APOE genotyping in cancer prognosis and treatment

Abstract

The present disclosure provides a method and reagent for cancer prognosis and treatment based on APOE genotyping.Specifically, the presence of APOE2 genotype indicates a poor prognosis for the subject, while the presence of APOE4 genotype indicates a good prognosis for the subject.The disclosed method and reagent are useful for treating cancer and making medical and clinical decisions regarding adjuvant therapy, tumor monitoring, and the likelihood of disease progression.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application No. 62 / 811,575, filed February 28, 2019, the contents of which are incorporated herein by reference in their entirety.

[0002] STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH This invention was made with Government support under 5R01CA184804 awarded by the National Institutes of Health. The Government has certain rights in this invention.

[0003] Technical Field The present invention relates generally to methods and reagents for cancer prognosis and treatment, and more specifically to methods and reagents for cancer prognosis and treatment based on APOE genotyping (also known as GENOTYPING). [Background technology]

[0004] Background technology Cancer remains one of the leading causes of death in the United States. Clinically, a wide variety of medical approaches, including surgery, radiation therapy, and chemotherapy drug therapy, are currently used to treat cancer in humans. However, it is recognized that such approaches continue to be limited by a fundamental inability to accurately predict the likelihood of metastasis and tumor recurrence, or the most effective treatment plan to minimize the occurrence of these negative outcomes.

[0005] The discovery and clinical validation of markers for all types of cancer that can predict prognosis, the likelihood of invasive or metastatic spread is one of the major challenges facing oncology today. For example, in breast cancer, 70% of the approximately 186,000 cases per year present as node-negative; however, 30% of these cases recur after local therapy (mastectomy or "lumpectomy") (Boring et al., Clin. J. Cancer 42: 19-38 (1992)). In order to determine the appropriate treatment for these patients, it remains unclear how to best identify patients whose risk of disease recurrence exceeds the risk of significant treatment toxicity (Osbourne, J. Clin. Oncol. 10: 679-682 (1992)).

[0006] Thus, there remains a great need to develop methods and reagents for cancer treatment and prognosis to determine the likelihood of adjuvant therapy, tumor monitoring, and disease progression. Summary of the Invention

[0007] Summary of the Invention The present disclosure addresses the above needs in several aspects. In one aspect, the present disclosure provides a method for treating cancer in a subject having at least one ε4 allele from rs7412 or rs429358 polymorphism, or ε3 allele from rs7412 and rs429358 polymorphism, in the ApoE gene on chromosome 19. The method comprises administering to the subject an effective amount of an LXRβ agonist or a pharma- ceutically acceptable salt thereof.

[0008] In another aspect, the present disclosure provides a method of treating cancer in a subject, the method comprising: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; and (b) administering to the subject an effective amount of an LXRβ agonist or a pharma- ceutically acceptable salt thereof.

[0009] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19, and identified as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof based on the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms; and (b) administering an effective amount of the LXRβ agonist or a pharma- ceutically acceptable salt thereof to the identified subject.

[0010] In some embodiments, the method comprises: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; (c) identifying a subject having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof; and (d) administering an effective amount of the LXRβ agonist or a pharma- ceutically acceptable salt thereof to the identified subject, thereby treating the cancer.

[0011] In another aspect, the disclosure also provides a method for identifying an individual having cancer who may benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof, comprising: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19; and (c) identifying a subject having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19, as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof. thereby identifying individuals with cancer who may benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof.

[0012] In some embodiments, the LXRβ agonist has the structure:

[0013] [ka]

[0014] or a pharma- ceutically acceptable salt thereof.

[0015] In another aspect, the present disclosure further provides a method of treating cancer in a subject having at least one ε4 allele from the rs7412 or rs429358 polymorphisms, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19. The method comprises administering to the subject an effective amount of a PD-1 inhibitor (e.g., nivolumab, pembrolizumab, pidilizumab, BMS 936559, and atezolizumab) or a PD-L1 inhibitor (e.g., atezolizumab and durvalumab), or a pharma- ceutically acceptable salt thereof.

[0016] In another aspect, the disclosure provides a method of treating cancer in a subject in need thereof, the method comprising: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; and (b) administering to the subject an effective amount of a PD-1 inhibitor (e.g., nivolumab, pembrolizumab, pidilizumab, BMS 936559, and atezolizumab) or a PD-L1 inhibitor (e.g., atezolizumab and durvalumab), or a pharma- ceutical acceptable salt thereof.

[0017] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19, and identified as likely to benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof, based on the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms; and (b) administering an effective amount of a PD-1 inhibitor or a PD-L1 inhibitor to the identified subject.

[0018] In some embodiments, the method comprises: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; (c) identifying subjects having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof, to the identified subject, thereby treating the cancer.

[0019] In some embodiments, the disclosure provides methods for identifying individuals with cancer who may benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor. The method includes: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; and (c) identifying subjects having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof, thereby identifying individuals having cancer who may benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof.

[0020] In some embodiments, the subject has previously been administered a CTLA-4 inhibitor, or a pharma- ceutically acceptable salt thereof.

[0021] In some embodiments, the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or the ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19 is determined by polymerase chain reaction (PCR).

[0022] In some embodiments, the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or the ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19 is determined by the expression level of the APOE3 or APOE4 protein of the subject.

[0023] In some embodiments, the cancer is breast cancer, colon cancer, renal cell carcinoma, lung cancer, hepatocellular carcinoma, gastric cancer, ovarian cancer, pancreatic cancer, esophageal cancer, prostate cancer, sarcoma, bladder cancer, head and neck cancer, glioblastoma, diffuse large B-cell lymphoma, leukemia, or melanoma. In some embodiments, the cancer is melanoma, small cell lung cancer, or non-small cell lung cancer. In some embodiments, the cancer is metastatic and / or locally advanced. In some embodiments, the cancer is unresectable.

[0024] In some embodiments, the effective amount includes an amount effective to inhibit metastatic colonization of the cancer (eg, metastatic colonization of the liver and / or brain).

[0025] In some embodiments, the cancer is resistant to platinum-containing chemotherapy, PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, mitosis inhibitors, topoisomerase inhibitors, antimetabolites, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents. In some embodiments, the cancer has progressed during or after treatment with platinum-containing chemotherapy, PD-1 inhibitors, PD-L1 inhibitors, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents. In some embodiments, the cancer has been determined or is predicted to be resistant to PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, topoisomerase inhibitors, antimetabolites, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents.

[0026] In some embodiments, the method further comprises administering to the subject an additional anti-cancer therapy. In some embodiments, the additional anti-cancer therapy comprises surgery, radiation therapy, chemotherapy, and / or immunotherapy. In some embodiments, the additional anti-cancer therapy comprises chemotherapy and / or immunotherapy. In some embodiments, the chemotherapy comprises docetaxel, carboplatin or cisplatin, pemetrexed, and / or pembrolizumab.

[0027] In some embodiments, the method further comprises administering to the subject an effective amount of folic acid, vitamin B12, a corticosteroid, a statin, an antiemetic, an antidiarrheal, an appetite stimulant, a general stimulant, a bisphosphonate, a gonadotropin releasing hormone agonist, a growth factor, and / or an LHRH agonist.

[0028] In some embodiments, the subject has an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene. In some embodiments, the subject has at least one ε4 allele from the rs7412 or rs429358 polymorphisms in the ApoE gene. In some embodiments, the subject has an ε4 allele from the rs7412 and rs429358 polymorphisms, an ε3 allele and an ε4 allele from the rs7412 and rs429358 polymorphisms, or an ε2 allele and an ε4 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene. In some embodiments, the subject has an ε4 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene.

[0029] In yet another aspect, the present disclosure further provides a method of treating cancer in a subject having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19. The method comprises administering an active treatment to the subject.

[0030] In another aspect, the disclosure provides a method of treating cancer in a subject in need thereof, comprising: (a) providing a subject identified as having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19; and (b) administering an active treatment to the subject.

[0031] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 and identified as likely to benefit from aggressive treatment based on the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism; and (b) administering aggressive treatment to the identified subject.

[0032] In some embodiments, the method comprises: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19; (c) identifying subjects having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 as likely to benefit from aggressive treatment; and (d) administering aggressive treatment to the identified subjects, thereby treating the cancer.

[0033] In another aspect, the present disclosure provides a method for identifying individuals with cancer who may benefit from aggressive treatment, the method comprising: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19; and (c) identifying subjects who have at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 as likely to benefit from aggressive treatment, thereby identifying individuals with cancer who may benefit from aggressive treatment.

[0034] In some embodiments, the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 is determined by PCR. In some embodiments, the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 is determined by the expression level of APOE2 protein in the subject.

[0035] In some embodiments, the subject has an ε2 allele from the rs7412 and rs429358 polymorphisms, or an ε2 allele and an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19.

[0036] In some embodiments, the active treatment comprises administration of 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof and concomitantly an effective amount of immunotherapy.

[0037] In some embodiments, the active treatment further comprises performing surgery on the subject. In some embodiments, the 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof is administered prior to surgery. In some embodiments, the 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof is administered post-surgery.

[0038] In some embodiments, the immunotherapy is a PD-1 inhibitor, a PD-L1 inhibitor, or a CTLA-4 inhibitor.

[0039] In another aspect, the disclosure further provides a kit comprising a probe having a first nucleic acid sequence complementary to a second nucleic acid sequence selected from the group consisting of APOE2, APOE3, and APOE4, wherein the probe hybridizes to the second nucleic acid sequence under stringent conditions. In some embodiments, the first nucleic acid sequence is 15-200 bases in length.

[0040] In some embodiments, the kit comprises a labeled probe having a sequence complementary to APOE2, APOE3, and APOE4, respectively. In some embodiments, the second nucleic acid comprises a sequence selected from the group consisting of SEQ ID NOs: 1-3.

[0041] In some embodiments, the kit further comprises a pair of primers configured to specifically bind to sequences flanking a genomic region to allow PCR amplification of at least one of APOE2, APOE3, and APOE4 that comprises the genomic region. In some embodiments, the pair of primers comprises primers having a sequence selected from the group consisting of SEQ ID NOs: 4-16.

[0042] In some embodiments, the probe is linked to a detectable label, hi some embodiments, the detectable label is selected from the group consisting of a fluorophore, a dye, a radioactive label, an enzyme, and biotin.

[0043] In yet other embodiments, the disclosure also provides an array comprising a support having a plurality of unique locations, said array consisting essentially of at least a nucleic acid having a sequence complementary to a nucleic acid sequence selected from the group consisting of APOE2, APOE3, and APOE4. In some embodiments, said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-3.

[0044] The foregoing summary is not intended to define all aspects of the disclosure, and additional aspects are described in other sections, such as the following detailed description. It is understood that this entire document is intended to relate as a unified disclosure, and that all combinations of features described herein are contemplated, even if the combinations of features are not found together in the same sentence, paragraph, or section of this document. Other features and advantages of the present invention will become apparent from the following detailed description. However, it should be understood that the detailed description and specific examples, while showing specific embodiments of the present disclosure, are given by way of illustration only, since various changes and modifications within the spirit and scope of the present disclosure will become apparent to those skilled in the art from this detailed description. [Brief description of the drawings]

