC). In some embodiments, the SCC is a lung SCC (LSCC). In some embodiments, the SCC is a thyroid SCC. In some embodiments, the SCC is an esophageal SCC. In some embodiments, the SCC is a bladder SCC. In some embodiments, the SCC is a urothelial carcinoma (UC).

[0238] The methods provided herein can also be used with other patient stratification approaches to further increase the response rate of a patient population to FTI treatment. For example, in some embodiments, the methods provided herein further include determining the mutation status of H-Ras and selecting the subject for FTI treatment if the subject carries an H-Ras mutation. As used herein, the term "H-Ras mutation" refers to an activating mutation in the HRAS gene or H-Ras protein. H-Ras mutation can refer to either a genetic change in the DNA sequence of the HRAS gene that results in the activation of the corresponding H-Ras protein, or a change in the amino acid sequence of the H-Ras protein that results in the activation of the H-Ras protein. Thus, as used herein, the term "H-Ras mutation" does not include a change in the HRAS gene that does not result in the activation of the H-Ras protein, or a change in the H-Ras protein sequence that does not induce its activation. Thus, a sample or subject that does not have any "H-Ras mutation" as used herein may still have a mutation in the HRAS gene that does not affect the activity of the H-Ras protein or a mutation that impairs the activity of the H-Ras protein, or may have a mutation in the H-Ras protein that does not affect the activity of the H-Ras protein or a mutation that impairs its activity. A sample or subject may have multiple copies of the HRAS gene. A sample or subject may also have both wild-type and mutant H-Ras proteins. As used herein, a sample or subject that has an H-Ras mutation may also have copies of the wild-type HRAS gene and / or wild-type H-Ras protein. As used herein, a sample or subject that is determined to have "wild-type H-Ras" refers to a sample or subject that has only wild-type HRAS gene and wild-type H-Ras protein, and does not have an H-Ras mutation.In some embodiments, the mutant HRAS gene encodes a mutant H-Ras protein, and the HRAS gene mutation is or includes a modification in a codon that encodes an amino acid substitution at a specific position selected from the group consisting of G12, G13, Q61, Q22, K117, A146, and any combination thereof, of the corresponding mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that encodes an amino acid substitution at the G12 position of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is in a codon that encodes a G12R substitution of the mutant H-Ras protein. The HRAS gene mutation can be a mutation in a codon that encodes a G12C, G12D, G12A, G12V, G12S, G12F, G12R, or G12N substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that encodes a G12V substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for an amino acid substitution at the G13 position of the mutant H-Ras protein. The HRAS gene mutation can be a mutation in a codon that codes for a G13A, G13C, G13V, G13D, G13R, G13S, or G13N substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for a G13C substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for a G13R substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for an amino acid substitution at the Q61 position of the mutant H-Ras protein. The HRAS gene mutation can be a mutation in a codon that codes for a Q61E, Q61K, Q61H, Q61L, Q61P, or Q61R substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for a Q61L substitution in a mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for a Q61R substitution in a mutant H-Ras protein.In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for an amino acid substitution at the Q22 position of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for a Q22K substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for an amino acid substitution at the K117 position of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for a K117N or K117L substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for an amino acid substitution at the A146 position of the mutant H-Ras protein. The HRAS gene mutation can be a mutation in a codon that codes for an A146V or A146P substitution of the mutant H-Ras protein. In some embodiments, the HRAS gene mutation is a mutation in a codon that codes for an A146P substitution of the mutant H-Ras protein. In some embodiments, the mutation can be a mutation in another codon that results in activation of the H-Ras protein.

[0239] Methods for determining mutation status are well known in the art. In some embodiments, the methods include sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high performance liquid chromatography (DHPLC), or restriction fragment length polymorphism (RFLP) assay. In some embodiments, the mutation status of the HRAS gene is determined using standard sequencing methods, including, for example, Sanger sequencing, next generation sequencing (NGS). In some embodiments, the mutation status of the HRAS gene can be determined by an NGS-based assay. In some embodiments, the mutation status of the HRAS gene can be determined by a qualitative PCR-based assay. In some embodiments, the SNV and / or mutation status is determined using MS. In some embodiments, the HRAS mutation status is determined by analyzing proteins obtained from the sample. Mutated Ras H protein can be detected by various immunohistochemistry (IHC) approaches, immunoblotting assays, enzyme-linked immunosorbent assays (ELISA), or other immunoassay methods known in the art.

[0240] As one of skill in the art will appreciate, any method for analyzing Ras mutations described herein or otherwise known in the art can be used to determine the presence or absence of an H-Ras mutation.

[0241] B. Pharmaceutical Compositions In some embodiments, provided herein is a method of treating a subject with an FTI or a pharmaceutical composition having an FTI. Provided herein is a pharmaceutical composition containing a therapeutically effective amount of an FTI and a pharma- ceutical acceptable carrier, diluent or excipient. In some embodiments, the FTI is tipifarnib, lonafarnib (also known as SCH-66336), aruglavin, perillyl alcohol, CP-609,754, BMS214662, L778123, L744832, L739749, R208176, AZD3409, or FTI-277. In some embodiments, the FTI is tipifarnib.

[0242] FTI can be formulated into suitable pharmaceutical preparations, such as solutions, suspensions, tablets, dispersible tablets, pills, capsules, powders, sustained release preparations or elixirs for oral administration, or sterile solutions or suspensions for ophthalmic or parenteral administration, as well as transdermal patch preparations and dry powder inhalants.Generally, FTI is formulated into pharmaceutical compositions using techniques and procedures well known in the art (see, for example, Ansel Introduction to Pharmaceutical Dosage Forms, Seventh Edition 1999).

[0243] In the composition, an effective concentration of the FTI and pharma- ceutically acceptable salts are mixed with a suitable pharmaceutical carrier or vehicle. In certain embodiments, the concentration of the FTI in the composition is effective to deliver an amount that, when administered, treats, prevents, or ameliorates one or more of the symptoms and / or progression of cancer, including hematological cancers and solid tumors.

[0244] Composition can be formulated for administration of a single dosage.To formulate composition, weight fraction of FTI is dissolved, suspended, dispersed or otherwise mixed in selected vehicle at effective concentration so that the treated condition is relieved or improved.The pharmaceutical carrier or vehicle suitable for administration of FTI provided herein includes any such carrier known to those skilled in the art to be suitable for specific administration mode.

[0245] Furthermore, FTIs can be formulated as the only pharmacoactive ingredient in the composition or can be combined with other active ingredients. Liposomal suspensions, including tissue-targeted liposomes, such as tumor-targeted liposomes, can also be suitable as pharmaceutically acceptable carriers. They can be prepared according to methods known to those skilled in the art. For example, liposomal formulations can be prepared as known in the art. Briefly, liposomes, such as multilamellar vesicles (MLVs), can be formed by drying egg phosphatidylcholine and brain phosphatidylserine (7:3 molar ratio) on the inside of a flask. A solution of FTIs provided herein in phosphate buffered saline (PBS) lacking divalent cations is added, and the flask is shaken until the lipid film is dispersed. The resulting vesicles are washed to remove unencapsulated compound, pelleted by centrifugation, and then resuspended in PBS.

[0246] The FTI is included in a pharma- ceutically acceptable carrier in an amount sufficient to exert a therapeutically useful effect without undesirable side effects on the patient being treated. Therapeutically effective concentrations can be empirically determined by testing the compounds in the in vitro and in vivo systems described herein, and then human dosages can be extrapolated therefrom.

[0247] The concentration of the FTI in the pharmaceutical composition depends on the absorption, tissue distribution, inactivation, and excretion rates of the FTI, the physicochemical properties of the FTI, the dosing schedule, and the amount administered, as well as other factors known to those skilled in the art. For example, the amount delivered is sufficient to ameliorate one or more symptoms of cancer, including hematopoietic cancers and solid tumors.

[0248] In certain embodiments, a therapeutically effective dosage should produce a serum concentration of the active ingredient of about 0.1 ng / ml to about 50-100 μg / ml. In one embodiment, the pharmaceutical composition provides a dosage of about 0.001 mg to about 2000 mg of the compound per kilogram of body weight per day. Pharmaceutical dosage unit forms are prepared to provide about 1 mg to about 1000 mg, and in certain embodiments, about 10 to about 500 mg of the essential active ingredient or combination of essential ingredients per dosage unit form.

[0249] The FTI may be administered once, or may be divided into several smaller doses administered at intervals of time. The exact dosage and duration of treatment will depend on the disease being treated and may be determined using known testing protocols or in vivo or in vivo. It is understood that concentration and dosage value can be experimentally determined by extrapolation from in vitro test data.It should be noted that concentration and dosage value can also vary according to the severity of the condition to be alleviated.It should be further understood that for any specific subject, specific dosage regimen should be adjusted over time according to individual need and the professional judgment of the person who manages or supervises administration of composition, and that the concentration ranges shown herein are merely exemplary and are not intended to limit the scope or practice of the claimed composition.

[0250] Thus, one or more of the compounds described herein or their pharma- ceutically acceptable salts are mixed with a pharmaceutical carrier or vehicle suitable for systemic, local, or topical administration to form a pharmaceutical composition at an effective concentration or amount.The compound is included in an amount effective for improving, treating, delaying, or preventing one or more symptoms.The concentration of the active compound in the composition depends on the absorption, tissue distribution, inactivation, and excretion rate of the active compound, dosage schedule, amount administered, specific formulation, and other factors known to those skilled in the art.

[0251] The compositions are intended to be administered by a suitable route, including but not limited to oral, parenteral, rectal, topical, and local. For oral administration, capsules and tablets can be formulated. The compositions are in liquid, semi-liquid, or solid form and are formulated in a manner suitable for each administration route.

[0252] Solutions or suspensions used for parenteral, intradermal, subcutaneous, or topical use can contain the following components: sterile diluents, such as water for injection, saline solution, non-volatile oils, polyethylene glycol, glycerin, propylene glycol, dimethylacetamide, or other synthetic solvents; antibacterial agents, such as benzyl alcohol and methylparaben; antioxidants, such as ascorbic acid and sodium bisulfite; chelating agents, such as ethylenediaminetetraacetic acid (EDTA); buffers, such as acetates, citrates, and phosphates; and agents for adjusting tonicity, such as sodium chloride or dextrose. Parenteral preparations can be enclosed in ampoules, pens, disposable syringes, or single or multiple dose vials made of glass, plastic, or other suitable materials.

[0253] When FTI shows insufficient solubility, methods can be used to dissolve the compound.Such methods are known to those skilled in the art and include, but are not limited to, using cosolvents such as dimethylsulfoxide (DMSO), using surfactants such as TWEEN®, or dissolving in aqueous sodium bicarbonate.