[0045] BRIEF DESCRIPTION OF THE DRAWINGS [Figure 1-1]Figure 1a, Figure 1b, Figure 1c, Figure 1d, Figure 1e, and Figure 1f are a series of figures showing that Apolipoprotein E (APOE) germline variants were used to predict human melanoma survival. Figure 1a shows the two amino acids that define the three common APOE variants, APOE2, APOE3, and APOE4. Structural representation of human APOE3 (PDB ID: 2L7B; Chen et al., PNAS, 2011). The presence of cysteine ​​or arginine at positions 112 and 158 distinguishes the alleles APOE2 (abbreviated as E2), APOE3 (abbreviated as E2), and APOE4 (abbreviated as E2). Figure 1b shows a computational pipeline for analyzing the impact of APOE genotypes on the outcome of melanoma patients in the TCGA-SKCM cohort. Figure 1c shows the proportion of E2 and E4 carriers in the Atherosclerosis Risk in Communities Study (ARIC) and TCGA-SKCM cohorts. As shown, non-E2 / E4 carriers were slightly over-represented in the TCGA-SKCM cohort versus the healthy population (P=0.0017, χ2 test). Figure 1d shows predicted survival of APOE carrier status in melanoma patients. Survival of the TCGA-SKCM cohort stratified by APOE carrier status (P=0.014, log-rank test for trend). Figure 1e shows that APOE variants exert a gene dosage effect on melanoma survival. Survival of the TCGA-SKCM cohort stratified by biallelic APOE genotype (P=0.016, log-rank test for trend). Figure 1f shows that APOE carrier status was associated with survival in patients with progressive localized disease. Survival of stage II-III patients in the TCGA-SKCM cohort stratified by APOE carrier status (P = 0.0025, log-rank test for trend). Numbers in parentheses represent sample sizes. [Figure 1-2]Figure 1a, Figure 1b, Figure 1c, Figure 1d, Figure 1e, and Figure 1f are a series of figures showing that Apolipoprotein E (APOE) germline variants were used to predict human melanoma survival. Figure 1a shows the two amino acids that define the three common APOE variants, APOE2, APOE3, and APOE4. Structural representation of human APOE3 (PDB ID: 2L7B; Chen et al., PNAS, 2011). The presence of cysteine ​​or arginine at positions 112 and 158 distinguishes the alleles APOE2 (abbreviated as E2), APOE3 (abbreviated as E2), and APOE4 (abbreviated as E2). Figure 1b shows a computational pipeline for analyzing the impact of APOE genotypes on the outcome of melanoma patients in the TCGA-SKCM cohort. Figure 1c shows the proportion of E2 and E4 carriers in the Atherosclerosis Risk in Communities Study (ARIC) and TCGA-SKCM cohorts. As shown, non-E2 / E4 carriers were slightly over-represented in the TCGA-SKCM cohort versus the healthy population (P=0.0017, χ2 test). Figure 1d shows predicted survival of APOE carrier status in melanoma patients. Survival of the TCGA-SKCM cohort stratified by APOE carrier status (P=0.014, log-rank test for trend). Figure 1e shows that APOE variants exert a gene dosage effect on melanoma survival. Survival of the TCGA-SKCM cohort stratified by biallelic APOE genotype (P=0.016, log-rank test for trend). Figure 1f shows that APOE carrier status was associated with survival in patients with progressive localized disease. Survival of stage II-III patients in the TCGA-SKCM cohort stratified by APOE carrier status (P = 0.0025, log-rank test for trend). Numbers in parentheses represent sample sizes. [Figure 1-3]Figure 1a, Figure 1b, Figure 1c, Figure 1d, Figure 1e, and Figure 1f are a series of figures showing that Apolipoprotein E (APOE) germline variants were used to predict human melanoma survival. Figure 1a shows the two amino acids that define the three common APOE variants, APOE2, APOE3, and APOE4. Structural representation of human APOE3 (PDB ID: 2L7B; Chen et al., PNAS, 2011). The presence of cysteine ​​or arginine at positions 112 and 158 distinguishes the alleles APOE2 (abbreviated as E2), APOE3 (abbreviated as E2), and APOE4 (abbreviated as E2). Figure 1b shows a computational pipeline for analyzing the impact of APOE genotypes on the outcome of melanoma patients in the TCGA-SKCM cohort. Figure 1c shows the proportion of E2 and E4 carriers in the Atherosclerosis Risk in Communities Study (ARIC) and TCGA-SKCM cohorts. As shown, non-E2 / E4 carriers were slightly over-represented in the TCGA-SKCM cohort versus the healthy population (P=0.0017, χ2 test). Figure 1d shows predicted survival of APOE carrier status in melanoma patients. Survival of the TCGA-SKCM cohort stratified by APOE carrier status (P=0.014, log-rank test for trend). Figure 1e shows that APOE variants exert a gene dosage effect on melanoma survival. Survival of the TCGA-SKCM cohort stratified by biallelic APOE genotype (P=0.016, log-rank test for trend). Figure 1f shows that APOE carrier status was associated with survival in patients with progressive localized disease. Survival of stage II-III patients in the TCGA-SKCM cohort stratified by APOE carrier status (P = 0.0025, log-rank test for trend). Numbers in parentheses represent sample sizes. [Figure 1-4]Figure 1a, Figure 1b, Figure 1c, Figure 1d, Figure 1e, and Figure 1f are a series of figures showing that Apolipoprotein E (APOE) germline variants were used to predict human melanoma survival. Figure 1a shows the two amino acids that define the three common APOE variants, APOE2, APOE3, and APOE4. Structural representation of human APOE3 (PDB ID: 2L7B; Chen et al., PNAS, 2011). The presence of cysteine ​​or arginine at positions 112 and 158 distinguishes the alleles APOE2 (abbreviated as E2), APOE3 (abbreviated as E2), and APOE4 (abbreviated as E2). Figure 1b shows a computational pipeline for analyzing the impact of APOE genotypes on the outcome of melanoma patients in the TCGA-SKCM cohort. Figure 1c shows the proportion of E2 and E4 carriers in the Atherosclerosis Risk in Communities Study (ARIC) and TCGA-SKCM cohorts. As shown, non-E2 / E4 carriers were slightly over-represented in the TCGA-SKCM cohort versus the healthy population (P=0.0017, χ2 test). Figure 1d shows predicted survival of APOE carrier status in melanoma patients. Survival of the TCGA-SKCM cohort stratified by APOE carrier status (P=0.014, log-rank test for trend). Figure 1e shows that APOE variants exert a gene dosage effect on melanoma survival. Survival of the TCGA-SKCM cohort stratified by biallelic APOE genotype (P=0.016, log-rank test for trend). Figure 1f shows that APOE carrier status was associated with survival in patients with progressive localized disease. Survival of stage II-III patients in the TCGA-SKCM cohort stratified by APOE carrier status (P = 0.0025, log-rank test for trend). Numbers in parentheses represent sample sizes. [Figure 2-1]Figure 2a, Figure 2b, Figure 2c, and Figure 2d are a series of diagrams showing that human APOE variants determine tumor progression in a mouse melanoma model. Figure 2a shows that human APOE variants regulate progression in a transplantable Braf-mutated YUMM1.7 mouse melanoma model. Tumor volumes of 100,000 YUMM1.7 cells injected into human APOE-targeted replacement mice (n=9-11 per group, *p<0.05, **p<0.01, one-tailed t-test; data representative of two independent experiments). Representative tumors correspond to day 26 (scale bar, 5 mm). Figure 2b shows a schematic of the experimental approach to evaluate the impact of human APOE alleles on the progression of genetically induced mouse melanoma. Human APOE3 and APOE4 knock-in mice were crossed with Tyr::CreER;BrafV600E / +;Ptenlox / lox mice, which develop genetically driven melanoma upon tamoxifen-induced melanocyte-specific Cre expression. Figure 2c shows that APOE4 / E4 mice exhibit reduced tumor burden compared to APOE3 / E3 mice in a genetically induced melanoma model. Melanoma burden measured as a percentage of the dorsal skin area of ​​the mice described in Figure 2c at day 35 after melanoma induction (p=0.01, one-sided Mann-Whitney test). Representative skin images are shown on the right. *p<0.05. Box plots show median, 1st and 3rd quartiles, whiskers represent minimum and maximum values. All data points are displayed with each circle corresponding to one mouse. Numbers in brackets indicate sample size. FIG. 2d shows that stromal APOE genotype also regulates metastatic progression of 100,000 intravenously injected B16F10-TR-shApoE cells (n=10 per group, one-tailed Mann-Whitney test; representative of two independent experiments). [Figure 2-2]Figure 2a, Figure 2b, Figure 2c, and Figure 2d are a series of diagrams showing that human APOE variants determine tumor progression in a mouse melanoma model. Figure 2a shows that human APOE variants regulate progression in a transplantable Braf-mutated YUMM1.7 mouse melanoma model. Tumor volumes of 100,000 YUMM1.7 cells injected into human APOE-targeted replacement mice (n=9-11 per group, *p<0.05, **p<0.01, one-tailed t-test; data representative of two independent experiments). Representative tumors correspond to day 26 (scale bar, 5 mm). Figure 2b shows a schematic of the experimental approach to evaluate the impact of human APOE alleles on the progression of genetically induced mouse melanoma. Human APOE3 and APOE4 knock-in mice were crossed with Tyr::CreER;BrafV600E / +;Ptenlox / lox mice, which develop genetically driven melanoma upon tamoxifen-induced melanocyte-specific Cre expression. Figure 2c shows that APOE4 / E4 mice exhibit reduced tumor burden compared to APOE3 / E3 mice in a genetically induced melanoma model. Melanoma burden measured as a percentage of the dorsal skin area of ​​the mice described in Figure 2c at day 35 after melanoma induction (p=0.01, one-sided Mann-Whitney test). Representative skin images are shown on the right. *p<0.05. Box plots show median, 1st and 3rd quartiles, whiskers represent minimum and maximum values. All data points are displayed with each circle corresponding to one mouse. Numbers in brackets indicate sample size. FIG. 2d shows that stromal APOE genotype also regulates metastatic progression of 100,000 intravenously injected B16F10-TR-shApoE cells (n=10 per group, one-tailed Mann-Whitney test; representative of two independent experiments). [Figure 3-1]Figure 3a, Figure 3b, Figure 3c, Figure 3d, Figure 3e, Figure 3f, Figure 3g, and Figure 3h are a series of figures showing biallelic APOE distribution and clinical characteristics of the TCGA-SKCM cohort. Figure 3a shows that the gender ratio was not significantly different between the APOE carrier groups (P = 0.717, χ2 test). Figure 3b shows that the age at diagnosis was not significantly different between the APOE carrier groups (P = 0.999, ANOVA). Figure 3c shows that the tumor stage at diagnosis was not significantly different between the APOE carrier groups (P = 0.1703, χ2 test). Figure 3d shows that the melanoma Clark level at diagnosis was not significantly different between the APOE carrier groups (P = 0.6579, χ2 test). Figure 3e shows that the Breslow depth at diagnosis was not significantly different between the APOE carrier groups (P = 0.2814, Kruskal-Wallis rank sum test). Figure 3f shows the proportion of APOE carrier status across molecular subtypes in the TCGA-SKCM cohort. As shown, APOE carrier status was not significantly associated with tumor mutation subtype (P=0.8703, χ2 test). Figure 3g shows the proportion of APOE carrier status across transcription clusters in the TCGA-SKCM cohort. As shown, APOE carrier status was not significantly associated with transcriptomics clusters (P=0.1176, χ2 test). Figure 3h shows the proportion of APOE genotypes in the Atherosclerosis Risk in Community (ARIC) and TCGA-SKCM cohorts. As shown, the distribution of biallelic APOE genotypes was somewhat skewed in the TCGA-SKCM cohort versus the healthy population (P=0.0056, χ2 test). [Figure 3-2]Figure 3a, Figure 3b, Figure 3c, Figure 3d, Figure 3e, Figure 3f, Figure 3g, and Figure 3h are a series of figures showing biallelic APOE distribution and clinical characteristics of the TCGA-SKCM cohort. Figure 3a shows that the gender ratio was not significantly different between the APOE carrier groups (P = 0.717, χ2 test). Figure 3b shows that the age at diagnosis was not significantly different between the APOE carrier groups (P = 0.999, ANOVA). Figure 3c shows that the tumor stage at diagnosis was not significantly different between the APOE carrier groups (P = 0.1703, χ2 test). Figure 3d shows that the melanoma Clark level at diagnosis was not significantly different between the APOE carrier groups (P = 0.6579, χ2 test). Figure 3e shows that the Breslow depth at diagnosis was not significantly different between the APOE carrier groups (P = 0.2814, Kruskal-Wallis rank sum test). Figure 3f shows the proportion of APOE carrier status across molecular subtypes in the TCGA-SKCM cohort. As shown, APOE carrier status was not significantly associated with tumor mutation subtype (P=0.8703, χ2 test). Figure 3g shows the proportion of APOE carrier status across transcription clusters in the TCGA-SKCM cohort. As shown, APOE carrier status was not significantly associated with transcriptomics clusters (P=0.1176, χ2 test). Figure 3h shows the proportion of APOE genotypes in the Atherosclerosis Risk in Community (ARIC) and TCGA-SKCM cohorts. As shown, the distribution of biallelic APOE genotypes was somewhat skewed in the TCGA-SKCM cohort versus the healthy population (P=0.0056, χ2 test). [Figure 4-1]Figure 4a, Figure 4b, Figure 4c, Figure 4d, Figure 4e, and Figure 4f are a series of figures showing that APOE genotype regulates melanoma progression under immunotherapy regimens. Figure 4a shows tumor growth and Figure 4b shows survival of human APOE knock-in mice injected with YUMMER1.7 tumors and treated with anti-PD1 antibodies (n=26 per group; P=0.022, two-tailed log-rank test; data pooled from two independent experiments; CR=complete remission). Figures 4c and 4d show survival of melanoma patients treated with anti-PD1 immunotherapy after failure of anti-CTLA4 treatment by Roh et al. and Riaz et al. Figure 4d shows the study stratified by APOE carrier status (p-value by log-rank test). Figure 4e shows the effect of LXR agonist treatment on YUMM1.7 tumor growth in human APOE knock-in mice (n=10 per group; two-tailed t-test; representative of two independent experiments). FIG. 4f shows the individual tumor volumes at 29 days post-injection from FIG. 4e. [Figure 4-2] Figure 4a, Figure 4b, Figure 4c, Figure 4d, Figure 4e, and Figure 4f are a series of figures showing that APOE genotype regulates melanoma progression under immunotherapy regimens. Figure 4a shows tumor growth and Figure 4b shows survival of human APOE knock-in mice injected with YUMMER1.7 tumors and treated with anti-PD1 antibodies (n=26 per group; P=0.022, two-tailed log-rank test; data pooled from two independent experiments; CR=complete remission). Figures 4c and 4d show survival of melanoma patients treated with anti-PD1 immunotherapy after failure of anti-CTLA4 treatment by Roh et al. and Riaz et al. Figure 4d shows the study stratified by APOE carrier status (p-value by log-rank test). Figure 4e shows the effect of LXR agonist treatment on YUMM1.7 tumor growth in human APOE knock-in mice (n=10 per group; two-tailed t-test; representative of two independent experiments). FIG. 4f shows the individual tumor volumes at 29 days post-injection from FIG. 4e. [Figure 4-3]Figure 4a, Figure 4b, Figure 4c, Figure 4d, Figure 4e, and Figure 4f are a series of figures showing that APOE genotype regulates melanoma progression under immunotherapy regimens. Figure 4a shows tumor growth and Figure 4b shows survival of human APOE knock-in mice injected with YUMMER1.7 tumors and treated with anti-PD1 antibodies (n=26 per group; P=0.022, two-tailed log-rank test; data pooled from two independent experiments; CR=complete remission). Figures 4c and 4d show survival of melanoma patients treated with anti-PD1 immunotherapy after failure of anti-CTLA4 treatment by Roh et al. and Riaz et al. Figure 4d shows the study stratified by APOE carrier status (p-value by log-rank test). Figure 4e shows the effect of LXR agonist treatment on YUMM1.7 tumor growth in human APOE knock-in mice (n=10 per group; two-tailed t-test; representative of two independent experiments). FIG. 4f shows the individual tumor volumes at 29 days post-injection from FIG. 4e. [Diagram 5] Figures 5a and 5b are a series of figures showing that APOE genotype modulates thyroid and breast cancer survival. Survival of stage II / III thyroid (Figure 5a) and breast (Figure 5b) cancer patients from the TCGA cohort stratified by APOE carrier status (log-rank test). [Figure 6] Figures 6a, 6b, and 6c are a series of figures showing that the effect of APOE genotype on breast cancer survival depends on tumor leukocyte infiltration. Figure 6a shows breast cancer patient survival in the TCGA cohort stratified by APOE genotype. Figures 6a, 6b, and 6c show breast cancer patient survival from (Figure 6a) stratified by high (Figure 6b) versus low (Figure 6c) leukocyte infiltration as assessed by RNA-seq deconvolution. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0046] Detailed Description of the Invention One of the most challenging features of human cancer is its unpredictable course after diagnosis. The present disclosure provides methods and reagents for cancer prognosis, based in part on the unexpected discovery that in human melanoma, a common genetic germline polymorphism of APOE, present in approximately 39% of Caucasians, predicts cancer progression and survival outcomes. Analysis of the Cancer Genome Atlas (TCGA) revealed that carriers of APOE2 variants have worse melanoma survival outcomes compared to carriers carrying the more common APOE3 variant. In contrast, carriers of APOE4 variants showed improved melanoma survival compared to APOE3 homozygotes. The effect of these alleles on melanoma outcomes was dose-dependent, with APOE2 homozygotes showing the shortest survival and APOE4 homozygotes showing the longest survival. Tumors grew more efficiently in human APOE2 than in APOE3 knock-in mice and least efficiently in APOE4 mice, suggesting that APOE variants causally regulate melanoma progression. Thus, APOE4 and APOE2 germline variants decrease and increase the likelihood of melanoma progression, respectively, and their risk-modifying roles are reversed in Alzheimer's disease.The findings are consistent with the idea that germline genetic makeup can influence future malignant trajectories.

[0047] The secreted glycoprotein apolipoprotein E (APOE) was previously found to suppress melanoma progression and metastasis through cancer cell autonomous and non-autonomous mechanisms. In humans, there are three common APOE variants, designated APOE2, APOE3, and APOE4, which differ by only two amino acids at positions 112 and 158 (Figure 1a) (Chen, J. et al., PNAS108, 14813-14818 (2011)). These variants are major genetic modifiers of risk for Alzheimer's disease and cardiovascular disease (Strittmatter, WJ et al., PNAS90, 1977-1981 (1993); Corder, EH et al., NatGenet7, 180-184 (1994); Mahley, RW, J Mol Med(Bed) 94, 739-746 (2016)), but their potential association with cancer outcome is so far inconclusive.

[0048] Given previous evidence supporting the role of APOE in melanoma progression, the association between germline APOE variant status and clinical outcomes in melanoma patients was investigated by determining APOE genotypes from normal tissue whole-exome sequencing data of 470 participants in the TCGA-SKCM study (Figure 1b) (Network, TCGA (2015), Cell, 161(7), 1681-1696). Compared to controls with similar age and ethnic composition, homozygotes for the most common APOE3 variants (i.e., non-E2 / E4 carriers) were somewhat overrepresented in the TCGA-SKCM cohort, indicating that both APOE2 and APOE4 carrier status do not predispose to increased melanoma incidence (Figure 1c). Surprisingly, however, APOE carrier status was significantly associated with survival. The median survival times for E2 carriers, E3;E3 homozygotes, and E4 carriers are 3.9, 5.5, and 10.1 years, respectively (Figure 1d). There were no significant differences in potential confounding characteristics, such as sex, age, tumor stage, melanoma Clark level, Breslow depth, mutations, or transcriptional subtypes, between the APOE carrier groups at diagnosis (Fig. 3a-g). Of note, stratifying patients by biallelic APOE genotype revealed an impact of gene dosing on survival (median survival was 3.6, 3.9, 5.8, and 9.4 years in E2;E2, E2;E3, E3;E3, E3;E4, and E4;E4, respectively, with median survival not reached) (Fig. 1f and Fig. 3h). Patients with advanced localized disease are at high risk of metastatic progression and therefore systemic therapy should be carefully considered. Such treatments carry risks of mortality and morbidity and should therefore ideally be administered to those at highest risk of progression. Therefore, we further evaluated whether the association between APOE genotype and survival was maintained in patients with melanoma stage in the TCGA-SKCM cohort. Indeed, APOE genotype stratified patient survival among this subgroup, suggesting that APOE genotype could be used to risk stratify these patients (Figure 1e).Thus, APOE genotype was significantly associated with melanoma survival in a gene dosage-dependent manner.

[0049] To assess whether APOE genotype simply correlates with altered melanoma outcome or is causally related, we utilized mice in which the endogenous mouse APOE locus was replaced with one of three human APOE variants. Using the Braf mutant YUMM1.7 melanoma model, we observed significantly slower tumor progression in E4;E4 compared with E3;E3 mice, and faster tumor progression in E2;E2 mice, consistent with APOE genotypes causally influencing melanoma progression (Figure 2a). The total allele frequency in Caucasians was 91.6%, with APOE3 and APOE4 being the most common alleles (Farrer, LA et al., JAMA278, 1349-1356 (1997)). Given their abundance, we assessed the impact of these APOE genotypes on a genetically driven melanoma model in which the tumor compartment also expresses the corresponding variant. To this end, APOE3 and APOE4 mice were transfected with Tyr:CreER;Braf V600E / + ;Pten lox / lox When the mice were crossed, melanoma formation could be initiated by tamoxifen-induced and Cre-mediated excision of Pten in melanocytes (Figure 2b). Consistent with the results of the transplantable melanoma model, we observed mice with the E4;E4 genotype exhibiting reduced melanoma tumor burden compared to E3;E3 mice (Figure 2c). Furthermore, we evaluated the impact of APOE genotype on metastatic progression using the highly aggressive B16F10-TR-shApoE model (in which endogenous mouse ApoE is depleted). Metastatic burden was found to progress significantly faster in APOE2 mice than in APOE3 and APOE4 mice (Figure 2d). Thus, human APOE alleles causally govern progression in a syngeneic mouse melanoma model consistent with the clinically relevant data presented above.

[0050] The results described herein reveal that genetic variants present in the germline can predict and influence the progression of common human cancers. In particular, common variants of APOE, a pleiotropic suppressor of metastatic melanoma phenotype, show different effects on tumor progression. Thus, the present disclosure provides methods for treating cancer based on the presence of APOE genotypes. Furthermore, the present disclosure provides methods for making medical and clinical decisions about neoadjuvant and adjuvant therapy, tumor surveillance, and the likelihood of disease progression based on the presence of APOE genotypes that are coincidentally associated with tumor progression.

[0051] I. METHODS FOR TREATING CANCER AND PROGNOSIS OF CANCER A. Methods of Treating Cancer The present disclosure addresses the above needs in several aspects. In one aspect, the present disclosure provides a method for treating cancer in a subject having at least one ε4 allele from rs7412 or rs429358 polymorphisms, or an ε3 allele from rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19. The method includes administering to the subject an effective amount of an anti-cancer or anti-tumor agent, or a pharma- ceutically acceptable salt thereof. In some embodiments, the anti-cancer or anti-tumor agent is an LXRβ agonist.

[0052] APOE is polymorphic with three major alleles / isoforms, as defined by two single nucleotide polymorphisms (SNPs), rs429358 and rs7412, known as ApoE-ε2, ApoE-ε3, and ApoE-ε4. The proteins produced by these genes are called ApoE2, ApoE3, and ApoE4. In some embodiments, APOE2 can include Cys112 and Cys158 residues, APOE3 can include Cys112 and Arg158 residues, and APOE4 can include Arg112 and Arg158 residues.

[0053] These allelic forms may differ from each other by only one or two amino acids at positions 112 and 158, but these differences alter the structure and function of APOE. The nucleotide sequences of human APOE2, APOE3, and APOE4 are shown in Table 1. In some embodiments, specific APOE genotypes may include APOE genes having the sequences of SEQ ID NOs: 1-3.

[0054] [Table 1-1]

[0055] [Table 1-2]

[0056] [Table 1-3]

[0057] In many embodiments, the terms "subject" and "patient" are used interchangeably, regardless of whether the subject has undergone or is currently undergoing any form of treatment. As used herein, the terms "subject" and "subjects" may refer to any vertebrate, including, but not limited to, mammals (e.g., cows, pigs, camels, llamas, horses, goats, rabbits, sheep, hamsters, guinea pigs, cats, dogs, rats, and mice, non-human primates (e.g., monkeys such as cynomolgus monkeys), chimpanzees, etc.), and humans). A subject may be human or non-human. In this context, a "normal," "control," or "reference" subject, patient, or population, respectively, is one that does not exhibit a detectable disease or disorder. In some embodiments, a "normal," "control," or "reference" subject has an APOE3 genotype.

[0058] In a more exemplary embodiment, the mammal is a human. As used herein, the phrase "subject in need thereof" or "patient in need thereof" refers to a human or non-human mammal that exhibits one or more symptoms or signs of cancer or tumor and / or has been diagnosed with a tumor or cancer, including a solid tumor, and is in need of treatment. The phrase includes subjects with primary, established, or recurrent tumor lesions. In certain embodiments, the phrase includes human subjects undergoing and / or in need of treatment for a solid tumor. The phrase also includes subjects with primary or metastatic tumors (advanced malignancies). In certain embodiments, the phrase includes patients with solid tumors that are resistant or refractory to, or poorly controlled by, previous treatments (e.g., surgery, or treatment with anticancer agents such as carboplatin or docetaxel). In certain embodiments, the phrase includes patients with tumor lesions that have been treated (e.g., surgically removed) with one or more lines of previous treatment, but have subsequently recurred. In some embodiments, the phrase includes subjects with tumors or cancers who are not candidates for curative surgery or curative radiation, or for whom conventional anti-cancer therapies are not recommended, e.g., due to toxic side effects. In other embodiments, the phrase includes subjects with tumor lesions for which surgical removal is planned. In other embodiments, the phrase includes subjects at high risk of recurrence due to a history of recurrence after surgery.

[0059] As used to describe the present invention, "cancer," "tumor," and "malignant tumor" all relate equally to hyperplasia of a tissue or organ. Where the tissue is part of the lymphatic or immune system, the malignant cells may include non-solid tumors of circulating cells. Malignant tumors of other tissues or organs may produce solid tumors. The methods of the present invention may be used to treat lymphatic cells, circulating immune cells, and solid tumors.

[0060] The cancers that can be treated include non-vascularized or substantially non-vascularized tumors and vascularized tumors.Cancers can include non-solid tumors (e.g., hematological tumors such as leukemia and lymphoma) or can include solid tumors.The types of cancers that can be treated with the compositions of the present invention include, but are not limited to, carcinomas, blastomas and sarcomas, as well as certain leukemias or malignant lymphoid tumors, benign and malignant tumors and malignant tumors, such as sarcomas, carcinomas, and melanomas.Adult tumors / cancers and pediatric tumors / cancers are also included.

[0061] In some embodiments, the cancer is breast cancer, colon cancer, renal cell carcinoma, lung cancer, hepatocellular carcinoma, gastric cancer, ovarian cancer, pancreatic cancer, esophageal cancer, prostate cancer, sarcoma, bladder cancer, head and neck cancer, glioblastoma, diffuse large B-cell lymphoma, leukemia, or melanoma. In some embodiments, the cancer is melanoma, small cell lung cancer, or non-small cell lung cancer. In some embodiments, the cancer is metastatic and / or locally advanced. In some embodiments, the cancer is unresectable.

[0062] As used herein, the terms "treating", "treat" and the like refer to alleviating or reducing the severity of at least one symptom or sign, temporarily or permanently eliminating the cause of a symptom, slowing or inhibiting tumor growth, reducing tumor cell load or tumor burden, promoting tumor regression, causing tumor shrinkage, necrosis and / or disappearance, preventing tumor recurrence, preventing or inhibiting metastasis, inhibiting metastatic tumor growth, eliminating the need for surgery, and / or prolonging survival in a subject.

[0063] The term "agent" is used herein to denote a compound, a mixture of compounds, a biopolymer (such as a nucleic acid, an antibody, a protein or portion thereof, e.g., a peptide, etc.), or an extract produced from biological material such as a bacterial, plant, fungus, or animal (especially mammalian) cell or tissue. The activity of such an agent may qualify it as a "therapeutic agent," which is a biologically, physiologically, or pharmacologically active substance (or substances) that acts locally or systemically in a subject.

[0064] The terms "therapeutic agent," "therapeutic agent," or "medical agent" are used interchangeably and refer to a molecule or compound that provides some beneficial effect upon administration to a subject. Beneficial effects include enabling a diagnostic determination; ameliorating a disease, symptom, disorder, or pathological condition; reducing or preventing the onset of a disease, symptom, disorder, or condition; and generally counteracting a disease, symptom, disorder, or pathological condition.

[0065] As used herein, the term "pharmaceutical acceptable" refers to a material, such as a carrier or diluent, that does not abrogate the biological activity or properties of the composition and is relatively non-toxic, i.e., the material may be administered to an individual without causing undesirable biological effects or interacting in a deleterious manner with any of the components of the composition in which it is contained.