[0254] Upon mixing or addition of the compound(s), the resulting mixture may be a solution, suspension, emulsion, etc. The form of the resulting mixture depends on several factors, including the intended mode of administration and the solubility of the compound in the selected carrier or vehicle. The effective concentration is sufficient to ameliorate the symptoms of the disease, disorder, or condition being treated and can be empirically determined.

[0255] Pharmaceutical compositions are provided for administration to humans and animals in unit dosage forms, such as tablets, capsules, pills, powders, granules, sterile parenteral solutions or suspensions, and oral solutions or suspensions, as well as oil-water emulsions, containing a suitable amount of the compound or its pharma- ceutically acceptable salts. Pharmaceutically, therapeutically active compounds and their salts are formulated and administered in unit dosage forms or multiple dosage forms. Unit dosage forms, as used herein, refer to physically separate units suitable for human and animal subjects and individually packaged as known in the art. Each unit dosage contains a predetermined amount of therapeutically active compound sufficient to produce the desired therapeutic effect, in association with the required pharmaceutical carrier, vehicle, or diluent. Examples of unit dosage forms include ampoules and syringes and individually packaged tablets or capsules. Unit dosage forms can be administered in fractions or multiples thereof. Multiple dosage forms are a plurality of identical unit dosage forms packaged in a single container to be administered in separate unit dosage forms. Examples of multiple dose forms include vials, bottles of tablets or capsules, or bottles of pints or gallons. Thus, a multiple dose form is a multiple of unit doses that are not segregated in packaging.

[0256] Sustained release preparations can also be prepared. Suitable examples of sustained release preparations include semipermeable matrices of solid hydrophobic polymers containing the compounds provided herein, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained release matrices include iontophoretic patches, polyesters, hydrogels (e.g., poly(2-hydroxyethyl-methacrylate) or poly(vinyl alcohol)), polylactides, copolymers of L-glutamic acid and ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as LUPRON DEPOT™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid allow the release of molecules for over 100 days, certain hydrogels release proteins for shorter periods of time. If the encapsulated compounds remain in the body for a long period of time, they may denature or aggregate as a result of exposure to moisture at 37°C, resulting in loss of biological activity and possible changes in their structure. Depending on the mechanism of action involved, rational strategies for stabilization can be taken. For example, if the aggregation mechanism is found to be intermolecular S--S bond formation via thio-disulfide exchange, stabilization can be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling the moisture content, using appropriate additives, and developing specific polymer matrix compositions.

[0257] Dosage forms or compositions can be prepared containing active ingredient in the range of 0.005%-100%, with the remainder consisting of non-toxic carriers. For oral administration, pharma- ceutically acceptable non-toxic compositions are formed by incorporation of any of the commonly used excipients, such as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, talcum, cellulose derivatives, croscarmellose sodium, glucose, sucrose, magnesium carbonate, or sodium saccharin. Such compositions include solutions, suspensions, tablets, capsules, powders, and sustained release formulations, including, but not limited to, implants and microencapsulated delivery systems, as well as biodegradable, biocompatible polymers, such as collagen, ethylene vinyl acetate, polyanhydrides, polyglycolic acid, polyorthoesters, polylactic acid, and the like. Methods for preparing these compositions are known to those skilled in the art. Contemplated compositions may contain about 0.001%-100%, and in certain embodiments, about 0.1-85% or about 75-95%, of the active ingredient.

[0258] The FTIs or pharma- ceutically acceptable salts may be prepared with carriers that protect the compound against rapid elimination from the body, such as time release formulations or coatings.

[0259] The composition may contain other active compounds to obtain a desired combination of properties. The compounds provided herein, or their pharma- ceutically acceptable salts as described herein, may also be administered with other pharmacological agents known in the general art to be useful in treating one or more of the above-mentioned diseases or conditions, such as diseases associated with oxidative stress.

[0260] The lactose-free compositions provided herein may contain excipients that are well known in the art and are described, for example, in the United States Pharmacopoeia (USP) SP(XXI) / NF(XVI).In general, lactose-free compositions contain active ingredients, binders / fillers, and lubricants in pharma- ceutically compatible and pharma-ceutically acceptable amounts.An exemplary lactose-free dosage form contains active ingredients, microcrystalline cellulose, pregelatinized starch, and magnesium stearate.

[0261] Further included are anhydrous pharmaceutical compositions and dosage forms that contain the compounds provided herein.For example, the addition of water (e.g., 5%) is widely accepted in the pharmaceutical field as a means of simulating long-term storage to determine properties such as shelf life or the stability of formulations over time.See, for example, Jens T. Carstensen, Drug Stability: Principles & Practice, 2d.Ed., Marcel Dekker, NY, NY, 1995, pp.379-80.In fact, water and heat accelerate the decomposition of some compounds.Therefore, the effect of water on formulations can be very significant, since they are often exposed to moisture and / or humidity during the manufacture, handling, packaging, storage, transportation, and use of formulations.

[0262] Anhydrous pharmaceutical compositions and dosage forms provided herein can be prepared using anhydrous or low moisture containing ingredients and low moisture or low humidity conditions. Pharmaceutical compositions and dosage forms that contain at least one active ingredient that comprises lactose and a primary or secondary amine are anhydrous if substantial contact with moisture and / or humidity is expected during manufacturing, packaging, and / or storage.

[0263] Anhydrous pharmaceutical composition should be prepared and stored so that its anhydrous nature is maintained.Therefore, anhydrous composition is packaged using a material known to prevent exposure to water so that it can be included in a suitable formulary kit.Examples of suitable packaging include, but are not limited to, hermetically sealed foils, plastics, unit dose containers (e.g., vials), blister packs, and strip packs.

[0264] Oral pharmaceutical dosage forms are either solid, gel, or liquid.Solid dosage forms are tablets, capsules, granules, and bulk powders.Types of oral tablets include compressed chewable lozenges and compressed chewable tablets, which may be enteric coated, sugar coated, or film coated.Capsules may be hard or soft gelatin capsules, while granules and powders may be provided in non-effervescent or effervescent form in combination with other ingredients known to those skilled in the art.

[0265] In certain embodiments, the formulation is a solid dosage form, such as a capsule or tablet. Tablets, pills, capsules, lozenges, etc. may contain any of the following ingredients: binders, diluents, disintegrants, lubricants, glidants, sweeteners, and flavoring agents, or compounds of a similar nature.

[0266] Examples of binders include microcrystalline cellulose, tragacanth gum, glucose solution, acacia mucilage, gelatin solution, sucrose, and starch paste. Lubricants include talc, starch, magnesium or calcium stearate, lycopodium, and stearic acid. Diluents include, for example, lactose, sucrose, starch, kaolin, salt, mannitol, and dicalcium phosphate. Glidants include, but are not limited to, colloidal silicon dioxide. Disintegrants include, for example, croscarmellose sodium, sodium starch glycolate, alginic acid, corn starch, potato starch, bentonite, methylcellulose, agar, and carboxymethylcellulose. Coloring agents include, for example, any of the approved certified water-soluble FD and C dyes, mixtures thereof; and water-insoluble FD and C dyes suspended on alumina hydrate. Sweeteners include sucrose, lactose, mannitol, and artificial sweeteners such as saccharin, and any number of spray-dried flavors.Flavors include natural flavors extracted from plants, such as fruits, and synthetic blends of compounds that produce a pleasant sensation, such as, but not limited to, peppermint and methyl salicylate.Wetting agents include propylene glycol monostearate, sorbitan monooleate, diethylene glycol monolaurate, and polyoxyethylene lauryl ether.Emetic coating agents include fatty acids, fats, waxes, shellac, ammoniated shellac, and cellulose acetate phthalate.Film coating agents include hydroxyethylcellulose, sodium carboxymethylcellulose, polyethylene glycol 4000, and cellulose acetate phthalate.

[0267] When the dosage unit form is a capsule, it may contain liquid carriers such as fatty oils in addition to the above-mentioned types of materials.Furthermore, the dosage unit form may contain various other materials that modify the physical form of the dosage unit, such as sugar and other enteric coatings.The compound may also be administered as a component of elixirs, suspensions, syrups, wafers, sprinkles, chewing gums, etc.Syrups may contain sucrose as a sweetener, as well as certain preservatives, dyes and colorings, and flavorings in addition to the active compound.

[0268] The pharma- ceutically acceptable carriers contained in the tablet are binders, lubricants, diluents, disintegrants, colorants, flavoring agents, and wetting agents. Enteric-coated tablets resist the action of stomach acid by the enteric coating and dissolve or disintegrate in neutral or alkaline intestines. Sugar-coated tablets are compressed tablets coated with various layers of pharma- ceutical acceptable materials. Film-coated tablets are compressed tablets coated with polymers or other suitable coatings. Multiple compressed tablets are compressed tablets produced by multiple compression cycles using the pharma- ceutical acceptable materials mentioned above. Coloring agents can also be used in the above dosage forms. Flavoring and sweetening agents are used in compressed tablets, sugar-coated tablets, multiple compressed tablets, and chewable tablets. Flavoring and sweetening agents are particularly useful in the formation of chewable tablets and lozenges.

[0269] Liquid oral dosage forms include aqueous solutions, emulsions, suspensions, solutions and / or suspensions reconstituted from non-effervescent granules, and effervescent preparations reconstituted from effervescent granules.Aqueous solutions include, for example, elixirs and syrups.Emulsions are either oil-in-water or water-in-oil.

[0270] Elixirs are clear, sweet, hydroalcoholic preparations. Pharmaceutically acceptable carriers used in elixirs include solvents. Syrups are concentrated aqueous solutions of a sugar, such as sucrose, and may contain preservatives. Emulsions are two-phase systems in which one liquid is dispersed in the form of small globules throughout the other liquid. Pharmaceutically acceptable carriers used in emulsions are non-aqueous liquids, emulsifying agents, and preservatives. In suspensions, pharma- ceutically acceptable suspending agents and preservatives are used. Pharmaceutically acceptable substances used in non-effervescent granules, to be reconstituted into liquid oral dosage forms, include diluents, sweeteners, and wetting agents. Pharmaceutically acceptable substances used in effervescent granules, to be reconstituted into liquid oral dosage forms, include organic acids and a source of carbon dioxide. Coloring and flavoring agents are used in all of the above dosage forms.