[0066] The term "pharmaceutically acceptable support" includes pharmaceutically acceptable salts, pharmaceutically acceptable materials, compositions, supports such as liquid or solid fillers, diluents, excipients, solvents, or encapsulating materials that are involved in carrying or transporting the compounds of the present invention in or to a subject so that they can perform their intended function. Typically, such compounds are carried or transported from one organ or part of the body to another organ or part of the body. Each salt or support must be "acceptable" in the sense of being compatible with the other components of the formulation and not harmful to the subject. Some examples of materials that can serve as pharmaceutically acceptable supports include sugars such as lactose, glucose, and sucrose; starches such as corn starch and potato starch; Cellulose and its derivatives such as sodium carboxymethylcellulose, ethylcellulose, and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository wax; oils such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil, and soybean oil; glycols such as propylene glycol; polyols such as glycerin, sorbitol, mannitol, and polyethylene glycol; esters such as ethyl oleate and ethyl laurate; agar-agar; Buffers such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; phosphate buffer; diluent; granulating agent; lubricant; binder; disintegrant; wetting agent; emulsifier; coloring agent; release agent; coating agent; sweetener; flavor; flavoring; preservative; antioxidant; plasticizer; gelling agent; thickener; hardening agent; setting agent; suspending agent; surfactant; humectant; carrier; stabilizer; and other non-toxic compatible materials used in formulation, or any combination thereof. As used herein, "pharmaceutically acceptable carrier" also includes any and all coatings, antibacterial and antifungal agents, and absorption retardants, and the like, which are compatible with the activity of one or more components of the present invention and are physiologically acceptable to the subject. Supplementary active compounds can also be incorporated into the composition.

[0067] The term "effective amount", "effective dose", or "effective dosage" is defined as an amount sufficient to achieve or at least partially achieve a desired effect. A "therapeutically effective amount" or "therapeutically effective dosage" of a drug or therapeutic agent is any amount of the drug that, when used alone or in combination with other therapeutic agents, promotes regression of a disease as evidenced by a decrease in the severity of disease symptoms, an increase in the frequency and duration of symptom-free periods of the disease, or prevention of disability or injury due to the affliction of the disease. A "prophylactically effective amount" or "prophylactically effective dosage" of a drug / agent is an amount of the drug that inhibits the onset or recurrence of a disease when administered alone or in combination with other therapeutic agents to a subject at risk of developing a disease or suffering from a recurrence of the disease. The ability of a therapeutic or prophylactic agent to promote regression of a disease or inhibit the onset or recurrence of a disease can be evaluated using a variety of methods known to those skilled in the art, such as assaying the activity of the agent in human subjects in clinical trials, in animal model systems predictive of efficacy in humans, or in in vitro assays.

[0068] In some embodiments, an effective amount includes an amount effective to inhibit metastatic colonization of a cancer.

[0069] In another aspect, the present disclosure provides a method of treating cancer in a subject, the method comprising: (a) providing a subject identified as having at least one ε4 allele from rs7412 or rs429358 polymorphisms, or an ε3 allele from rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19; and (b) administering to the subject an effective amount of an anti-cancer or anti-tumor agent (e.g., an LXRβ agonist) or a pharma- ceutically acceptable salt thereof.

[0070] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19, and identified as likely to benefit from treatment with an anti-cancer or anti-tumor agent (e.g., an LXRβ agonist) or a pharmaceutically acceptable salt thereof based on the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms; and (b) administering an effective amount of an anti-cancer or anti-tumor agent (e.g., an LXRβ agonist) or a pharmaceutically acceptable salt thereof to the identified subject.

[0071] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19, and identified as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof based on the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms; and (b) administering an effective amount of an LXRβ agonist or a pharma- ceutically acceptable salt thereof to the identified subject.

[0072] In some embodiments, the method includes: (a) obtaining a sample comprising nucleic acid from a subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; (c) identifying a subject having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with an anti-cancer or anti-tumor agent (e.g., an LXRβ agonist) or a pharma- ceutically acceptable salt thereof; and (d) administering an effective amount of an anti-cancer or anti-tumor agent (e.g., an LXRβ agonist) or a pharma- ceutically acceptable salt thereof to the identified subject, thereby treating cancer.

[0073] In some embodiments, the method includes: (a) obtaining a sample comprising nucleic acid from a subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; (c) identifying a subject having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof; and (d) administering an effective amount of an LXRβ agonist or a pharma- ceutically acceptable salt thereof to the identified subject, thereby treating cancer.

[0074] "Sample", "test sample", and "patient sample" may be used interchangeably herein. A sample may be a sample of serum, urine, plasma, amniotic fluid, cerebrospinal fluid, cells (e.g., antibody-producing cells), or tissue. Such samples may be used directly as obtained from a patient, or may be pretreated by filtration, distillation, extraction, concentration, centrifugation, inactivation of interfering components, addition of reagents, etc., to modify the characteristics of the sample in some way, as described herein or known in the art. As used herein, the terms "sample" and "biological sample" generally refer to biological material that is being tested for and / or suspected of containing an analyte of interest, such as an antibody. A sample may be any tissue sample from a subject. A sample may contain proteins from a subject.

[0075] To obtain the sample, any cell type, tissue, or body fluid may be utilized. Such cell types, tissues, and body fluids may include sections of tissue such as biopsy and autopsy samples, frozen sections taken for histological purposes, blood (such as whole blood), plasma, serum, sputum, stool, tears, mucus, saliva, hair, skin, red blood cells, platelets, interstitial fluid, ocular lens fluid, cerebrospinal fluid, sweat, nasal fluid, synovial fluid, vaginal discharge, amniotic fluid, semen, and the like. Cell types and tissues may also include lymphatic fluid, peritoneal fluid, gynecological fluid, urine, peritoneal fluid, cerebrospinal fluid, fluid collected by vaginal lavage, or fluid collected by vaginal lavage. Tissues or cell types may be provided by removing a sample of cells from an animal, but may also be achieved by using previously isolated cells (e.g., by another person, at another time, and / or for another purpose). Archival tissues, such as those with treatment history or outcome history, may also be used. Purification of the protein may not be necessary.

[0076] Methods well known in the art for collecting, handling, and processing urine, blood, serum, plasma, and other bodily fluids may be used in the practice of the present disclosure, for example, when the antibodies provided herein are used as immunodiagnostic reagents and / or in immunoassay kits. A test sample may contain additional moieties in addition to the analyte of interest, such as antibodies, antigens, haptens, hormones, drugs, enzymes, receptors, proteins, peptides, polypeptides, oligonucleotides, or polynucleotides. For example, a sample may be a whole blood sample obtained from a subject. It may be necessary or desirable for a test sample, particularly whole blood, to be treated prior to immunoassay, for example with a pretreatment reagent, as described herein. Even if pretreatment is not required, pretreatment may be performed simply for convenience (e.g., as part of a commercial platform regimen). The sample may be used directly as obtained from the subject, or may be used to modify the characteristics of the sample after pretreatment. Pretreatment may include extraction, concentration, inactivation of interfering components, and / or addition of reagents.

[0077] The terms "increased", "increase" or "enhancement" or "activation" are all used herein generally to mean an increase by a statically significant amount; for the avoidance of doubt, the terms "increased", "increase", "enhancement", or "activation" mean an increase of at least 10% compared to a reference level, for example, at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or up to 100%, or an increase of 10-100% compared to a reference level, or at least about 2-fold, or at least about 3-fold, or at least about 4-fold, or at least about 5-fold, or at least about 10-fold increase, or a 2-fold to 10-fold or more increase compared to a reference level.

[0078] In other aspects, the disclosure also provides methods for identifying individuals having cancer who may benefit from treatment with an LXRβ agonist, or a pharma- ceutically acceptable salt thereof. The method includes: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; and (c) identifying subjects having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof, thereby identifying individuals having cancer who may benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof.

[0079] In some embodiments, the LXRβ agonist can be 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof. In some embodiments, the LXRβ agonist has the structure represented by:

[0080] [ka]

[0081] In other aspects, the disclosure further provides a method of treating cancer in a subject having at least one ε4 allele from the rs7412 or rs429358 polymorphisms, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19. The method includes administering to the subject an effective amount of a PD-1 inhibitor (e.g., nivolumab, pembrolizumab, pidilizumab, BMS 936559, and atezolizumab) or a PD-L1 inhibitor (e.g., atezolizumab and durvalumab), or a pharma- ceutically acceptable salt thereof.

[0082] In other aspects, a method of treating cancer in a subject in need of treatment comprises: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphisms, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19; and (b) administering to the subject an effective amount of a PD-1 inhibitor (e.g., nivolumab, pembrolizumab, pidilizumab, BMS 936559, and atezolizumab) or a PD-L1 inhibitor (e.g., atezolizumab and durvalumab), or a pharma- ceutical acceptable salt thereof.

[0083] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19, and identified as likely to benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof, based on the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms; and (b) administering an effective amount of a PD-1 inhibitor or a PD-L1 inhibitor to the identified subject.

[0084] In some embodiments, the method comprises: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; (c) identifying subjects having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof; and (d) administering an effective amount of a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof, to the identified subjects, thereby treating cancer.

[0085] In some embodiments, the disclosure provides methods for identifying individuals with cancer who may benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor. The method includes: (a) obtaining a sample comprising nucleic acid from the subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19; and (c) identifying subjects having at least one ε4 allele from the rs7412 or rs429358 polymorphism, or an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, as likely to benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof, thereby identifying individuals having cancer who may benefit from treatment with a PD-1 inhibitor or a PD-L1 inhibitor, or a pharma- ceutically acceptable salt thereof.

[0086] In some embodiments, the subject has previously been administered a CTLA-4 inhibitor, or a pharma- ceutically acceptable salt thereof.

[0087] In some embodiments, the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or the ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19 is determined by polymerase chain reaction (PCR).

[0088] In some embodiments, the presence of at least one ε4 allele from the rs7412 or rs429358 polymorphism, or the ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19 is determined by the expression level of the subject's APOE3 protein or APOE4 protein.

[0089] The level of APOE protein can be measured by determining or estimating protein level or mRNA level.Methods for determining or estimating protein level or mRNA level are well known in the art.For example, the protein level (e.g., protein expression level) of APOE protein can be determined by SDS-PAGE, Western blot, or immunoassay (e.g., immunoblotting assay, immunoprecipitation assay).The mRNA level can be determined by RT-PCR.

[0090] Measurement of the levels of APOE proteins can be performed by assaying the proteins themselves (by Western blotting, ELISA, RIA, and other techniques known to those skilled in the art), by assaying the mRNAs encoding these proteins (such as quantitative PCR, Northern blotting, RNAse protection assays, RNA dot blotting, and other techniques known to those skilled in the art), or by assaying the activity of regulatory elements of the genes of APOE proteins. For example, the activity of regulatory elements can be assessed by reporter constructs consisting of DNA segments from promoters, enhancers, and / or intronic elements linked to cDNAs encoding reporters (such as luciferase, beta-galactosidase, green fluorescent protein, or other easily assayed reporter genes). These reporter constructs can be stably or transiently transfected into cells.

[0091] In some embodiments, the cancer is resistant to or has not responded to previous treatment with platinum-containing chemotherapy, PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, antimetabolites, topoisomerase inhibitors, antimetabolites, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents. In some embodiments, the cancer has progressed during or after treatment with platinum-containing chemotherapy, PD-1 inhibitors, PD-L1 inhibitors, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents. In some embodiments, the cancer has been determined or is predicted to be resistant to PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, topoisomerase inhibitors, antimetabolites, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents.

[0092] In some embodiments, the method further comprises administering to the subject an additional anti-cancer therapy. In some embodiments, the additional anti-cancer therapy comprises surgery, radiation therapy, chemotherapy, and / or immunotherapy. In some embodiments, the additional anti-cancer therapy comprises chemotherapy and / or immunotherapy. In some embodiments, the chemotherapy comprises docetaxel, carboplatin or cisplatin, pemetrexed, and / or pembrolizumab.

[0093] In some embodiments, the method further comprises administering to the subject an effective amount of folic acid, vitamin B12, a corticosteroid, a statin, an antiemetic, an antidiarrheal, an appetite stimulant, a general stimulant, a bisphosphonate, a gonadotropin releasing hormone agonist, a growth factor, and / or an LHRH agonist.

[0094] In some embodiments, the subject has an ε3 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene. In some embodiments, the subject has at least one ε4 allele from the rs7412 or rs429358 polymorphisms in the ApoE gene. In some embodiments, the subject has an ε4 allele from the rs7412 and rs429358 polymorphisms, an ε3 allele and an ε4 allele from the rs7412 and rs429358 polymorphisms, or an ε2 allele and an ε4 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene. In some embodiments, the subject has an ε4 allele from the rs7412 and rs429358 polymorphisms in the ApoE gene.

[0095] In yet another aspect, the disclosure further provides a method of treating cancer in a subject having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19. The method includes administering an active treatment to the subject.

[0096] In another aspect, the disclosure provides a method of treating cancer in a subject in need thereof, the method comprising: (a) providing a subject identified as having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19; and (b) administering an active treatment to the subject.

[0097] In some embodiments, the method comprises: (a) providing a subject identified as having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 and identified as likely to benefit from aggressive treatment based on the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism; and (b) administering aggressive treatment to the identified subject.

[0098] In some embodiments, the method includes (a) obtaining a sample comprising nucleic acid from a subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19; (c) identifying subjects having at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 as likely to benefit from aggressive treatment; and (d) administering aggressive treatment to the identified subjects, thereby treating the cancer.

[0099] In another aspect, the present disclosure provides a method for identifying individuals with cancer who may benefit from aggressive treatment, the method comprising: (a) obtaining a sample comprising nucleic acid from a subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19; and (c) identifying subjects who have at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 as likely to benefit from aggressive treatment, thereby identifying individuals with cancer who may benefit from aggressive treatment.

[0100] In some embodiments, the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 is determined by polymerase chain reaction (PCR). In some embodiments, the presence of at least one ε2 allele from the rs7412 or rs429358 polymorphism in the ApoE gene on chromosome 19 is determined by the expression level of APOE2 protein in the subject.

[0101] In some embodiments, the subject has an ε2 allele from the rs7412 and rs429358 polymorphisms, or an ε2 allele and an ε3 allele from the rs7412 and rs429358 polymorphisms, in the ApoE gene on chromosome 19.

[0102] In some embodiments, the active treatment comprises administration of 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof and concomitantly an effective amount of immunotherapy.

[0103] In some embodiments, the active treatment further comprises performing surgery on the subject. In some embodiments, the 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof is administered prior to surgery. In some embodiments, the 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof is administered post-surgery.

[0104] In some embodiments, the immunotherapy is a PD-1 inhibitor, a PD-L1 inhibitor, or a CTLA-4 inhibitor.

[0105] In some embodiments, the additional therapeutic agent may be administered to the subject before, after, or simultaneously with the second therapeutic agent. The anti-cancer or anti-tumor agent (e.g., LXRβ agonist, PD-1 inhibitor, or PD-L1 inhibitor), or pharmaceutical composition thereof, may be administered as a single dose, or more commonly, multiple doses. The interval between single doses may be, for example, weekly, monthly, every three months, or yearly. The interval may also be irregular, as indicated by measuring the blood level of the anti-cancer or anti-tumor agent (e.g., LXRβ agonist, PD-1 inhibitor, or PD-L1 inhibitor) in the patient.

[0106] Anti-cancer or anti-tumor agents (e.g., LXRβ agonists, PD-1 inhibitors, or PD-L1 inhibitors), or pharmaceutical compositions thereof, may be administered via one or more routes of administration using one or more of a variety of methods known in the art. As will be appreciated by those skilled in the art, the route and / or mode of administration may vary depending on the desired outcome. For example, routes of administration of anti-cancer or anti-tumor agents include intravenous, intramuscular, intradermal, intraperitoneal, subcutaneous, spinal, or other parenteral routes of administration, such as by injection or infusion. As used herein, the phrase "parenteral administration" refers to modes of administration other than enteral and topical administration, usually by injection, including, but not limited to, intravenous, intramuscular, intra-arterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcutaneous, intra-articular, subcapsular, subarachnoid, intraspinal, epidural, and intrasternal injection and infusion. Alternatively, the anti-cancer or anti-tumor agent may be administered via a parenteral route, such as, for example, intranasally, orally, vaginally, rectally, sublingually or topically, including topical, epidermal or mucosal routes of administration.

[0107] In some embodiments, the anti-cancer or anti-agent, or pharmaceutical composition thereof, may be administered intratumorally, intravenously, subcutaneously, intraosseously, orally, transdermally, sustained release, extended release, as a suppository, or sublingually.

[0108] The dosage regimen is adjusted to provide the optimum desired response (e.g., therapeutic response). For example, a single bolus can be administered, several divided doses can be administered over time, or the dose can be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is particularly advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. As used herein, dosage unit form refers to physically discrete units suitable as unitary dosages for the subject to be treated; each unit contains a predetermined amount of active ingredient calculated to produce the desired therapeutic effect in association with the required pharmaceutical support. The specifications for the dosage unit forms of the present invention are determined by and directly depend on (a) the unique characteristics of the active compound and the specific therapeutic effect to be achieved, and (b) the limitations inherent in the technology of compounding such active ingredients for the treatment of individual susceptibility.

[0109] For administration of anti-cancer or anti-tumor agents, dosages range from about 0.0001 to 100 mg / kg, more usually 0.01 to 5 mg / kg, of the host body weight. Exemplary treatment regimes involve administration once a week, once every two weeks, once every three weeks, once every four weeks, once a month, once every three months, or once every three to six months.

[0110] Alternatively, the anti-cancer or anti-tumor agent may be administered as a sustained release formulation, in which case less frequent administration is required. The dosage and frequency will vary depending on the half-life of the anti-cancer or anti-tumor agent in the patient. The dosage and frequency may vary depending on whether the treatment is preventive or therapeutic. In preventive applications, relatively low doses are administered at relatively infrequent intervals over a long period of time. Some patients continue to receive treatment for the rest of their lives. In therapeutic applications, relatively high doses may be required at relatively short intervals until the progression of the disease is reduced or terminated, preferably until the patient shows partial or complete improvement of the symptoms of the disease. The patient may then be administered a prophylactic regime.

[0111] The actual dosage level of the active ingredient in the pharmaceutical composition of the present invention may be varied to obtain an effective amount of the active ingredient to achieve the desired therapeutic response for a particular patient, composition, and mode of administration without causing toxicity to the patient. The dosage level selected may depend on various pharmacokinetic factors such as the activity of the particular composition of the present invention used, the route of administration, the time of administration, the excretion rate of the particular active ingredient being used, the duration of treatment, other drugs, the particular composition being used, the age, sex, weight, condition, general health, and previous medical history of the patient being treated, and the compounds and / or materials used in combination with similar factors well known in the medical art.

[0112] In some embodiments, the anti-cancer or anti-tumor agent (e.g., an LXRβ agonist, a PD-1 inhibitor, or a PD-L1 inhibitor), or a pharmaceutical composition thereof, may be administered in combination therapy, i.e., with an additional therapeutic agent. For example, the combination therapy may include an LXRβ agonist, a PD-1 inhibitor, or a PD-L1 inhibitor, in combination with at least one additional therapeutic agent, such as another anti-cancer or anti-tumor agent, such as the chemotherapeutic and immunotherapeutic agents described above.

[0113] A "chemotherapeutic agent" is a compound useful in the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclophosphamide (CYTOXANTM); alkylsulfonates such as busulfan, improsulfan, and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelanamines such as altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphaolamide, and trimethylolomelanamine; acetogenins (especially bullatacin and bullatacinone); camptothecins (including the synthetic analog topotecan); bryostatin; kallistatin; CC-1065 (including its synthetic analogs adozelesin, carzelesin, and bizelesin); cryptophycins (especially bromophenytoin); and the like. steroids (especially cryptophycin 1 and cryptophycin 8); dolastatins; duocarmycins (synthetic analogs, such as KW-2189 and CBI-TMI); eleutherobin; pancratistatin; sarcodictin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, chlorophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine hydrochloride, melphalan, nobembitine, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimustine; enediyne antibiotics (e.g., calicheamicins, e.g., Agnew See Chem. Intl. Ed. Engl. 33: 183-186 (1994); the dynemicins, including dynemicin A; the esperamicins;Neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores), aclacinomycin, actinomycin, autramycin, azaserine, bleomycin, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycin, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, Antibiotics such as cyclosporine, idarubicin, marcelomycin, mitomycin, mycophenolic acid, nogalamycin, olivomycin, peplomycin, potfilomycin, puromycin, keramycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, and zorubicin; antimetabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogs such as denopterin, methotrexate, pteropterin, and trimetrexate; fludarabine, 6-mercaptopurine, thiamiprine, and thioamiprine. Purine analogues such as guanine; pyrimidine analogues such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine, 5-FU; androgens such as calucelone, drostanolone propionate, epithiostanol, mepitiostane, testolactone; antiadrenal drugs such as aminoglutethimide, mitotane, trilostane; folic acid supplements such as floric acid; aceglatone; aldophosphamide glycosides; aminolevulinic acid; amsacrine; bestravsil; bisantre edatrexate;defofamine;demecolcine;diaziquone;elformitin;elliptinium acetate;epothilone;etoglucide;gallium nitrate;hydroxyurea;lentinan;lonidamine;maytansinoids such as maytansine and ansamitocin;mitoguazone;mitoxantrone;mopidamol;nitracrine;pentostatin;phenamet;pirarubicin;podophyllic acid;2-ethylhydrazide;procarbazine;PSK(registered trademark);razoxane;rhizoxin;schizofuran;spirogermanium;tenuazonic acid;triaziquone;2,2',2''-Trichlorotriethylamine; trichothecenes (especially T-2 toxin, veracrine A, roridin A, and anguidine); urethane; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); cyclophosphamide; thiotepa; taxoids such as paclitaxel (TAXOL®, Bristol-Myers Squibb Oncology, Princeton, NJ) and docetaxel (TAXOTERE®, Rhône-Poulenc Roller, Antony, France); chlorambucil. These include cyclosporine; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogues such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine; navelbine; novantrone; teniposide; daunomycin; aminopterin; xeloda; ibandronate; CPT-11; the topoisomerase inhibitor RFS2000; difluoromethylornithine (DMFO); retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids, or derivatives of any of the above. Also included within this definition are antiestrogens such as, for example, tamoxifen, raloxifene, aromatase inhibiting 4(5)-imidazole, 4-hydroxytamoxifen, trioxifene, keoxifene, LY117018, onapristone, and toremifene (Farestone); antiandrogens such as flutamide, nilutamide, bicalutamide, leuprolide, goserelin; and antihormonal agents that act to regulate or inhibit hormone action on tumors, such as pharmaceutically acceptable salts, acids, or derivatives of any of the above;

[0114] "Immunotherapeutic agents" are biological agents useful in the treatment of cancer. Examples of immunotherapeutic agents include atezolizumab, avelumab, blinatumomab, daratumumab, cemiplimab, durvalumab, elotuzumab, laherparepvec, ipilimumab, nivolumab, obinutuzumab, ofatumumab, pembrolizumab, and talimogene.

[0115] In some embodiments, the subject is administered an immune checkpoint inhibitor or an LXR agonist (e.g., RGX-104). Examples of immune checkpoint inhibitors may include antibodies targeting CTLA-4, PD-1, PD-L1, PD-L2, killer immunoglobulin receptors (KIR), LAG3, B7-H3, B7-H4, TIM3, A2aR, CD40L, CD27, OX40, 4-IBB, TCR, BTLA, ICOS, CD28, CD80, CD86, ICOS-L, B7-H4, HVEM, 4-1BBL, OX40L, CD70, CD40, or GALS. In some embodiments, the immune checkpoint inhibitor is an anti-PD-1 antibody.

[0116] As used herein, the term "co-administration" or "co-administered" refers to the administration of at least two agents or therapies to a subject. In some embodiments, the co-administration of two or more agents / therapies occurs simultaneously. In other embodiments, a first agent / treatment is administered prior to a second agent / treatment. One of skill in the art will appreciate that the formulations and / or routes of administration of the various agents / therapies used may vary.

[0117] b. Methods of cancer prognosis This disclosure also provides a method for assessing the prognosis of a subject having or at risk of having cancer. The method includes: (i) obtaining a sample from a subject; (ii) determining the presence of a specific APOE genotype in the sample; and (iii) determining a prognostic outcome of the subject based on the presence of a specific APOE genotype, such as an APOE2, APOE3, or APOE4 genotype. In some embodiments, the method further includes administering a drug for treating cancer to the subject based on the presence of the specific APOE genotype to achieve a better prognostic outcome than the determined prognostic outcome.

[0118] In some embodiments, the sample may include a sample of cells, tissue, or bodily fluids from a subject, such as a tumor tissue or blood sample. The presence of a particular APOE genotype in a sample may be determined by PCR. PCR primers are preferably selected based on known sequences of the genome that result in the amplification of a particular fragment of genomic DNA. Computer programs well known in the art are useful for designing primers with the required specificity and optimal amplification properties, such as Oligo version 5.0 (National Biosciences). In some embodiments, the PCR primers include the sequences of SEQ ID NOs: 4-16.

[0119] In some embodiments, determining the presence of a particular APOE genotype includes determining the presence of a particular APOE variant protein in a sample. Determining the presence of a particular APOE variant protein in a sample can be performed using an antibody or a fragment thereof that specifically binds to a particular APOE variant protein. Such an APOE variant protein specific antibody can include, but is not limited to, APOE2 specific antibody: clone F48.1 (Research Diagnostics, NJ, USA), APOE4 specific antibody: clone 4E4 (Novus Biologicals, Catalog No. NBP1-49529). To determine the presence of a particular APOE variant protein using an antibody or a fragment thereof, various assays can be used, such as electrochemiluminescence assay, enhanced chemiluminescence assay, enzyme-linked immunosorbent assay (ELISA), co-immunoprecipitation (co-IP), etc.

[0120] Genotyping of APOE polymorphisms in biological samples such as tumor tissue samples or peripheral blood samples can provide early indication of recovery or lack thereof.For example, the presence of APOE2 genotype indicates poor prognosis of the subject, while the presence of APOE4 genotype indicates good prognosis of the subject.Prognosis of disease course includes risk of metastasis, recurrence, and recurrence.Good prognosis indicates longer survival rate compared to subjects with poor prognosis.

[0121] The prognostic method described herein identifies the progression and management of conditions characterized by uncontrolled autonomous cell proliferation, providing information useful for prognosis. For example, the information assists clinicians to more specifically design chemotherapy or other treatment regimens to eradicate such conditions from the body of an afflicted subject, such as a human. For example, the method can be used to determine whether a subject is suitable for administration with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) for treating a disorder associated with uncontrolled autonomous cell proliferation.