[0271] Solvents include glycerin, sorbitol, ethyl alcohol, and syrup. Examples of preservatives include glycerin, methyl and propyl parabens, benzoic add, sodium benzoate, and alcohol. Examples of non-aqueous liquids utilized in emulsions include mineral oil and cottonseed oil. Examples of emulsifying agents include gelatin, gum arabic, gum tragacanth, bentonite, and surfactants such as polyoxyethylene sorbitan monooleate. Suspending agents include sodium carboxymethylcellulose, pectin, gum tragacanth, veegum, and gum arabic. Diluents include lactose and sucrose. Sweetening agents include sucrose, syrup, glycerin, and artificial sweetening agents such as saccharin. Wetting agents include propylene glycol monostearate, sorbitan monooleate, diethylene glycol monolaurate, and polyoxyethylene lauryl ether. Organic adds include citric acid and tartaric acid. Carbon dioxide sources include sodium bicarbonate and sodium carbonate. Coloring agents include any of the approved certified water soluble FD and C dyes, and mixtures thereof. Flavoring agents include natural flavors extracted from plants, e.g., fruits, and synthetic blends of compounds that produce a pleasant taste sensation.

[0272] For solid dosage forms, solutions and suspensions in, for example, propylene carbonate, vegetable oils, or triglycerides are encapsulated in a gelatin capsule. Such solutions and their preparation and encapsulation are disclosed in U.S. Patent Nos. 4,328,245, 4,409,239, and 4,410,545. For liquid dosage forms, solutions in, for example, polyethylene glycols can be diluted with a sufficient quantity of a pharma- ceutically acceptable liquid carrier, for example, water, to be easily measured for administration.

[0273] Alternatively, liquid or semi-solid oral formulations can be prepared by dissolving or dispersing the active compound or salt in vegetable oils, glycols, triglycerides, propylene glycol esters (e.g., propylene carbonate), and other such carriers, and encapsulating these solutions or suspensions in hard or soft gelatin capsule shells. Other useful formulations include those comprising a compound provided herein and a dialkylated mono- or polyalkylene glycol, including, but not limited to, 1,2-dimethoxymethane, diglyme, triglyme, tetraglyme, polyethylene glycol-350-dimethyl ether, polyethylene glycol-550-dimethyl ether, polyethylene glycol-750-dimethyl ether (where 350, 550, and 750 refer to the approximate average molecular weight of the polyethylene glycol), and one or more antioxidants, such as butylated hydroxytoluene (BHT), butylated hydroxyanisole (BHA), propyl gallate, vitamin E, hydroquinone, hydroxycoumarin, ethanolamine, lecithin, cephalin, ascorbic acid, malic acid, sorbitol, phosphoric acid, thiodipropionic acid and its esters, and dithiocarbamates.

[0274] Other formulations include, but are not limited to, aqueous alcohol solutions containing pharmaceutically acceptable acetals.The alcohols used in these formulations are any pharmaceutically acceptable water-miscible solvents with one or more hydroxyl groups, including, but not limited to, propylene glycol and ethanol.Acetals include, but are not limited to, di(lower alkyl) acetals of lower alkyl aldehydes, such as acetaldehyde diethyl acetal.

[0275] In all embodiments, tablet and capsule formulations may be coated as known to those skilled in the art to modify or sustain dissolution of the active ingredient. Thus, for example, they may be coated with conventional enteric coatings such as phenylsalicylate, waxes, and cellulose acetate phthalate.

[0276] Parenteral administration, generally characterized by injection either subcutaneously, intramuscularly, or intravenously, is also provided herein. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for dissolving or suspending in liquid before injection, or as emulsions. Suitable excipients are, for example, water, saline, dextrose, glycerol, or ethanol. In addition, if desired, the pharmaceutical composition to be administered can also contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, pH buffers, stabilizers, solubility enhancers, and other such agents, such as, for example, sodium acetate, sorbitan monolaurate, triethanolamine oleate, and cyclodextrins. Implantation of a slow-release or sustained-release system, such that a constant level of dosage is maintained, is also contemplated herein. Briefly, the compounds provided herein are dispersed in a solid internal matrix, such as polymethyl methacrylate, polybutyl methacrylate, plasticized or unplasticized polyvinyl chloride, plasticized nylon, plasticized polyethylene terephthalate, natural rubber, polyisoprene, polyisobutylene, polybutadiene, polyethylene, ethylene-vinyl acetate copolymers, silicone rubber, polydimethylsiloxane, silicone carbonate copolymers, hydrophilic polymers (e.g., hydrogels of esters of acrylic and methacrylic acid), collagen, cross-linked polyvinyl alcohol, and partially hydrolyzed cross-linked polyvinyl acetate, and the solid internal matrix is ​​then immersed in the hydrophilic polymer. The trix is ​​surrounded by an outer polymeric membrane that is insoluble in body fluids, such as polyethylene, polypropylene, ethylene / propylene copolymers, ethylene / ethyl acrylate copolymers, ethylene / vinyl acetate copolymers, silicone rubber, polydimethylsiloxane, neoprene rubber, chlorinated polyethylene, polyvinyl chloride, vinyl acetate, vinylidene chloride, ethylene and propylene copolymers, ionomeric polyethylene terephthalate, butyl rubber epichlorohydrin rubber, ethylene / vinyl alcohol copolymers, ethylene / vinyl acetate / vinyl alcohol terpolymers, and ethylene / vinyloxyethanol copolymers. The compound diffuses through the outer polymeric membrane in a release rate controlling step.The percentage of active compound contained in such parenteral compositions highly depends on the specific nature thereof, as well as the activity of the compound and the needs of the subject.

[0277] Parenteral administration of the composition includes intravenous administration, subcutaneous administration and intramuscular administration.Preparation for parenteral administration includes sterile liquid ready for injection, sterile dry soluble product ready for mixing with solvent immediately before use, such as freeze-dried powder, including subcutaneous tablet, sterile suspension ready for injection, sterile dry insoluble product ready for mixing with vehicle immediately before use, and sterile emulsion.Liquid can be either aqueous or non-aqueous.

[0278] If administered intravenously, suitable carriers include saline or phosphate buffered saline (PBS), as well as solutions containing thickening and solubilizing agents, such as glucose, polyethylene glycol, and polypropylene glycol, and mixtures thereof.

[0279] Pharmaceutically acceptable carriers used in parenteral preparations include aqueous vehicles, non-aqueous vehicles, antibacterial agents, isotonic agents, buffers, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents, and other pharma- ceutically acceptable substances.

[0280] Examples of aqueous vehicles include sodium chloride injection, Ringer's injection, isotonic dextrose injection, sterile water injection, dextrose, and lactated Ringer's injection. Non-aqueous parenteral vehicles include fixed oils of vegetable origin, cottonseed oil, corn oil, sesame oil, and peanut oil. Antibacterial agents in bacteriostatic or fungistatic concentrations must be added to parenteral preparations packaged in multi-dose containers, and include phenols or cresols, mercurials, benzyl alcohol, chlorobutanol, p-hydroxybenzoic acid methyl ester and p-hydroxybenzoic acid propyl ester, thimerosal, benzalkonium chloride, and benzethonium chloride. Isotonic agents include sodium chloride and dextrose. Buffers include phosphates and citrates. Antioxidants include sodium bisulfate. Local anesthetics include procaine hydrochloride. Suspending and dispersing agents include sodium carboxymethylcellulose, hydroxypropyl methylcellulose, and polyvinylpyrrolidone. Emulsifying agents include polysorbate 80 (TWEEN® 80). Sequestering or chelating agents for metal ions include EDTA. Pharmaceutical carriers also include ethyl alcohol, polyethylene glycol, and propylene glycol for water-miscible vehicles, and sodium hydroxide, hydrochloric acid, citric acid, or lactic acid for pH adjustment.

[0281] The concentration of FTI is adjusted so that injection provides an effective amount to produce the desired pharmacological effect.As is known in the art, the exact dose depends on the age, weight, and condition of the patient or animal.Unit-dose parenteral preparations are filled into ampoules, vials, or syringes with needles.All preparations for parenteral administration must be sterile, as is known and practiced in the art.

[0282] Illustratively, intravenous or intraarterial infusion of a sterile aqueous solution containing an FTI is an effective mode of administration. Another embodiment is a sterile aqueous or oily solution or suspension containing an active material injected as necessary to produce the desired pharmacological effect.

[0283] Injectables are designed for local and systemic administration. Typically, a therapeutically effective dosage is formulated to contain a concentration of at least about 0.1 w / w% to up to about 90 w / w% or more, e.g., more than 1 w / w%, of the active compound relative to the tissue(s) being treated. The active ingredient may be administered once or divided into several smaller doses administered at time intervals. It is understood that the exact dosage and duration of treatment will depend on the tissue being treated and can be determined empirically using known testing protocols or by extrapolation from in vivo or in vitro test data. It is noted that concentration and dosage values ​​may also vary with the age of the individual being treated. It should be further understood that for any particular subject, the specific dosage regimen should be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the formulation, and that the concentration ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed formulations.

[0284] FTI can be suspended in micronized form or other suitable form, or can be derivatized to produce more soluble active product or to produce prodrug.The form of the resulting mixture depends on several factors, including the intended mode of administration and the solubility of the compound in the selected carrier or vehicle.The effective concentration is sufficient to ameliorate the symptoms of the condition, and can be empirically determined.

[0285] Also of interest herein are lyophilized powders that can be reconstituted for administration as solutions, emulsions, and other mixtures. They can also be reconstituted and formulated as solids or gels.

[0286] The sterile lyophilized powder is prepared by dissolving the FTI or a pharma- ceutically acceptable salt thereof provided herein in a suitable solvent. The solvent may contain excipients that improve the stability or other pharmacological elements of the powder or the reconstituted solution prepared from the powder. Excipients that may be used include, but are not limited to, dextrose, sorbital, fructose, corn syrup, xylitol, glycerin, glucose, sucrose, or other suitable agents. The solvent may also contain a buffer, such as citrate, sodium or potassium phosphate, or other such buffer known to those of skill in the art, in one embodiment, a buffer with a pH of about neutral. The solution is then sterile filtered under standard conditions known to those of skill in the art, followed by lyophilization to provide the desired formulation. Generally, the resulting solution is apportioned into vials for lyophilization. Each vial contains a single dose (including, but not limited to, 1-1000 mg or 100-500 mg) or multiple doses of the compound. The lyophilized powder can be stored under appropriate conditions, for example, at about 4° C. to room temperature.

[0287] Reconstitution of this lyophilized powder with water for injection provides a formulation for use in parenteral administration. For reconstitution, about 1-50 mg, about 5-35 mg, or about 9-30 mg of lyophilized powder is added per mL of sterile water or other suitable carrier. The exact amount will depend on the compound selected. Such amounts can be determined empirically.