[0122] The term "prognosis" as used herein refers to the prediction of the expected course and outcome of a clinical condition or disease. Prognosis is usually performed by evaluating disease factors or symptoms that indicate a favorable or unfavorable course or outcome of the disease. The phrase "assessing prognosis" or "determining prognosis" as used herein refers to a process by which a person skilled in the art may predict the course or outcome of a patient's condition. The term "prognosis" does not refer to the ability to predict the course or outcome of a condition with 100% accuracy, but rather, a person skilled in the art will understand that the term "prognosis" refers to an increased likelihood of a particular course or outcome occurring, i.e., a higher likelihood of a course or outcome occurring in a patient exhibiting a particular condition, as compared to an individual not exhibiting the particular condition.

[0123] The terms "good prognosis", "favorable prognosis" and "benign prognosis", or "poor prognosis", "unfavorable prognosis" and "poor prognosis" as used herein are relative terms for predicting the expected course and / or expected outcome of a condition or disease. A good, favorable or benign prognosis predicts a better outcome of a condition than a poor, unfavorable or poor prognosis. In a general sense, a "good prognosis", "favorable prognosis" and "benign prognosis" are relatively better outcomes than many other possible prognoses that may be associated with a particular condition, whereas a "poor prognosis", "unfavorable prognosis" and "poor prognosis" predict a relatively worse outcome than many other possible prognoses that may be associated with a particular condition. Typical examples of a good, favorable or benign prognosis include a better than average cure rate, a lower tendency to metastasis, a longer than expected life expectancy, differentiation between benign and cancerous processes, etc. For example, a benign prognosis is when a patient has a 50% chance of being cured of a particular cancer after treatment, whereas an average patient with the same cancer has only a 25% chance of being cured. In some embodiments, the "good prognosis", "favorable prognosis" and "benign prognosis" of APOE4 carriers are associated with the prognostic outcome of APOE3 carriers (considered to be the "neutral" APOE genotype). Similarly, the "poor prognosis", "unfavorable prognosis" and "poor prognosis" of APOE2 carriers are associated with the prognostic outcome of APOE3 carriers.

[0124] The prognostic methods described herein can be used to determine whether a subject is suitable for or in need of treatment, such as surgery or administration of a therapeutic agent (such as an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug). For example, such methods can be used to determine whether a subject can be administered an antibody or other therapy (e.g., surgery such as amputation). Thus, certain methods described herein can further include treating the subject (e.g., with one or more pharmaceutical compositions for a period of time or by surgery) if the subject receives a poor prognosis.

[0125] In some embodiments, the subject undergoing prognostic analysis has or is at risk of having cancer, the cancer being any of oral cavity cancer, oropharyngeal cancer, nasopharyngeal cancer, respiratory cancer, genitourinary cancer, gastrointestinal cancer, central or peripheral nervous system tissue cancer, endocrine or neuroendocrine or hematopoietic cancer, glioma, sarcoma, carcinoma, lymphoma, melanoma, fibroma, meningioma, brain tumor, oropharyngeal cancer, nasopharyngeal cancer, renal cancer, biliary tract cancer, pheochromocytoma, pancreatic islet cell carcinoma, Li-Fraumeni tumor, thyroid cancer, parathyroid cancer, pituitary cancer, adrenal tumor, osteogenic sarcoma tumor, multiple neuroendocrine type I and type II tumors, breast cancer, lung cancer, head and neck cancer, prostate cancer, esophageal cancer, tracheal cancer, liver cancer, bladder cancer, gastric cancer, pancreatic cancer, ovarian cancer, uterine cancer, cervical cancer, testicular cancer, colon cancer, rectal cancer, and skin cancer.

[0126] II. Kits and arrays for cancer prognosis The present disclosure also provides kits and arrays embodying the above methods. Such kits can be prepared from readily available materials and reagents and can be provided in a variety of embodiments.

[0127] In some embodiments, the kit comprises a probe having a nucleic acid sequence complementary to a nucleic acid sequence of APOE2, APOE3, or APOE4. Such a probe may hybridize to a nucleic acid sequence of APOE2, APOE3, or APOE4 under stringent conditions. In some embodiments, the kit comprises a labeled probe having a sequence complementary to APOE2, APOE3, and APOE4, respectively. In some embodiments, the nucleic acid sequences of APOE2, APOE3, and APOE4 comprise the sequences of SEQ ID NOs: 1-3, respectively. In some embodiments, the nucleic acid sequence of the probe is 15-200 bases in length. In some embodiments, the probe is linked to a detection label. The detection label may be a fluorophore, a dye, a radioactive label, an enzyme, biotin, or an antibody (or a fragment thereof).

[0128] In some embodiments, the kit also includes primers configured to specifically bind to sequences flanking the genomic region to allow PCR amplification of at least one of APOE2, APOE3, and APOE4 that includes the genomic region. In some embodiments, the primers may have the sequences of SEQ ID NOs: 4-16.

[0129] The kit may include a calibrator or control, e.g., an antigen, an antibody, or a combination thereof, optionally purified and lyophilized. The kit may include at least one container for performing the assay (e.g., a tube, a microtiter plate or a strip, which may already be coated with the appropriate antigen or antibody), and / or one of the following may be provided as either a buffer, such as an assay buffer or a wash buffer, a concentrate solution, a substrate solution for a detectable label (e.g., an enzyme label), or a stop solution. Preferably, the kit includes all components necessary to perform the assay, i.e., reagents, standards, buffers, diluents, etc. Antibodies, calibrators, and / or controls may be provided in separate containers or pre-dispensed into a suitable assay format, e.g., a microtiter plate.

[0130] The kit may also include quality control components (e.g., sensitivity panels, calibrators, positive controls). Preparation of quality control reagents is known in the art and is described on various diagnostic product inserts. Sensitivity panel members may be used to establish assay performance characteristics and may also be useful indicators of kit reagent integrity and assay standardization.

[0131] The kit may also include other reagents necessary to perform the diagnostic assay or to facilitate quality control evaluation, such as buffers, salts, enzymes, enzyme cofactors, substrates, detection reagents, etc. Other components, such as buffers and solutions for isolation and / or treatment of test samples (e.g., pretreatment reagents), may also be included in the kit. The kit may additionally include one or more other controls. One or more components of the kit may be lyophilized, in which case the kit may further include reagents suitable for reconstitution of the lyophilized components.

[0132] The various components of the kit may be provided in suitable containers, such as microtiter plates. The kit may further include containers for holding or storing samples (e.g., containers or cartridges for urine samples). Optionally, the kit may include reaction vessels, mixing vessels, and other components to facilitate preparation of reagents or test samples. The kit may also include one or more devices to assist in collection of test samples, such as syringes, pipettes, forceps, spatulas, etc.

[0133] Optionally, the kit may include a solid phase such as a magnetic particle, a bead, a test tube, a microtiter plate, a cuvette, a membrane, a scaffold molecule, a film, a filter paper, a crystal, a disk, or a chip. The kit may also include a detectable label that may be an antigen or an antibody, or may be bound thereto. The detectable label may be, for example, an enzyme, an oligonucleotide, a nanoparticle chemiluminophore, a fluorophore, a fluorescence quencher, a chemiluminescence quencher, or a direct label that may be biotin. The kit may also include additional reagents necessary for detection of the label.

[0134] In some examples, the kits may include one or more additional anti-cancer therapeutic agents, such as one or more chemotherapeutic or immunotherapeutic agents described herein or known in the art. Such kits may include commercially available packaging and / or printed information regarding the antibodies, antimicrobial therapeutic agents, and their methods of use.

[0135] The kit may include instructions for use. The instructions included in the kit may be attached to the packaging material or may be included as a package insert. The instructions are typically, but are not limited to, written or printed materials. Any medium capable of storing such instructions and communicating them to an end user is contemplated by the present disclosure. Such media include, but are not limited to, electronic storage media (e.g., magnetic disks, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. As used herein, the term "instructions" may include an address of an internet site that provides the instructions. The instructions may also include instructions for generating a standard curve or reference standard for the purpose of quantifying the target.

[0136] Biochips or arrays are also provided in the present disclosure. Biochips / arrays may include a solid or semi-solid substrate to which a probe or multiple probes described herein are attached. The probes may be capable of hybridizing to the target sequence under stringent hybridization conditions. The probes may be attached to spatially defined addresses on the substrate. Multiple probes may be used per target sequence, either with overlapping probes or probes to different sections of a particular target sequence. The probes may be capable of hybridizing to target sequences associated with a single disorder recognized by those skilled in the art. The probes may be first synthesized and then attached to the biochip, or may be directly synthesized on the biochip.

[0137] In another aspect, the present disclosure provides an array comprising a support having a plurality of unique locations. The array may comprise at least a nucleic acid or probe having a sequence complementary to a nucleic acid sequence of APOE2, APOE3, or APOE4. In some embodiments, the nucleic acid sequence is one of SEQ ID NOs: 1-3.

[0138] The solid substrate may be modified to contain individual unique sites suitable for attachment or binding of probes and may be of a material suitable for at least one detection method. Examples of such substrates include glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethane, Teflon, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, and plastics. The substrate may allow for optical detection without appreciably fluorescing.

[0139] The substrate can be planar, although other forms of substrates can also be used. For example, the probes can be placed on the inside surface of a tube for flow-through sample analysis to minimize sample volume. Similarly, the substrate can be flexible, such as a flexible foam, including closed-cell foams made of certain plastics.

[0140] The array / biochip and the probes can be derivatized with chemical functional groups for subsequent linkage of the two. For example, the biochip can be derivatized with chemical functional groups, including but not limited to amino, carboxyl, oxo or thiol groups. Using these functional groups, the probes can be linked directly or indirectly with functional groups on the probes using linkers. The probes can be linked to the solid support either by the 5' end, the 3' end, or by an internal nucleotide. The probes can also be linked to the solid support non-covalently. For example, biotinylated oligonucleotides can be made that can be attached to a surface covalently coated with streptavidin to effect linkage. Alternatively, the probes can be synthesized on the surface using techniques such as photopolymerization and photolithography. Detailed discussion of methods for linking nucleic acids to support substrates can be found, for example, in U.S. Patent Nos. 5,837,832, 6,087,112, 5,215,882, 5,707,807, 5,807,522, 5,958,342, 5,994,076, 6,004,755, 6,048,695, 6,060,240, 6,090,556, and 6,040,138.

[0141] III. Definition To aid in understanding the detailed description of the compositions and methods according to the present disclosure, some explicit definitions are provided to facilitate a clear disclosure of the various aspects of the present disclosure. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

[0142] As used herein, the term "allele" refers to one or more alternative forms of a gene occupying a given locus on a chromosome.

[0143] The term "gene" as used herein refers to a naturally occurring (e.g., genomic) or synthetic gene, including transcriptional and / or translational regulatory sequences and / or coding regions and / or non-translated sequences (e.g., introns, 5'-non-translated sequences and 3'-non-translated sequences). The coding region of a gene can be a nucleotide sequence that encodes an amino acid sequence or a functional RNA (such as tRNA, rRNA, catalytic RNA, siRNA, miRNA, or antisense RNA). A gene can also be an mRNA or a cDNA that corresponds to a coding region (e.g., exons and miRNA) that may include 5'-non-translated sequences or 3'-non-translated sequences linked thereto. A gene can also be an in vitro generated, amplified nucleic acid molecule that includes all or a portion of a coding region and / or 5'-non-translated sequences or 3'-non-translated sequences linked thereto. The term also includes pseudogenes, which are dysfunctional relatives of known genes that have lost the ability to code for a protein or are no longer expressed in a cell.

[0144] As used herein, "nucleic acid" or "oligonucleotide" or "polynucleotide" refers to at least two nucleotides covalently linked together. The depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. Many variants of a nucleic acid can be used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and their complements. A single strand provides a probe that can hybridize to a target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions.

[0145] Nucleic acids may be single-stranded or double-stranded, or may contain portions of both double-stranded and single-stranded sequences. Nucleic acids may be DNA, both genomic and cDNA, RNA, or hybrids, where the nucleic acid may contain combinations of deoxyribonucleotides and ribonucleotides, and combinations of bases such as uracil, adenine, thymine, cytosine, guanine, inosine, xanthine, hypoxanthine, isocytosine, and isoguanine. Nucleic acids may be obtained by chemical synthesis or recombinant methods.

[0146] "Polypeptide" is used in its conventional sense, i.e., as a sequence of amino acids. A polypeptide is not limited to a particular length of product. Peptides, polypeptides, and proteins are included in the definition of polypeptide, and such terms may be used interchangeably herein, unless otherwise indicated. The term also includes post-expression modifications of the polypeptide, such as glycosylation, acetylation, phosphorylation, and the like, as well as other modifications, both naturally occurring and non-naturally occurring, known in the art. A polypeptide may be an entire protein or a subsequence thereof.

[0147] The term "primer" refers to any nucleic acid that can hybridize at its 3' end to a complementary nucleic acid molecule and provide a free 3' hydroxyl end that can be extended by a nucleic acid polymerase. As used herein, amplification primers are a pair of nucleic acid molecules that can anneal to the 5' or 3' region of a gene (the positive and negative strands, respectively, or vice versa) and can include a short region therebetween. Under appropriate conditions and with appropriate reagents, such primers allow the amplification of a nucleic acid molecule having a nucleotide sequence adjacent to the primer. For in situ methods, a cell or tissue sample can be prepared and immobilized on a support, such as a glass slide, and then contacted with a probe that can hybridize to RNA. Alternative methods for amplifying nucleic acids corresponding to expressed RNA samples include, for example, those described in U.S. Pat. No. 7,897,750.