[0288] Topical mixtures are prepared as described for local and systemic administration. The resulting mixture may be a solution, suspension, emulsion, etc., and is formulated as a cream, gel, ointment, emulsion, liquid, elixir, lotion, suspension, tincture, paste, foam, aerosol, irrigate, spray, suppository, bandage, transdermal patch, or any other formulation suitable for topical administration.

[0289] FTIs or pharmaceutical compositions having FTIs can be formulated as aerosols for topical application, for example, by inhalation (see, for example, U.S. Patent Nos. 4,044,126, 4,414,209, and 4,364,923, which describe aerosols for the delivery of steroids useful in the treatment of inflammatory diseases, particularly asthma). These formulations for administration to the respiratory tract can be in the form of an aerosol or liquid for a nebulizer, or as a fine powder for insufflation, alone or in combination with an inert carrier such as lactose. In such cases, the particles of the formulation have a diameter of less than 50 microns or less than 10 microns.

[0290] FTIs or pharmaceutical compositions having FTIs can be formulated for local or topical application, for example, in the form of gels, creams, and lotions, for topical application to the skin and mucous membranes, for example, in the eye, as well as for application to the eye or for intracisternal or intrathecal application. Topical administration is contemplated for transdermal delivery, as well as for administration to the eye or mucous membranes, or for inhalation therapy. Nasal solutions of the active compounds can also be administered alone or in combination with other pharma- ceutically acceptable excipients. These solutions, particularly those intended for ophthalmic use, can be formulated as 0.01%-10% isotonic solutions with appropriate salts and a pH of about 5-7.

[0291] Other routes of administration, such as transdermal patches and rectal administration, are also contemplated herein. For example, pharmaceutical dosage forms for rectal administration are rectal suppositories, capsules, and tablets for systemic effect. Rectal suppositories, as used herein, refer to solid bodies for insertion into the rectum that melt or soften at body temperature to release one or more pharmacologically or therapeutically active ingredients. Pharmaceutically acceptable substances utilized in rectal suppositories are bases or vehicles and agents to raise the melting point. Examples of bases include cocoa butter (theobroma oil), glycerin, gelatin, carbowax (polyoxyethylene glycol), and suitable mixtures of fatty acid mono-, di-, and triglycerides. Combinations of various bases may be used. Agents to raise the melting point of the suppository include spermaceti and wax. Rectal suppositories may be prepared by either the compressed method or by molding. An exemplary weight of a rectal suppository is about 2 to 3 grams. Tablets and capsules for rectal administration are manufactured using the same pharma- ceutically acceptable substance and by the same methods as for preparations for oral administration.

[0292] The FTIs or pharmaceutical compositions comprising an FTI provided herein can be administered by controlled release means or by delivery devices that are well known to those of ordinary skill in the art. Examples include U.S. Patent Nos. 3,845,770; 3,916,899; 3,536,809; 3,598,123; and 4,008,719, 5,674,533, 5,059,595, 5,591,767, 5,120,548, 5,073,543, 5,639,476, 5,354,556, 5,639,480, 5,733,566, 5,739,108, 5,891,474, 5,922,356, 5,972,891, 5, Nos. 5,980,945, 5,993,855, 6,045,830, 6,087,324, 6,113,943, 6,197,350, 6,248,363, 6,264,970, 6,267,981, 6,376,461, 6,419,961, 6,589,548, 6,613,358, 6,699,500, and 6,740,634 (each of which is incorporated herein by reference). Such dosage forms can be used to provide slow or controlled release of the FTI, for example, using hydropropylmethylcellulose, other polymer matrices, gels, permeable membranes, osmotic systems, multilayer coatings, microparticles, liposomes, microspheres, or combinations thereof in various proportions to provide the desired release profile. Controlled release formulations known to those of skill in the art, including those described herein, can be readily selected for use with the active ingredients provided herein.

[0293] All controlled release pharmaceutical products have a common goal of improving drug therapy over that achieved by their non-controlled counterparts. In one embodiment, the use of optimally designed controlled release preparations in medical treatment is characterized by the use of a minimum amount of drug substance to cure or control a condition in a minimum amount of time. In certain embodiments, the advantages of controlled release formulations include extended drug activity, reduced dosing frequency, and improved patient compliance. In addition, controlled release formulations can be used to affect other characteristics, such as the time of onset of action or blood levels of the drug, thereby affecting the occurrence of side effects (e.g., adverse effects).

[0294] Many controlled release formulations are designed to initially release an amount of drug (active ingredient) that quickly produces the desired therapeutic effect, and then slowly and continuously release another amount of drug that maintains this level of therapeutic effect over an extended period of time.To maintain this constant level of drug in the body, the drug must be released from the dosage form at a rate that compensates for the amount of drug that is metabolized and excreted from the body.The controlled release of the active ingredient can be stimulated by various conditions, including but not limited to pH, temperature, enzymes, water, or other physiological conditions or compounds.

[0295] In certain embodiments, FTIs can be administered using intravenous infusion, implantable osmotic pumps, transdermal patches, liposomes, or other modes of administration. In one embodiment, pumps can be used (see Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med. 321:574 (1989)). In another embodiment, polymeric materials can be used. In yet another embodiment, the controlled release system can be placed in close proximity to the therapeutic target, i.e., so that only a small fraction of the systemic dose is required (see, e.g., Goodson, Medical Applications of Controlled Release, vol. 2, pp. 115-138 (1984)).

[0296] In some embodiments, the controlled release device is introduced into the subject in proximity to the site of inappropriate immune activation or tumor. Other controlled release systems are discussed in the review by Langer (Science 249:1527-1533 (1990)). F can be dispersed in a solid internal matrix, such as polymethyl methacrylate, polybutyl methacrylate, plasticized or unplasticized polyvinyl chloride, plasticized nylon, plasticized polyethylene terephthalate, natural rubber, polyisoprene, polyisobutylene, polybutadiene, polyethylene, ethylene-vinyl acetate copolymers, silicone rubber, polydimethylsiloxane, silicone carbonate copolymers, hydrophilic polymers (e.g., hydrogels of esters of acrylic and methacrylic acid), collagen, cross-linked polyvinyl alcohol, and partially hydrolyzed cross-linked polyvinyl acetate, which solid internal matrix is ​​dispersed in the body. It is surrounded by an outer polymeric membrane that is insoluble in liquid, such as polyethylene, polypropylene, ethylene / propylene copolymer, ethylene / ethyl acrylate copolymer, ethylene / vinyl acetate copolymer, silicone rubber, polydimethylsiloxane, neoprene rubber, chlorinated polyethylene, polyvinyl chloride, vinyl acetate, vinylidene chloride, ethylene and propylene vinyl chloride copolymer, ionomeric polyethylene terephthalate, butyl rubber epichlorohydrin rubber, ethylene / vinyl alcohol copolymer, ethylene / vinyl acetate / vinyl alcohol terpolymer and ethylene / vinyloxyethanol copolymer.Then, the active ingredient diffuses out of the outer polymeric membrane in the release rate control step.The percentage of active ingredient contained in such parenteral composition is highly dependent on its specific nature and the needs of the subject.

[0297] The FTI or pharmaceutical composition of an FTI can be packaged as an article of manufacture that includes packaging materials; a compound provided herein, or a pharma- ceutically acceptable salt thereof, for use in the treatment, prevention, or amelioration of one or more symptoms or progression of cancer, including hematological cancers and solid tumors; and a label indicating that the compound, or a pharma-ceutically acceptable salt thereof, is used for the treatment, prevention, or amelioration of one or more symptoms or progression of cancer, including hematological cancers and solid tumors.

[0298] The products provided herein include packaging materials. Packaging materials used for packaging pharmaceutical products are well known to those skilled in the art. For example, see U.S. Patent Nos. 5,323,907, 5,052,558, and 5,033,252. Examples of pharmaceutical packaging materials include, but are not limited to, blister packs, bottles, tubes, inhalers, pumps, bags, vials, containers, syringes, pens, bottles, and any packaging material suitable for the selected formulation and intended administration and treatment mode. A wide range of formulations of the compounds and compositions provided herein are contemplated.

[0299] In some embodiments, a therapeutically effective amount of a pharmaceutical composition having an FTI is administered orally or parenterally.

[0300] In some embodiments, the FTI is administered in a daily dose of 0.05 up to 1800 mg / kg. In some embodiments, the FTI is administered in a daily dose of 0.05 up to 1500 mg / kg. In some embodiments, the FTI is administered in a daily dose of 0.05 up to 500 mg / kg. In some embodiments, the FTI is administered in a daily dose of 0.05 mg / kg per day, 0.1 mg / kg per day, 0.2 mg / kg per day, 0.5 mg / kg per day, 1 mg / kg per day, 2 mg / kg per day, 5 mg / kg per day, 10 mg / kg per day, 20 mg / kg per day, 50 mg / kg per day, 100 mg / kg per day, 200 mg / kg per day, 300 mg / kg per day, or 400 mg / kg per day. In some embodiments, the FTI is administered at 1 mg / kg per day. In some embodiments, the FTI is administered at 2 mg / kg per day. In some embodiments, the FTI is administered at 5 mg / kg per day. In some embodiments, the FTI is administered at 10 mg / kg per day. In some embodiments, the FTI is administered at 20 mg / kg per day. In some embodiments, the FTI is administered at 5 mg / kg per day. In some embodiments, the FTI is administered at 10 mg / kg per day. In some embodiments, the FTI is administered at 20 mg / kg per day. In some embodiments, the FTI is administered at 50 mg / kg per day. In some embodiments, the FTI is administered at 100mg / kg per day. In some embodiments, the FTI is administered at 200mg / kg per day. In some embodiments, the FTI is administered at 500mg / kg per day. The FTI can be administered either as a single dose or divided into two or more doses. In some embodiments, the FTI is tipifarnib.