[0148] The term "probe" as used herein refers to an oligonucleotide that can bind to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairs, usually through the formation of hydrogen bonds. A probe can bind to a target sequence that lacks complete complementarity with the probe sequence, depending on the stringency of the hybridization conditions. There can be any number of base pair mismatches that prevent hybridization between the target sequence and the single-stranded nucleic acid described herein. However, if the number of mutations is so great that no hybridization occurs even under the least stringent hybridization conditions, the sequence is not a complementary target sequence. A probe can be single-stranded or partially single-stranded and partially double-stranded. The stranding of the probe is determined by the structure, composition, and properties of the target sequence. A probe can also be directly labeled or indirectly labeled, such as with biotin, to which a streptavidin complex can later bind.

[0149] "Complement" or "complementary" as used herein to refer to a nucleic acid can refer to Watson-Crick (e.g., AT / U and CG) or Hoogsteen base pairing between the nucleotides or nucleotide analogs of a nucleic acid molecule. A perfect complement or perfect complementary can refer to 100% complementary base pairing between the nucleotides or nucleotide analogs of a nucleic acid molecule.

[0150] As used herein, "stringent hybridization conditions" refers to conditions under which a first nucleic acid sequence (e.g., a probe) hybridizes to a second nucleic acid sequence (e.g., a target), such as in a complex mixture of nucleic acids. Stringent conditions are sequence-dependent, will vary under different circumstances, and can be appropriately selected by one of skill in the art. Stringent conditions can be selected to be about 5-10°C lower than the thermal melting point (Tm) of a particular sequence at a defined ionic strength pH. Tm can be the temperature (under defined ionic strength, pH, and nucleic acid concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (because the target sequence is present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions can be conditions in which the salt concentration is less than about 1.0 M sodium ion, for example, about 0.01-1.0 M sodium ion concentration (or other salt) at pH 7.0-8.3, and the temperature is at least about 30° C. for short probes (e.g., about 10-50 nucleotides) and at least about 60° C. for long probes (e.g., more than about 50 nucleotides). Stringent conditions can also be achieved by adding destabilizing agents such as formamide. For selective or specific hybridization, a positive signal can be at least 2-10 times the background hybridization. Exemplary stringent hybridization conditions include: 50% formamide, 5xSSC and 1% SDS incubated at 42° C., or 5xSSC, 1% SDS incubated at 65° C. with a wash in 0.2xSSC and 0.1% SDS at 65° C. However, several factors other than temperature, such as salt concentration, can affect the stringency of hybridization, and one skilled in the art can appropriately select the factors to achieve similar stringency.

[0151] "Hybridization" means the Watson-Crick base pairing of essentially complementary nucleotide sequences (polymers of nucleic acid) to form a double-stranded molecule.

[0152] As used herein, "linking" or "immobilization" in reference to a nucleic acid (e.g., a probe) and a solid support may mean that the bond between the probe and the solid support is sufficient to be stable under conditions of binding, washing, analysis, and removal. The bond may be covalent or non-covalent. A covalent bond may be formed directly between the probe and the solid support, or may be formed by a cross-linking agent, or by including specific reactive groups on either the solid support or the probe or both molecules. A non-covalent bond may be one or more of electrostatic interactions, hydrophilic interactions, and hydrophobic interactions. Non-covalent bonds include covalent binding of a molecule such as streptavidin to the support, and non-covalent binding of a biotinylated probe to streptavidin. Immobilization may also include a combination of covalent and non-covalent interactions.

[0153] The terms "determining," "measuring," "assessing," and "assaying" are used interchangeably and include both quantitative and qualitative measurements, including determining whether a property, attribute, or characteristic is present. Assessment can be relative or absolute. "Assessing the presence" of a target includes determining the amount of target present, as well as determining the presence or absence of a target.

[0154] The term "treat" or "treatment" refers to the administration of a compound or agent to a subject having or at risk of developing a disorder for the purpose of curing, alleviating, mitigating, curing, delaying, preventing or ameliorating the disorder, a symptom of the disorder, a condition secondary to the disorder, or a predisposition to the disorder.

[0155] As used herein, the term "in vitro" refers to events that take place not within a multicellular organism, but in an artificial environment, e.g., a test tube or reaction vessel, cell culture, and the like.

[0156] As used herein, the term "in vivo" refers to events that occur within a multicellular organism, such as a non-human animal.

[0157] It should be noted that as used in this specification and the appended claims, the singular forms "a," "an," and "the" include plural references unless the context clearly dictates otherwise.

[0158] The terms "including," "including," "containing," or "having" and variations thereof are meant to encompass the items listed thereafter and equivalents thereof, as well as additional subject matter, unless expressly stated otherwise.

[0159] The phrases "in one embodiment," "in various embodiments," "in some embodiments," and the like are used repeatedly. Such phrases do not necessarily refer to the same embodiment, although they can, unless the context dictates otherwise.

[0160] The term "and / or" or " / " means any one of the items, any combination of the items, or all of the items with which this term is associated.

[0161] The word "substantially" does not exclude "completely." For example, a composition that is "substantially free" of Y may be completely free of Y. If desired, the word "substantially" may be omitted from the definition of the invention.

[0162] As used herein, the term "approximately" or "about" when applied to one or more values ​​of interest refers to a value similar to the stated reference value. In some embodiments, the term "approximately" or "about" refers to a range of values ​​that falls within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater or less) of the stated reference value, unless otherwise stated or clear from the context (except where such number exceeds 100% of possible values). Unless otherwise indicated herein, the term "about" is intended to include values, e.g., weight percentages, that are close to the stated range that are equivalent in terms of the function of the individual components, compositions, or embodiments.

[0163] As disclosed herein, several ranges of values ​​are provided. Unless the context clearly dictates otherwise, it is understood that each intervening value, to the tenth of the unit of the lower limit, is also specifically disclosed between the upper and lower limits of that range. Each smaller range between a stated value or intervening value in a stated range and another stated or intervening value in that stated range is included in the invention. The upper and lower limits of these smaller ranges may be individually included or excluded in the range, and each range in which either, neither, or both limits are included in the smaller range is also included in the invention, subject to the specifically excluded limit in the stated range. When a stated range includes one or both limits, ranges excluding either or both of those included limits are also included in the invention.

[0164] As used herein, the term "each," when used in reference to a collection of items, is intended to identify an individual item in the collection, but does not necessarily refer to every item in the collection. Exceptions may occur where explicit disclosure or context clearly dictates otherwise.

[0165] Any and all examples provided herein, or the use of exemplary language (e.g., "etc.") are intended merely to better illuminate the invention and do not limit the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.

[0166] All methods described herein may be performed in any suitable order unless otherwise indicated herein or clearly contradicted by context. For any of the methods provided, the method steps may occur simultaneously or sequentially. When method steps occur sequentially, the steps may occur in any order unless otherwise stated. When a method includes a combination of steps, any and all combinations or subcombinations of steps are included within the scope of the present disclosure unless otherwise stated herein.

[0167] Each publication, patent application, patent, and other reference cited herein is incorporated by reference in its entirety to the extent that it is not inconsistent with this disclosure. Publications disclosed herein are provided solely for their disclosure prior to the filing date of the present invention. Nothing herein should be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, publication dates provided may differ from the actual publication dates, which may need to be independently confirmed.

[0168] It is understood that the examples and embodiments described herein are for illustrative purposes only, and that various modifications or changes in light thereof will be suggested to those skilled in the art and are to be included within the spirit and scope of this application and the appended claims.

[0169] IV. Working Examples Example 1: Effect of APOE genotype on human melanoma survival in the TCGA-SKCM cohort We downloaded the aligned whole-exome sequence BAM files sliced ​​for genomic coordinates chr19:44904748-44910394 (GRCh38) from the TCGA-SKCM project using the Genomic Data Commons API (Network, TCGA (2015) Cell, 161(7), 1681-1696) to assess the APOE genotype of melanoma patients. APOE variants were detected using the samtools / bcftools package (Li, H. (2011) Bioinformatics, 27(21), 2987-2993), providing the allele frequencies of chr19:44908684 (rs429358) and chr19:44908822 (rs7412) determined in the Atherosclerosis Risk in Communities (ARIC) study as prior distributions (Blair, CK et al., (2005) Neurology, 64(2), 268-276). Mutation detection at these two loci was then annotated with the APOE allele in R. 470 patients had normal tissue samples available (normal blood, normal solid tissue, or normal buccal tissue). Patients who presented with the E2;E4 genotype (n=5) were excluded from analyses other than genotype frequency assessment. Given that participants were comparable in terms of age and ethnicity, APOE genotype abundance in the normal population, as assessed for Caucasian patients in the ARIC study, has been reported (Blair, CK et al., (2005) Neurology, 64(2), 268-276). To test for differences in genotype distribution, χ 2 The test was adopted.

[0170] Clinical data including survival time and clinical response were used as recently curated (Liu, J. et al., (2018) Cell, 173(2), 400-416). Breslow depth and Clark level clinical data were added using the R package "TCGAbiolinks" (Colaprico, A. et al., (2016) Nucleic Acids Res, 44(8), e71). To assess the impact of APOE genotype on survival, Kaplan-Meier survival analyses were performed and statistical significance was tested with the log-rank test for trend using the 'survival' and 'survminer' packages (Therneau, TM (2015). A Package for Survival Analysis in S. Retrieved from https: / / CRAN.R-project.org / package=survival); (Alboukadel, K. et al., (2018) survminer: Drawing Survival Curves using 'ggplot2'. Retrieved from https: / / CRAN.R-project.org / package=survminer). All analyses were performed using R v3.5 (The R Foundation for Statistical Computing) and RStudiov1.1.3.

[0171] Example 2: Animal Experiments All animal experiments were performed in accordance with protocols approved by the Rockefeller University Institutional Animal Care and Use Committee. Human APOE2 (strain #1547), APOE3 (#1548) and APOE4 (#1549) targeted replacement (knock-in) mice were obtained from TACONIC BIOSCIENCES. Tyrr.CreER;Braf V600E / + ;Pten lox / lox Mice (Dankort, D. et al., Nature genetics 41, 544-552 (2009) were obtained from The Jackson Laboratory (#013590).

[0172] Example 3: Tumor Growth Studies To evaluate the effect of APOE genotype on syngeneic melanoma growth, 100,000 (YUMM1.7) cells were injected subcutaneously into the flank of 7-10 week-old APOE-targeted replacement male mice. For all injections, cells were mixed 1:1 with growth factor-reduced Matrigel (356231, CORNING) and injected in a total volume of 100 μL. Tumor size was measured on the indicated days using digital calipers, and tumor volumes were calculated (minor diameter) 2 The metastatic progression was evaluated by injecting 100,000 B16F10-TR-shApoE cells intravenously into the tail vein of human ApoE knock-in mice, and bioluminescence was measured twice a week.

[0173] Example 4: A genetically initiated model of melanoma progression Human APOE knock-in mice were generated using the Tyrr.CreER;Braf V600E / + ;Pten lox / lox Mice were mated with 10-mg tamoxifen (T5648, Sigma-Aldrich) mice. To induce melanoma, 6-7 week-old female mice were intraperitoneally injected with 1 mg tamoxifen (T5648, Sigma-Aldrich) for three consecutive days. Tamoxifen solution was prepared by dissolving tamoxifen powder in 100% ethanol at 50 °C for 5 min, followed by 10-fold dilution with peanut oil to generate a 10 mg / mL working solution. To assess melanoma burden, dorsal skin samples extending from the ear to the hip joint were collected 35 days after induction, depilated with a commercial depilatory cream (Nair), washed with water, and fixed in 4% PFA. The skin was then scanned and the percentage of pigmented melanoma lesion area was quantified using Cellprofiler v3 (McQuin, C. et al. CellProfiler 3.0: Next-generation image processing for biology. PLoS Blot 16, e2005970 (2018)).

[0174] Example 5: Cell Lines Murine B16F10 melanoma cells were obtained from the American Tissue Type Collection and cultured according to the supplier's conditions. B16F10 cells transduced with a retroviral construct to express luciferase (Therneau, TM (2015). A Package for Survival Analysis in S. Retrieved from https: / / CRAN.R-project.org / package=survival) and shRNA targeting Apoe (shRNA clone TRCN0000011799) were previously described (Pencheva, N. et al., (2014) Cell, 156(5), 986-1001). Braf V600E / + ;Pten - / - YUMM1.7 cells derived from mouse Cdkn2amouse melanoma were first provided in full by Marcus Bosenberg (Meeth, K. et al., Pigment Cell Melanoma Res 29, 590-597 (2016)). B16F10 cells were cultured in DMEM medium with pyruvate and glutamine (11995, GIBCO) supplemented with 10% FBS (F4135, SIGMA), penicillin-streptomycin (15140, GIBCO), and amphotericin B (17-936E, LONZA). YUMM1.7 cells were cultured in DMEM / F-12 medium with L-glutamine and 15 mM HEPES (11330, Gibco) supplemented with 10% FBS, penicillin-streptomycin, amphotericin B, and 1% non-essential amino acids (111400, GIBCO). Mycoplasma contamination was excluded by PCR testing according to standard protocols (Young, L. et al., Nature Protocols 5, 929-934 (2010)).