[0301] In some embodiments, the FTI is administered at a dose of 50-2400 mg per day. In some embodiments, the FTI is administered at a dose of 100-1800 mg per day. In some embodiments, the FTI is administered at a dose of 100-1200 mg per day. In some embodiments, the FTI is administered at a dose of 50 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, 1000 mg, 1100 mg, 1200 mg, 1300 mg, 1400 mg, 1500 mg, 1600 mg, 1700 mg, 1800 mg, 1900 mg, 2000 mg, 2100 mg, 2200 mg, 1200 mg, or 2400 mg per day. In some embodiments, the FTI is administered at a dose of 200 mg per day. The FTI may be administered at a dose of 300 mg per day. The FTI may be administered at a dose of 400 mg per day. The FTI may be administered at a dose of 500 mg per day. The FTI may be administered at a dose of 600 mg per day. The FTI may be administered at a dose of 700 mg per day. The FTI may be administered at a dose of 800 mg per day. The FTI may be administered at a dose of 900 mg per day. The FTI may be administered at a dose of 1000 mg per day. The FTI may be administered at a dose of 1100 mg per day. The FTI may be administered at a dose of 1200 mg per day. The FTI may be administered at a dose of 1300 mg per day. The FTI may be administered at a dose of 1400 mg per day. The FTI may be administered at a dose of 1500 mg per day. The FTI may be administered at a dose of 1600 mg per day. The FTI may be administered at a dose of 1700 mg per day. The FTI may be administered at a dose of 1800 mg per day. The FTI may be administered at a dose of 1900 mg per day. The FTI may be administered at a dose of 2000 mg per day. The FTI may be administered at a dose of 2100 mg per day. The FTI may be administered at a dose of 2200 mg per day. The FTI may be administered at a dose of 2300 mg per day. The FTI may be administered at a dose of 2400 mg per day. The FTI may be administered either as a single dose or sub-divided into two or more doses.In some embodiments, the FTI is tipifarnib.

[0302] In some embodiments, the FTI is 100, 200, 225, 250, 275, The FTI is administered at a dose of 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 875, 900, 925, 950, 975, 1000, 1025, 1050, 1075, 1100, 1125, 1150, 1175, or 1200 mg twice daily (bid). In some embodiments, the FTI is administered at a dose of 100-1400 mg bid. In some embodiments, the FTI is administered at a dose of 100-1200 mg bid. In some embodiments, the FTI is administered at a dose of 300-1200 mg bid. In some embodiments, the FTI is administered at a dose of 300-900 mg bid. In some embodiments, the FTI is administered at a dose of 300 mg bid. In some embodiments, the FTI is administered at a dose of 400 mg bid. In some embodiments, the FTI is administered at a dose of 500 mg bid. In some embodiments, the FTI is administered at a dose of 600 mg bid. In some embodiments, the FTI is administered at a dose of 700 mg bid. In some embodiments, the FTI is administered at a dose of 800 mg bid. In some embodiments, the FTI is administered at a dose of 900 mg bid. In some embodiments, the FTI is administered at a dose of 1000 mg bid. In some embodiments, the FTI is administered at a dose of 1100 mg bid. In some embodiments, the FTI is administered at a dose of 1200 mg bid. In some embodiments, the FTI used in the compositions and methods provided herein is tipifarnib.

[0303] As one skilled in the art will appreciate, dosage will vary depending on the dosage form used, the condition and sensitivity of the patient, the route of administration, and other factors. The exact dosage will be determined by the physician, taking into account factors related to the subject that needs to be treated. Dosage and administration will be adjusted to provide sufficient levels of the active ingredient or to maintain the desired effect. Factors that may be considered include the severity of the disease state, the general health of the subject, the age, weight, and sex of the subject, diet, time and frequency of administration, drug combination(s), response sensitivity, and tolerability / response to therapy. During the treatment cycle, the daily dose may vary. In some embodiments, the starting dose may be tapered within the treatment cycle. In some embodiments, the starting dose may be tapered within the treatment cycle. The final dose may depend on the occurrence of dose-limiting toxicity and other factors. In some embodiments, the FTI is administered at a starting dose of 300 mg per day and increased to a maximum dose of 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, 1000 mg, 1100 mg, or 1200 mg per day. In some embodiments, the FTI is administered at a starting dose of 400 mg per day and increased to a maximum dose of 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, 1000 mg, 1100 mg, or 1200 mg per day. In some embodiments, the FTI is administered at a starting dose of 500 mg per day and increased to a maximum dose of 600 mg, 700 mg, 800 mg, 900 mg, 1000 mg, 1100 mg, or 1200 mg per day. In some embodiments, the FTI is administered at a starting dose of 600 mg per day and increased to a maximum dose of 700 mg, 800 mg, 900 mg, 1000 mg, 1100 mg, or 1200 mg per day. In some embodiments, the FTI is administered at a starting dose of 700 mg per day and increased to a maximum dose of 800 mg, 900 mg, 1000 mg, 1100 mg, or 1200 mg per day. In some embodiments, the FTI is administered at a starting dose of 800 mg per day and increased to a maximum dose of 900 mg, 1000 mg, 1100 mg, or 1200 mg per day.In some embodiments, FTI is administered at a starting dose of 900mg per day, and is increased to a maximum dose of 1000mg, 1100mg, or 1200mg per day.Dose increase can be performed all at once or stepwise.For example, starting dose of 600mg per day can be increased by 100mg per day for 4 days, or by 200mg per day for 2 days, or by 400mg at once to a final dose of 1000mg per day.In some embodiments, FTI is tipifarnib.

[0304] In some embodiments, FTI is administered at a relatively high starting dose and tapered to a lower dose depending on patient response and other factors.In some embodiments, FTI is administered at a starting dose of 1200mg per day and reduced to a final dose of 1100mg, 1000mg, 900mg, 800mg, 700mg, 600mg, 500mg, 400mg, or 300mg per day.In some embodiments, FTI is administered at a starting dose of 1100mg per day and reduced to a final dose of 1000mg, 900mg, 800mg, 700mg, 600mg, 500mg, 400mg, or 300mg per day.In some embodiments, FTI is administered at a starting dose of 1000mg per day and reduced to a final dose of 900mg, 800mg, 700mg, 600mg, 500mg, 400mg, or 300mg per day. In some embodiments, the FTI is administered at a starting dose of 900mg per day and reduced to a final dose of 800mg, 700mg, 600mg, 500mg, 400mg, or 300mg per day. In some embodiments, the FTI is administered at a starting dose of 800mg per day and reduced to a final dose of 700mg, 600mg, 500mg, 400mg, or 300mg per day. In some embodiments, the FTI is administered at a starting dose of 600mg per day and reduced to a final dose of 500mg, 400mg, or 300mg per day. The dose reduction can be done all at once or stepwise. In some embodiments, the FTI is tipifarnib. For example, the starting dose of 900mg per day can be reduced to a final dose of 600mg by reducing 100mg per day over three days or by reducing 300mg at once. In some embodiments, the FTI is tipifarnib.

[0305] The length of the treatment cycle can vary. In some embodiments, the treatment cycle is 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 3 months, 4 months, It may be 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, or 12 months. In some embodiments, the treatment cycle is 4 weeks. The treatment cycle may have an intermittent schedule. In some embodiments, a 2-week treatment cycle may have 5 days of administration followed by 9 days of rest. In some embodiments, a 2-week treatment cycle may have 6 days of administration followed by 8 days of rest. In some embodiments, a 2-week treatment cycle may have 7 days of administration followed by 7 days of rest. In some embodiments, a 2-week treatment cycle may have 8 days of administration followed by 6 days of rest. In some embodiments, a 2-week treatment cycle may have 9 days of administration followed by 5 days of rest. In some embodiments, a 4-week treatment cycle may have 7 days of administration followed by 21 days of rest. In some embodiments, a 4-week treatment cycle may have 21 days of administration followed by 7 days of rest. In some embodiments, a four week treatment cycle can have administrations on days 1-7 and days 15-21, and rest on days 8-14 and days 22-28.

[0306] In some embodiments, the FTI may be administered for at least one treatment cycle. In some embodiments, the FTI may be administered for at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, or at least twelve treatment cycles. In some embodiments, the FTI may be administered for at least two treatment cycles. In some embodiments, the FTI may be administered for at least three treatment cycles. In some embodiments, the FTI may be administered for at least six treatment cycles. In some embodiments, the FTI may be administered for at least nine treatment cycles. In some embodiments, the FTI may be administered for at least twelve treatment cycles. In some embodiments, the FTI is tipifarnib.

[0307] In some embodiments, the FTI is administered for up to 2 weeks. In some embodiments, the FTI is administered for up to 3 weeks, up to 1 month, up to 2 months, up to 3 months, up to 4 months, up to 5 months, up to 6 months, up to 7 months, up to 8 months, up to 9 months, up to 10 months, up to 11 months, or up to 12 months. In some embodiments, the FTI is administered for up to 1 month. In some embodiments, the FTI is administered for up to 3 months. In some embodiments, the FTI is administered for up to 6 months. In some embodiments, the FTI is administered for up to 9 months. In some embodiments, the FTI is administered for up to 12 months.

[0308] In some embodiments, the FTI is administered daily for 3 out of 4 weeks of a repeated 4 week cycle. In some embodiments, the FTI is administered daily (1 week on, 1 week off) every other week of a repeated 4 week cycle. In some embodiments, the FTI is administered orally at a dose of 300 mg bid for 3 out of 4 weeks of a repeated 4 week cycle. In some embodiments, the FTI is administered orally at a dose of 600 mg bid for 3 out of 4 weeks of a repeated 4 week cycle. In some embodiments, the FTI is administered orally at a dose of 900 mg bid every other week of a repeated 4 week cycle (1 week on, 1 week off). In some embodiments, the FTI is administered orally at a dose of 1200 mg bid every other week (on days 1-7 and 15-21 of a repeated 28 day cycle). In some embodiments, the FTI is administered orally at a dose of 1200 mg bid on days 1-5 and 15-19 of a repeated 28 day cycle.

[0309] In some embodiments, a biweekly regimen of 300 mg b.id tipifarnib may be employed and used. Under this regimen, patients receive a starting dose of 300 mg po, bid on days 1-7 and 15-21 of a 28-day treatment cycle. In the absence of unmanageable toxicity, subjects may continue to receive tipifarnib treatment for up to 12 months. If the subject tolerates the treatment well, the dose may be increased to 1200 mg bid. Gradual 300 mg dose reductions may also be included to control treatment-related and treatment-emergent toxicities.

[0310] In some embodiments, a biweekly regimen of 600 mg bid of tipifarnib may be employed. Under this regimen, patients are administered a starting dose of 600 mg po bid on days 1-7 and 15-21 of a 28-day treatment cycle. In the absence of unmanageable toxicity, subjects may continue to receive tipifarnib treatment for up to 12 months. If the subject tolerates the treatment well, the dose may be increased to 1200 mg bid. A gradual 300 mg dose reduction may also be included to control treatment-related, treatment-emergent toxicity.

[0311] In some embodiments, a biweekly regimen of tipifarnib at 900 mg bid may be employed. Under this regimen, patients receive a starting dose of 900 mg po bid on days 1-7 and 15-21 of a 28-day treatment cycle. In the absence of unmanageable toxicity, subjects may continue to receive tipifarnib treatment for up to 12 months. If the subject tolerates the treatment well, the dose may be increased to 1200 mg bid. Stepwise 300 mg dose reductions may also be included to control treatment-related, treatment-emergent toxicities.

[0312] In some other embodiments, tipifarnib is administered orally at a dose of 300 mg bid daily for 21 days followed by 1 week of rest in a 28-day treatment cycle (21-day schedule; Cheng DT, et al., J Mol Diagn. (2015) 17(3): 251-64). In some embodiments, 5 days of bid dosing in the range of 25-1300 mg followed by 9 days of rest is employed (5-day schedule; Zujewski J., J Clin Oncol., (2000) Feb; 18(4): 927-41). In some embodiments, 7 days of bid dosing followed by 7 days of rest is employed (7-day schedule; Lara PN Jr., Anticancer Drugs., (2005) 16(3): 317-21, Kirschbaum MH, Leukemia., (2011) Oct; 25(10): 1543-7). In the 7-day schedule, patients can be given a starting dose of 300 mg bid and escalated doses of 300 mg up to a maximum planned dose of 1800 mg bid. In the 7-day schedule study, patients can also be given tipifarnib bid on days 1-7 and 15-21 of a 28-day cycle at doses up to 1600 mg bid.

[0313] In previous studies, FTIs have been shown to inhibit the growth of mammalian tumors when administered as a twice-daily dosing schedule. It has been found that administering FTIs daily for 1-5 days in a single dose results in significant inhibition of tumor growth that lasts for at least 21 days. In some embodiments, FTIs are administered in a dosage range of 50-400 mg. In some embodiments, FTIs are administered at 200 mg / kg. Dosing regimens for specific FTIs are also well known in the art (e.g., U.S. Patent No. 6,838,467, which is incorporated herein by reference in its entirety). For example, suitable dosages of the compounds Arglabin (WO 98 / 28303), Perillyl Alcohol (WO 99 / 45712), SCH-66336 (U.S. Pat. No. 5,874,442), L778123 (WO 00 / 01691), 2(S)-[2(S)-[2(R)-amino-3-mercapto]propylamino-3(S)-methyl]-pentyloxy-3-phenylpropionyl-methionine sulfone (WO 94 / 10138), BMS 214662 (WO 97 / 30992), AZD3409; Pfizer's Compounds A and B (WO 00 / 12499 and WO 00 / 12498) are set forth in the aforementioned patent specifications, which are incorporated herein by reference, or are known to or can be readily determined by one of ordinary skill in the art.

[0314] For perillyl alcohol, the drug may be administered at 1-4 g per 150 lb human patient per day. In one embodiment, 1-2 g per 150 lb human patient per day. SCH-66336 may be administered at a unit dose of about 0.1 mg to 100 mg, more preferably about 1 mg to 300 mg, depending on the particular application. Compounds L778123 and 1-(3-chlorophenyl)-4-[1-(4-cyanobenzyl)-5-imidazolylmethyl]-2-piperazinone may be administered to a human patient in an amount of about 0.1 mg / kg body weight to about 20 mg / kg body weight per day, preferably 0.5 mg / kg body weight to about 10 mg / kg body weight per day.

[0315] Pfizer's Compounds A and B may be administered in single or divided (i.e., multiple) doses at dosages ranging from about 1.0 mg up to about 500 mg per day, preferably from about 1 to about 100 mg per day. Therapeutic compounds are typically administered in daily dosages ranging from about 0.01 to about 10 mg per kg body weight per day, in single or divided doses. BMS214662 may be administered in a dosage range of about 0.05 to 200 mg / kg / day, preferably less than 100 mg / kg / day, in a single dose or in 2 to 4 divided doses.

[0316] C. Combination Therapy The FTI treatments described herein may also be used in combination with additional second therapies in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio. The FTI treatments described herein may also be used in combination with additional second therapies in selectively treating SCC in subjects carrying H-Ras gene mutations. In some embodiments of the methods provided herein, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC may be a specific type of SCC described herein or otherwise known in the art. The SCC may be HNSCC. The SCC may be esophageal SCC. The SCC may be a thyroid SCC. The SCC may be a LSCC. The SCC may be a bladder SCC. The SCC may be a urothelial carcinoma (UC).

[0317] FTI can be any FTI described herein or otherwise known in the art.In some embodiments, FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409 or BMS-214662.In some embodiments, FTI is tipifarnib.

[0318] In some embodiments, FTI treatment is administered in combination with radiotherapy or radiation therapy.Radiation therapy includes the use of gamma rays, X-rays, and / or the directed delivery of radioisotopes to tumor cells.Other forms of DNA damage agents are also contemplated, such as microwaves, proton beam irradiation (US Pat. Nos. 5,760,395 and 4,870,287; all of which are incorporated herein by reference in their entirety), and UV irradiation.All of these agents most likely affect a wide range of damage to DNA, to the precursors of DNA, to DNA replication and repair, and to chromosome assembly and maintenance.

[0319] In some embodiments, a therapeutically effective amount of a pharmaceutical composition having an FTI is administered, which effectively sensitizes the host tumor to irradiation. (US Pat. No. 6,545,020, which is incorporated herein by reference in its entirety). The irradiation can be ionizing radiation, particularly gamma radiation. In some embodiments, the gamma radiation is emitted by a linear accelerator or a radionuclide. The irradiation of the tumor by a radionuclide can be external or internal.

[0320] The radiation can also be X-ray radiation. X-ray doses range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 weeks), to single doses of 2000 to 6000 roentgens. Dosage ranges for radioisotopes vary widely and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.

[0321] In some embodiments, administration of the pharmaceutical composition begins up to one month, particularly up to ten days or one week, prior to irradiation of the tumor.Furthermore, irradiation of the tumor is fractionated and administration of the pharmaceutical composition is maintained in the interval between the first and last irradiation sessions.

[0322] The amount of FTI, the dose of radiation, and the interruption of radiation administration depend on a number of parameters, such as the type of tumor, its location, and the patient's response to chemotherapy or radiation therapy, and are ultimately determined by the physician and radiologist in each individual case. In some embodiments, the FTI is administered before the administration of radiation therapy. In some embodiments, the FTI is administered simultaneously with radiation therapy. In some embodiments, the FTI is administered after the administration of radiation therapy. In some embodiments, the FTI is tipifarnib.

[0323] In some embodiments, the methods provided herein further comprise administering a therapeutically effective amount of a second active agent or supportive care therapy. The second active agent can be a chemotherapeutic agent. Chemotherapeutic agents or drugs can be classified according to their mode of activity in cells, for example, whether they affect the cell cycle and at what stage they affect the cell cycle. Alternatively, agents can be characterized based on their ability to directly crosslink DNA, intercalate into DNA, or induce chromosomal and mitotic abnormalities by affecting nucleic acid synthesis. The FTI can be administered prior to administration of the second active agent. The FTI can be administered simultaneously with the second active agent. The FTI can be administered after administration of the second active agent.

[0324] Examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclophosphamide; alkyl sulfonates such as busulfan, improsulfan, and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide, and trimethylolomelamine; acetogenins (particularly bullatacin and bullatacinone); camptothecins (including the synthetic analog topotecan); bryostatin; kallistatin; CC-1065 (including its adozelesin, carzelesin, and bizelesin synthetic analogs); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatins; duocarmycins (synthetic including analogs KW-2189 and CB1-TM1); erytherobin; pancratistatin; sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednisone cin, trofosfamide, and uracil mustard; nitrosureas, such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimustine; antibiotics, such as enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gamma 1I and calicheamicin omega 11); dynemicins, including dynemicin A; bisphosphonates, such as clodronate; esperamicin;and neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores, aclacinomycin, actinomycin, anthramycin, azaserine, bleomycin, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin, and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalarnycin, olivomycin, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, and zorubicin; antimetabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogs such as denopterin, pteropterin, and trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, and Thioguanine; pyrimidine analogues such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, and floxuridine; androgens such as calsterone, dromostanolone propionate, epithiostanol, mepitiostane, and testolactone; antiadrenal drugs such as mitotane and trilostane; folic acid supplements such as folinic acid; aceglatone; aldophosphamide glycosides; aminolevulinic acid; eniluracil; amsacrine; bestravcil; bisantrene; edatrexate; defofamine; demecolcine; diazicon; elformithine; elliptinium acetate; epothilone; etoglucide; gallium nitrate; hydroxyurea; lentinan;lonidainine; maytansinoids, such as maytansine and ansamitocin; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllic acid; 2-ethylhydrazide; procarbazine; PSK polysaccharide complex; razoxane; rhizoxin; schizophyllan; spirogermanium; tenuazonic acid; triazicon; 2,2',2''-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A) A), Roridin A, and Anguidine); urethane; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); cyclophosphamide; taxoids, such as paclitaxel and docetaxel gemcitabine; 6-thioguanine; mercaptopurine; platinum coordination complexes, such as cisplatin, oxaliplatin, and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine ; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitors RFS2000; difluorometlhylornithine (DMFO); retinoids, such as retinoic acid; capecitabine; carboplatin, procarbazine, plicomycin, gemcitabine, navelbine, transplatinum, as well as pharmaceutically acceptable salts, acids, or derivatives of any of the above;

[0325] The second active agent may be a large molecule (e.g., a protein) or a small molecule (e.g., a synthetic inorganic, organometallic, or organic molecule). In some embodiments, the second active agent is a DNA hypomethylating agent, an alkylating agent, a topoisomerase inhibitor, a CDK inhibitor, a PI3K-α inhibitor, an AKT inhibitor, an MTOR1 / 2 inhibitor, or a therapeutic antibody that specifically binds to a cancer antigen. The second active agent may also be a hematopoietic growth factor, a cytokine, an antibiotic, a cox-2 inhibitor, an immunomodulator, an antithymocyte globulin, an immunosuppressant, a corticosteroid, or a pharmacologically active variant or derivative thereof.

[0326] In some embodiments, the second therapy is a chemotherapy, such as cisplatin, 5-FU, carboplatin, paclitaxel, or a platinum-based doublet (e.g., cisplatin / 5-FU or carboplatin / paclitaxel). In some embodiments, the second therapy is a taxane and / or methotrexate. In some embodiments, the second therapy may be selected from those targeting the PI3K pathway: BKM120 (buparlisib), BYL719 (PI3K-α inhibitor), temsirolimus, rigosertib; those targeting the MET pathway: tivantinib, ficlatuzumab; those targeting the HER3 pathway: patritumab; those targeting the FGFR pathway: BGJ398; those targeting the CDK4 / 6-cell cycle pathway: palbociclib, LEE011, abemaciclib, and ribociclib; RTK inhibitors: anlotinib; AKT inhibitors: MK2206, GSK2110183, and GSK2141795; MTOR1 / 2 inhibitors: INK-128; and chemotherapy: oral azacitidine. In some embodiments, the second therapy is an immunotherapy, such as an anti-PD1 antibody, an anti-PDL1 antibody, or an anti-CTLA-4 antibody. In some embodiments, the second therapy is a taxane.

[0327] In some embodiments, the second active agent is an alkylating agent, and provided herein is a combination of an alkylating agent and an FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the second active agent is an alkylating agent, and provided herein is a combination of an alkylating agent and an FTI in selectively treating SCC in subjects with H-Ras gene mutations. In some embodiments, the alkylating agent is altretamine, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cyclophosphamide, dacarbazine, lomustine, melphalan, oxaliplatin, temozolomide, or thiotepa. In some embodiments, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. The FTI can be administered before the administration of the alkylating agent. The FTI can be administered simultaneously with the alkylating agent. The FTI can be administered after the administration of the alkylating agent.

[0328] In some embodiments, the second active agent is cisplatin, and provided herein is the combined use of cisplatin and FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio.In some embodiments, the second active agent is cisplatin, and provided herein is the combined use of cisplatin and FTI in selectively treating SCC in subjects with H-Ras gene mutation. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of cisplatin and tipifarnib in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio.In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of cisplatin and tipifarnib in selectively treating SCC in subjects with H-Ras gene mutation.Tipifarnib can be administered before administration of cisplatin.Tipifarnib can be administered simultaneously with cisplatin.Tipifarnib can be administered after administration of cisplatin.

[0329] In some embodiments, the SCC is human papilloma virus (HPV) negative. In some embodiments, the SCC is in an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC described herein or otherwise known in the art. The SCC can be HNSCC. The SCC can be esophageal SCC. The SCC can be thyroid SCC. The SCC can be LSCC. The SCC can be bladder SCC. The SCC can be urothelial carcinoma (UC). The FTI can be any FTI described herein or otherwise known in the art. Cisplatin can be administered at standard doses known in the art or other doses deemed appropriate by the oncologist. For example, cisplatin can be administered at 20 mg / m 2 , 50 mg / m 2 , 80 mg / m 2 , 100 mg / m 2 , 120 mg / m 2 , 150 mg / m 2 , or 200 mg / m 2 Cisplatin may be administered intravenously at a daily dose of 100 mg / m. Cisplatin may be administered weekly (QW), every 14 days (Q14D), every 21 days (Q21D), or every 28 days (Q28D). Cisplatin may be administered for at least 1 cycle, at least 2 cycles, at least 3 cycles, at least 4 cycles, at least 5 cycles, or at least 6 cycles. In some embodiments, cisplatin is administered at a daily dose of 100 mg / m. 2 daily dose of 10 mg Q21D for three cycles.

[0330] In some embodiments, the second active agent is a CDK inhibitor, and provided herein is the combined use of an FTI and a CDK inhibitor in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio. The CDK inhibitor can be palbociclib (Ibrance), ribociclib (Kisqali), or abemaciclib. The FTI can be tipifarnib, lonafarnib, aruglavin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. The FTI may be administered prior to administration of the CDK inhibitor. The FTI may be administered simultaneously with the CDK inhibitor. The FTI may be administered after administration of the CDK inhibitor. In some embodiments, the SCC is human papilloma virus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC may be a specific type of SCC described herein or otherwise known in the art. The SCC may be HNSCC. The SCC may be esophageal SCC. The SCC may be thyroid SCC. The SCC may be LSCC. The SCC may be bladder SCC. The SCC may be urothelial carcinoma (UC).

[0331] For example, in some embodiments, the CDK inhibitor is palbociclib, and provided herein is the combined use of FTI and palbociclib in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to K-Ras and N-Ras combined expression higher than a reference ratio.In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of tipifarnib and palbociclib in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to K-Ras and N-Ras combined expression higher than a reference ratio.In some embodiments, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC described herein or otherwise known in the art. The SCC can be HNSCC. The SCC can be esophageal SCC. The SCC can be thyroid SCC. The SCC can be LSCC. The SCC can be bladder SCC. The SCC can be urothelial carcinoma (UC).

[0332] Tipifarnib may be administered prior to administration of palbociclib. Tipifarnib may be administered simultaneously with palbociclib. Tipifarnib may be administered after administration of palbociclib. Palbociclib may be administered at standard doses known in the art or other doses deemed appropriate by an oncologist. For example, palbociclib may be administered orally at doses of 25 mg / day, 50 mg / day, 75 mg / day, 100 mg / day, 125 mg / day, 150 mg / day, 175 mg / day, 200 mg / day, 225 mg / day, or 250 mg / day. Palbociclib may be administered in a 14-day treatment cycle or a 28-day treatment cycle. In some embodiments, a 2-week treatment cycle may have 7 days of administration followed by 7 days of rest. In some embodiments, a 4-week treatment cycle may have 7 days of administration followed by 21 days of rest. In some embodiments, a 4-week treatment cycle can have 21 days of dosing followed by a 7-day rest. In some embodiments, a 4-week treatment cycle can have dosing on days 1-7 and 15-21, followed by rest on days 8-14 and 22-28. In some embodiments, palbociclib can be administered for at least 1 cycle, at least 2 cycles, at least 3 cycles, at least 4 cycles, at least 5 cycles, or at least 6 cycles. In some embodiments, palbociclib is administered orally at 125 mg / kg on days 1-21 of a 28-day cycle.

[0333] In some embodiments, the second active agent is an EGFR inhibitor, and provided herein is the combined use of an FTI and an EGFR inhibitor in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio.The EGFR inhibitor can be an anti-EGFR antibody, such as gefitinib, erlotinib, neratinib, lapatinib, vandetanib, cetuximab, necitumumab, osimertinib, or panitumumab.The FTI can be administered before administration of the EGFR inhibitor.The FTI can be administered simultaneously with the EGFR inhibitor.The FTI can be administered after administration of the EGFR inhibitor.

[0334] In some embodiments, the second active agent is cetuximab, and provided herein is the combined use of FTI and cetuximab in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to K-Ras and N-Ras combined expression higher than a reference ratio.In some embodiments, the second active agent is panitumumab, and provided herein is the combined use of FTI and panitumumab in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to K-Ras and N-Ras combined expression higher than a reference ratio.In some embodiments, SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC described herein or otherwise known in the art. The SCC can be HNSCC. The SCC can be esophageal SCC. The SCC can be thyroid SCC. The SCC can be LSCC. The SCC can be bladder SCC. The SCC can be urothelial carcinoma (UC).

[0335] The FTI can be any FTI described herein or otherwise known in the art.The FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662.In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of tipifarnib and an EGFR inhibitor in selectively treating SCC in subjects with H-Ras overexpression, the ratio of H-Ras expression to K-Ras expression that is higher than a reference ratio, the ratio of H-Ras expression to N-Ras expression that is higher than a reference ratio, or the ratio of H-Ras expression to the combined expression of K-Ras and N-Ras that is higher than a reference ratio.

[0336] In some embodiments, provided herein is a combination use of tipifarnib and panitumumab in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the SCC is in an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC may be a specific type of SCC described herein or otherwise known in the art. The SCC may be HNSCC. The SCC may be esophageal SCC. The SCC may be thyroid SCC. The SCC may be LSCC. The SCC may be bladder SCC. The SCC may be urothelial carcinoma (UC).

[0337] Tipifarnib can be administered before administration of panitumumab. Tipifarnib can be administered simultaneously with panitumumab. Tipifarnib can be administered after administration of panitumumab. Panitumumab can be administered at standard doses known in the art or other doses deemed appropriate by oncologists. For example, panitumumab can be orally administered at a daily dose of 1 mg / kg, 2 mg / kg, 3 mg / kg, 4 mg / kg, 5 mg / kg, 6 mg / kg, 7 mg / kg, 8 mg / kg, 9 mg / kg, 10 mg / kg, 11 mg / kg, 12 mg / kg, 13 mg / kg, 14 mg / kg, 15 mg / kg, 16 mg / kg, 17 mg / kg, or 18 mg / kg body weight. Cetuximab may be administered every week (QW), every 14 days (Q14D), every 21 days (Q21D), or every 28 days (Q28D). Panitumumab may be administered for at least 1 cycle, at least 2 cycles, at least 3 cycles, at least 4 cycles, at least 5 cycles, or at least 6 cycles. In some embodiments, panitumumab is administered at 6 mg / kg Q14D.

[0338] In some embodiments, provided herein is a combination use of tipifarnib and cetuximab in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the SCC is in an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC may be a specific type of SCC described herein or otherwise known in the art. The SCC may be HNSCC. The SCC may be esophageal SCC. The SCC may be thyroid SCC. The SCC may be LSCC. The SCC may be bladder SCC. The SCC may be urothelial carcinoma (UC).

[0339] Tipifarnib may be administered prior to administration of cetuximab. Tipifarnib may be administered simultaneously with cetuximab. Tipifarnib may be administered after administration of cetuximab. Cetuximab may be administered at standard doses known in the art or other doses deemed appropriate by an oncologist. For example, cetuximab may be administered at 50 mg / m 2 , 100 mg / m 2 , 150 mg / m 2 , 200 mg / m 2 , 250 mg / m 2 , 300 mg / m 2 , 350 mg / m 2 , 400 mg / m 2 , 450 mg / m 2 , or 500 mg / m 2 Cetuximab may be administered orally at a daily dose of 400 mg / m. Cetuximab may be administered weekly (QW), every 14 days (Q14D), every 21 days (Q21D), or every 28 days (Q28D). Cetuximab may be administered with a loading dose followed by a standard dose. The loading dose may be at least 1.5, 2, 2.5, or 3 times the standard dose. In some embodiments, the loading dose is 400 mg / m 2 , 450 mg / m 2 , 500 mg / m 2 , 600 mg / m 2 , 700 mg / m 2 , 800 mg / m 2 , 900 mg / m 2 or 1000 mg / m 2 Cetuximab may be administered for at least 1 cycle, at least 2 cycles, at least 3 cycles, at least 4 cycles, at least 5 cycles, or at least 6 cycles. In some embodiments, cetuximab is administered at 400 mg / m 2 loading dose of 250 mg / m 2 Administered QW.

[0340] In some embodiments, the second active agent targets the PI3K pathway, and provided herein is the combined use of a PI3K pathway targeting agent and an FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the second active agent targets the PI3K pathway, and provided herein is the combined use of a PI3K pathway targeting agent and an FTI in selectively treating SCC in subjects with an H-Ras genetic mutation. In some embodiments, the second active agent targets the PI3K pathway, and provided herein is the combined use of a PI3K pathway targeting agent and an FTI in selectively treating SCC in subjects with an H-Ras genetic mutation and a PIK3CA genetic mutation. In some embodiments, the PI3K pathway targeting agent is BKM120 (buparlisib), BYL719 (PI3K-α inhibitor), temsirolimus, or rigosertib. In some embodiments, the PI3K pathway targeting agent is a PI3K-α inhibitor. In some embodiments, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. The FTI can be administered prior to administration of the PI3K pathway targeting agent. The FTI can be administered simultaneously with the PI3K pathway targeting agent. The FTI can be administered after administration of the PI3K pathway targeting agent. The FTI can be administered prior to administration of the PI3K-α inhibitor. The FTI can be administered simultaneously with the PI3K-α inhibitor. The FTI may be administered following administration of the PI3K-α inhibitor.

[0341] In some embodiments, the PI3K-α inhibitor is BYL719, and provided herein is the combined use of BYL719 and an FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the second active agent is BYL719, and provided herein is the combined use of BYL719 and an FTI in selectively treating SCC in subjects carrying an H-Ras genetic mutation. In some embodiments, the second active agent is BYL719, and provided herein is the combined use of BYL719 and an FTI in selectively treating SCC in subjects carrying an H-Ras genetic mutation and a PIK3CA genetic mutation. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of BYL719 and tipifarnib in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of BYL719 and tipifarnib in selectively treating SCC in subjects carrying an H-Ras gene mutation. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of BYL719 and tipifarnib in selectively treating SCC in subjects carrying an H-Ras gene mutation and a PIK3CA gene mutation. Tipifarnib can be administered prior to administration of BYL719. Tipifarnib can be administered simultaneously with BYL719. Tipifarnib can be administered following administration of BYL719.

[0342] In some embodiments, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC described herein or otherwise known in the art. The SCC can be HNSCC. The SCC can be esophageal SCC. The SCC can be thyroid SCC. The SCC can be LSCC. The SCC can be bladder SCC. The SCC can be urothelial carcinoma (UC).

[0343] In some embodiments, the second active agent is an AKT inhibitor, and the present disclosure provides a combination of an AKT inhibitor and an FTI for selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression that is higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression that is higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras that is higher than a reference ratio.In some embodiments, the second active agent is an AKT inhibitor, and the present disclosure provides a combination of an AKT inhibitor and an FTI for selectively treating SCC in subjects with H-Ras gene mutation.In some embodiments, the AKT inhibitor is MK2206, GSK2110183, or GSK2141795. In some embodiments, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. The FTI can be administered before the administration of the AKT inhibitor. The FTI can be administered simultaneously with the AKT inhibitor. The FTI can be administered after the administration of the AKT inhibitor.

[0344] In some embodiments, the AKT inhibitor is GSK2141795, and provided herein is the combined use of GSK2141795 and FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the second active agent is GSK2141795, and provided herein is the combined use of GSK2141795 and FTI in selectively treating SCC in subjects with H-Ras gene mutations. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of GSK2141795 and tipifarnib in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of GSK2141795 and tipifarnib in selectively treating SCC in subjects with H-Ras gene mutations. Tipifarnib can be administered before administration of GSK2141795. Tipifarnib can be administered simultaneously with GSK2141795. Tipifarnib can be administered after administration of GSK2141795.

[0345] In some embodiments, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC described herein or otherwise known in the art. The SCC can be HNSCC. The SCC can be esophageal SCC. The SCC can be thyroid SCC. The SCC can be LSCC. The SCC can be bladder SCC. The SCC can be urothelial carcinoma (UC).

[0346] In some embodiments, the second active agent is an MTOR1 / 2 inhibitor, and provided herein is the combined use of an MTOR1 / 2 inhibitor and an FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio.In some embodiments, the second active agent is an MTOR1 / 2 inhibitor, and provided herein is the combined use of an MTOR1 / 2 inhibitor and an FTI in selectively treating SCC in subjects with H-Ras gene mutation.In some embodiments, the MTOR1 / 2 inhibitor is INK-128. In some embodiments, the FTI can be tipifarnib, lonafarnib, arglabin, perillyl alcohol, L778123, L739749, FTI-277, L744832, CP-609,754, R208176, AZD3409, or BMS-214662. The FTI can be administered prior to administration of the MTOR1 / 2 inhibitor. The FTI can be administered simultaneously with the MTOR1 / 2 inhibitor. The FTI can be administered after administration of the MTOR1 / 2 inhibitor.

[0347] In some embodiments, the MTOR1 / 2 inhibitor is INK-128, and provided herein is the combined use of INK-128 and FTI in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to the combined expression of K-Ras and N-Ras higher than a reference ratio.In some embodiments, the second active agent is INK-128, and provided herein is the combined use of INK-128 and FTI in selectively treating SCC in subjects with H-Ras gene mutations. In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of INK-128 and tipifarnib in selectively treating SCC in subjects with H-Ras overexpression, a ratio of H-Ras expression to K-Ras expression higher than a reference ratio, a ratio of H-Ras expression to N-Ras expression higher than a reference ratio, or a ratio of H-Ras expression to combined expression of K-Ras and N-Ras higher than a reference ratio.In some embodiments, the FTI is tipifarnib, and provided herein is the combined use of INK-128 and tipifarnib in selectively treating SCC in subjects with H-Ras gene mutation.Tipifarnib can be administered before administration of INK-128.Tipifarnib can be administered simultaneously with INK-128.Tipifarnib can be administered after administration of INK-128.

[0348] In some embodiments, the SCC is human papillomavirus (HPV) negative. In some embodiments, the SCC is at an advanced stage. In some embodiments, the SCC is metastatic SCC. In some embodiments, the SCC is recurrent SCC. In some embodiments, the SCC is refractory. The SCC can be a specific type of SCC described herein or otherwise known in the art. The SCC can be HNSCC. The SCC can be esophageal SCC. The SCC can be thyroid SCC. The SCC can be LSCC. The SCC can be bladder SCC. The SCC can be urothelial carcinoma (UC).

[0349] In some embodiments, the second active agent is a DNA hypomethylating agent, such as a cytidine analog (e.g., azacytidine) or 5-azadeoxycytidine (e.g., decitabine). In some embodiments, the second active agent is a cytoreductive agent, including but not limited to, Induction, topotecan, hydrea, PO etoposide, lenalidomide, LDAC, and thioguanine. In some embodiments, the second active agent is mitoxantrone, etoposide, cytarabine, or valspodar. In some embodiments, the second active agent is mitoxantrone + valspodar, etoposide + valspodar, or cytarabine + valspodar. In some embodiments, the second active agent is idarubicin, fludarabine, topotecan, or ara-C. In some other embodiments, the second active agent is idarubicin + ara-C, fludarabine + ara-C, mitoxantrone + ara-C, or topotecan + ara-C. In some embodiments, the second active agent is quinine. Other combinations of the above agents can be used, and dosages can be determined by a physician.

[0350] The treatments described herein or otherwise available in the art can be used in combination with FTI treatments. For example, drugs that can be used in combination with FTIs include belinostat (Beleodaq®) and pralatrexate (Folotyn®) marketed by Spectrum Pharmaceuticals, romidepsin (Istodax®) marketed by Celgene, and brentuximab vedotin (Adcetris®) marketed by Seattle Genetics; azacitidine (Vidaza®) and lenalidomide (Revlimid®) marketed by Celgene, and decitabine (Dacogen®) marketed by Otsuka and Johnson & Johnson; vandetanib (Caprelsa®), sorafenib (Nexavar®) from Bayer, cabozantinib (Cometriq®) from Exelixis, and lenvatinib (Lenvima®) from Eisai.

[0351] Non-cytotoxic therapies, such as pralatrexate (Folotyn®), romidepsin (Istodax®), and belinostat (Beleodaq®), can also be used in combination with FTI treatment.

[0352] In some embodiments, the secondary active agent is a DNA hypomethylating agent. In some embodiments, the secondary active agent is cytarabine, daurubicin, idarubicin, or gemtuzumab, or ozogamicin. In some embodiments, the secondary active agent is a DNA hypomethylating agent, such as azacitidine or decitabine.

[0353] In some embodiments, the second active agent is an immunotherapeutic agent. In some embodiments, the second active agent is an anti-PD1 antibody. In some embodiments, the second active agent is an anti-PDL1 antibody. In some embodiments, the second active agent is an anti-CTLA-4 antibody.

[0354] It is contemplated that in some embodiments, a second active agent or second therapy used in combination with an FTI may be administered prior to, simultaneously with, or after FTI treatment. In some embodiments, a second active agent or second therapy used in combination with an FTI may be administered prior to FTI treatment. In some embodiments, a second active agent or second therapy used in combination with an FTI may be administered simultaneously with FTI treatment. In some embodiments, a second active agent or second therapy used in combination with an FTI may be administered after FTI treatment.

[0355] In some embodiments, the FTI treatment is administered in conjunction with a bone marrow transplant. In some embodiments, the FTI is administered prior to the performance of the bone marrow transplant. In some embodiments, the FTI is administered simultaneously with the bone marrow transplant. In some embodiments, the FTI is administered after the performance of the bone marrow transplant.

[0356] In some embodiments, the FTI treatment is administered in combination with stem cell transplantation. In some embodiments, the FTI is administered before stem cell transplantation. In some embodiments, the FTI is administered simultaneously with stem cell transplantation. In some embodiments, the FTI is administered after stem cell transplantation.

[0357] One of skill in the art will understand that the methods described herein include the use of any permutation or combination of the particular FTIs, formulations, dosing regimens, and additional therapies to treat the subjects described herein.

[0358] It is understood that modifications that do not substantially affect the operation of the various embodiments of the present invention are also provided within the definition of the present invention provided herein.Thus, the following examples are intended to illustrate the present invention, but are not intended to limit the present invention.All references cited herein are incorporated by reference in their entirety. EXAMPLES

[0359] Example I Increased in vivo efficacy of tipifarnib in HNSCC with high H-Ras expression or high H / N+K ratio To generate tumors, primary human tumor model fragments (2–3 mm in diameter) were inoculated subcutaneously into the right flank of female BALB / c nude mice or Nu / nu mice (6–8 weeks old). The average tumor size was approximately 250–350 mm. 3 When tumor size reached 100 mg / kg, mice were randomly grouped into treatment groups. Animals were orally administered tipifarnib vehicle (20% w / v hydroxypropyl-β-cyclodextrin) or tipifarnib at a dose of 80 mg / kg BID for 3–4 weeks, and tumor dimensions were measured twice weekly.

[0360] The ability of tipifarnib to inhibit tumor growth was determined using selected patient-derived xenograft (PDX) models of HNSCC. The selected models expressed...

Claims

[Claim 1] The invention described in the specification.

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