[0175] Example 6: Mouse genotyping Tyrr.CreER;Braf V600E / + ;Pten - / -Genotyping of mice was performed to distinguish between mouse and human APOE using standard PCR with independent reactions for mouse and human APOE (PCR product lengths of 200 bp and approximately 600 bp, respectively). PCR restriction fragment length polymorphism genotyping (Hixson, JE and Vernier, DT Journal of lipid research 31, 545-548 (1990)) was used to distinguish human APOE alleles. Briefly, a 244 bp fragment of APOE was amplified using standard PCR, digested with Hhal (R0139S, New England Biolabs), and allele-specific products were resolved on a 15% polyacrylamide gel. The following primers were used for the indicated PCR reactions: Tyr::CreER; Braf V600E / + ; Pten lox / lox mouse Cre transgene forward: 5'-GCG GTC TGG CAG TAA AAA CTA TC-3' (SEQ ID NO: 4) Cre transgene reverse: 5'-GTG AAA CAG CAT TGC TGT CAC TT-3' (SEQ ID NO:5) Cre internal control forward: 5'-CAC GTG GGC TCC AGC ATT-3' (SEQ ID NO: 6) Cre internal control reverse: 5'-TCA CCA GTC ATT TCT GCC TTT G-3' (SEQ ID NO: 7) Braf forward: 5'-TGA GTA TTT TTG TGG CAA CTG C-3' (SEQ ID NO: 8) Braf reverse: 5'-CTC TGC TGG GAA AGC GGC-3' (SEQ ID NO: 9) Pten forward: 5'-CAA GCA CTC TGC GAA CTG AG -3' (SEQ ID NO: 10) Pten reverse: 5'-AAG TTT TTG AAG GCA AGA TGC-3' (SEQ ID NO: 11) Mouse vs. human knock-in APOE mice Common forward: 5-TAC CGG CTC AAC TAG GAA CCA T-3' (SEQ ID NO: 12) Mouse Apoe reverse: 5'-TTT AAT CGT CCT CCA TCC CTG C-3' (SEQ ID NO: 13) Human APOE reverse: 5'-GTT CCA TCT CAG TCC CAG TCTC-3' (SEQ ID NO: 14) Human APOE allele-restricted length polymorphisms Human APOE forward: 5'-ACA GAA TTC GCC CCG GCC TGG TAC AC-3' (SEQ ID NO: 15) Human APOE reverse: 5'-TAA GCT TGG CAC GGC TGT CCA AGG A-3' (SEQ ID NO: 16) Example 7: Tumor Growth Study and Treatment To assess the effect of APOE genotype on syngeneic melanoma growth, 1 × 10 5 YUMM1.7 cells were injected subcutaneously into the flank of 6-10 week old gender-matched human APOE targeted replacement mice. Cells were injected in a total volume of 100 μL, and YUMM1.7 cells were mixed 1:1 with growth factor reduced Matrigel (356231, Corning) prior to injection. Tumor size was measured on the indicated days using digital calipers, and tumor volumes were calculated as (small diameter) 2 × (large diameter) × Π / 6. In experiments using YUMMER1.7 cells, 5 × 10 5Cells were injected subcutaneously into the flank. For LXR agonist treatment, mice were fed chow supplemented with synthetic LXR agonist RGX-104 (Rgenix (Tavazoie, M. et al., (2018) Cell, 172(4), 825-840)) at 628.5 mg / kg chow (Research Diets, approximate target dose 100 mg / kg body weight) starting 3 days after injection. For anti-PD1 treatment, mice were injected intraperitoneally with 250 μg and 125 μg of anti-PD-1 antibody (BioXCell, clone RMP1-14) on days 6 and 9 after tumor cell injection, respectively. Control mice received PBS injections on the same days. Survival analysis in the YUMMER1.7 model showed that mice with tumor volumes of 1000 mm 3 Mice were euthanized when tumor volumes exceeded 16 mm 3 If the IL-10 level was below the lower limit of detection, the treatment response was considered complete (CR, complete response).

[0176] Example 8: Analysis of APOE genotypes in the TCGA cohort The Cancer Genome Atlas (TCGA) assessed the APOE genotype of cancer patients by downloading aligned whole-exome sequence BAM files sliced ​​for genomic coordinates chr19:44904748-44910394 (GRCh38) using the Genomic Data Commons API (Network, TCGA (2015) Cell, 161(7), 1681-1696). APOE variants were detected using the samtools / bcftools package (Li, H. (2011) Bioinformatics, 27(21), 2987-2993) to provide allele frequencies for chr19:44908684 (rs429358) and chr19:44908822 (rs7412) as prior distributions, as determined in the Atherosclerosis Risk in Communities (ARIC) study (Blair, CK et al. (2005) Neurology, 64(2), 268-276). Patients who presented with the APOE2;APOE4 genotype (n=5) were excluded from the analysis, except for the genotype frequency assessment.

[0177] Clinical data including survival time and clinical response were used as recently curated (Liu, J. et al., (2018) Cell, 173(2), 400-416.). Clinical data at Breslow depth and Clark level were added using the R package "TCGAbiolinks" (Colaprico, A. et al., (2016) Nucleic Acids Res, 44(8), e71). To evaluate the impact of APOE genotype on survival, Kaplan-Meier survival analysis was performed and statistical significance was assessed with the log-rank test using the “survival” and “survminer” packages (Therneau, TM (2015) A Package for Survival Analysis in S. Retrieved from https: / / CRAN.R-project.org / package=survival); (Alboukadel, K. et al., (2018)survminer: Drawing Survival Curves using 'ggplot2'. Retrieved from https: / / CRAN.R-project.org / package=survival). Hazard ratios were calculated according to the Cox proportional hazards regression model using the “survival” R package (Therneau, TM (2015) A Package for Survival Analysis in S. Retrieved from https: / / CRAN.R-project.org / package=survival). For visualization purposes, survival data were truncated at 12 years. All analyses were performed using R v3.5 (The R Foundation for Statistical Computing) and RStudiov1.1.3.

[0178] Example 9: Analysis of APOE genotypes in anti-PD1 melanoma studies Analyses of the cohorts of Roh et al. (Roh, W. et al., (2017) Sci Transl Med, 9(379).) and Riaz et al. (Riaz, N. et al., (2017) Cell, 171(4), 934-949) were performed as described for the TCGA-SKCM cohort. Briefly, whole-exome sequencing data of normal tissues were downloaded from dbGaP (BioProject IDs PRJNA369259 and PRJNA359359) and APOE genotypes were detected as described above. In the cohort of Roh et al., the genotype of one patient could not be determined. In the cohort of Roh et al., only patients who received both anti-CTLA4 and anti-PD1 treatment were considered. In the cohort of Riaz et al., patients were stratified by previous CTLA4 treatment status. Kaplan-Meier survival analysis was performed using the “survival” and “survminer” packages as described above.

[0179] Example 10: APOE genotype modulates cancer survival in the context of immunotherapy To evaluate whether APOE genotype could affect melanoma progression in the context of immunotherapy, we analyzed the impact of APOE genotype on the progression of the immunogenic YUMMER1.7 melanoma model, which is amenable to anti-PD1 checkpoint therapy (Wang, J. et al., (2017) Pigment Cell & Melanoma Research, 30(4), 428-435). APOE4 mice survived significantly longer than APOE2 mice upon anti-PD1 treatment, suggesting that APOE genotype modulates melanoma outcome also in the context of immunotherapy (Figure 4a-b). To evaluate whether this effect can also be observed in humans, we analyzed melanoma patients who received anti-PD1 checkpoint inhibitor therapy after proceeding with anti-CTLA4 checkpoint inhibition (Roh, W. et al., (2017) Sci Transl Med, 9(379)). Indeed, APOE genotype was significantly associated with survival in this cohort (p=0.017, log-rank test). Consistent with the observations on survival of early stage patients above, APOE4 and APOE2 carriers showed the longest and shortest survival, respectively, with anti-PD1 therapy (Figure 4c). These findings were validated in an independent cohort of patients receiving anti-PD1 therapy upon progression of CTLA4 blockade (Riaz, N. et al., (2017) Cell, 171(4), 934-949). Consistent with the cohort studied by Roh, W. et al., APOE4 and APOE2 carriers also showed the longest and shortest survival outcomes, respectively, in this study by Riaz et al. (Figure 4d). Thus, in both of these cohorts, APOE genotype was associated with survival of patients who progressed on previous immunotherapy.

[0180] Pharmacological activation of APOE may enhance the differential impact of APOE variants on melanoma progression. Liver X receptor (LXR) is a nuclear hormone receptor that transcriptionally activates many genes involved in cholesterol and lipid metabolism, including APOE (Evans, RM et al., (2014) Cell, 157(1), 255-266; Hong, C. et al., (2014) Nat Rev Drug Discov, 13(6), 433-444). LXR agonism has been shown to enhance antitumor immunity, an effect that is primarily mediated by APOE (Tavazoie, M. et al., (2018) Cell, 172(4), 825-840.e18; Pencheva, N. et al., (2014) Cell, 156(5),986-1001). Indeed, the efficacy of LXR agonism was completely abrogated in APOE2 mice, whereas APOE4 mice benefited from the strong antitumor effect of the treatment, amplifying the differences in tumor progression between APOE2 and APOE4 mice (Figure 4e-f). Thus, different APOE genotypes may induce different responsiveness to LXR agonist therapy and serve as potential biomarkers for current clinical efforts investigating the use of LXR agonism in cancer treatment (Tavazoie, M. et al., (2018) Cell, 172(4), 825-840).

[0181] Example 11: APOE genotype modulates thyroid and breast cancer outcome To assess the impact of APOE genotype on thyroid and breast cancer patient outcomes, we analyzed normal tissue whole-exome sequencing data from patients with stage II / III disease in The Cancer Genome Atlas (TCGA) cohorts. In both cohorts, APOE genotype was significantly associated with survival (Figure 5a-b), with patients carrying the APOE2 genotype exhibiting the shortest survival.

[0182] Example 12: The effect of APOE genotype on breast cancer survival interacts with tumor immune cell infiltration Analysis of the entire TCGA breast cancer cohort revealed that patients carrying the APOE2 or APOE4 allele had shorter survival than APOE3 homozygotes (Figure 6a-c). In light of this difference between the melanoma and thyroid cancer cohorts, the effect of APOE on breast cancer survival may be modulated by other factors that determine cancer outcome. Considering the influence of APOE on tumor immunity, we tested the interaction of the degree of immune cell infiltration as assessed by (tumor transcriptome analysis (Thorsson, V. et al., (2018) Immunity, 48(4), 812-830. e14.) and APOE genotype. Immune infiltration interacted with APOE genotype, whereby there was a significant association of APOE genotype with overall survival in both groups of patients with low and high leukocyte infiltration, whereas survival of APOE2 and APOE4 carriers was reversed between the two groups. Thus, it was concluded that the effect of APOE genotype on breast cancer survival interacts with immune cell infiltration of the tumor.

[0183] Example 13: Statistical Analysis Unless otherwise stated, all data are expressed as mean ± standard error of the mean and groups were compared using t-test for normally distributed data or Mann-Whitney test for non-normally distributed data as indicated in the figure legends. Significant differences were concluded at p<0.05. To compare survival times, the log-rank test was employed. Throughout all figures: *p<0.05, **p<0.01, ***p<0.001, and *”*”p<0.0001.

[0184] Other objects, features, and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and examples, while indicating specific embodiments of the present invention, are given by way of illustration only. Moreover, it is contemplated that changes and modifications within the spirit and scope of the present invention will become apparent to those skilled in the art from this detailed description.

[0185] Example 14 RGX-104 was administered to patients with solid tumors as monotherapy or in combination with either docetaxel, nivolumab, or ipilimumab. Fifty-one patients were evaluable for both radiographic assessment of tumor response and ApoE genotype. Below is a table showing the number of patients with each genotype and the number of clinical responses (partial responses) to treatment.

[0186] [Table 2]

Claims

1. 1. A method for treating a subject having at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, comprising administering to said subject an effective amount of an LXRβ agonist or a pharma- ceutically acceptable salt thereof; The LXRβ agonist is 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof.

2. an effective amount of an LXRβ agonist or a pharma- ceutical acceptable salt thereof for administration to a subject identified as having at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19, and identified as likely to benefit from treatment with an LXRβ agonist or a pharma- ceutical acceptable salt thereof based on the presence of at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms; The LXRβ agonist is 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof.

3. The cancer therapeutic agent according to claim 1 or 2, wherein the presence of at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19 is detected by performing a genotyping assay on a sample containing nucleic acid obtained from the subject.

4. 1. A method for detecting susceptibility of a subject having cancer to benefit from treatment with an LXRβ agonist, or a pharma- ceutically acceptable salt thereof, comprising: (a) obtaining a sample comprising nucleic acid from said subject; (b) performing a genotyping assay on the sample to detect the presence of at least one ε4 allele in the ApoE gene on chromosome 19, the allele being defined by the rs7412 and rs429358 polymorphisms; and (c) detecting that a subject having at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19 is susceptible to benefit from treatment with an LXRβ agonist or a pharma- ceutically acceptable salt thereof; wherein the LXRβ agonist is 2-[3-[(3R)-3-[[2-chloro-3-(trifluoromethyl)phenyl]methyl-(2,2-diphenylethyl)amino]butoxy]phenyl]acetic acid or a pharma- ceutically acceptable salt thereof; This provides a method for detecting the likelihood that a subject with cancer would benefit from treatment with an LXRβ agonist, or a pharma- ceutically acceptable salt thereof.

5. The cancer therapeutic agent according to any one of claims 1 to 3, wherein the presence of at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19 is determined by polymerase chain reaction (PCR).

6. 5. The method of claim 4, wherein the presence of at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19 is determined by polymerase chain reaction (PCR).

7. The cancer therapeutic agent according to any one of claims 1 to 3, wherein the presence of at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19 is determined by the expression level of the APOE3 protein or APOE4 protein of the subject.

8. 5. The method of claim 4, wherein the presence of at least one ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene on chromosome 19 is determined by the expression level of the APOE4 protein in the subject.

9. The cancer therapeutic agent according to any one of claims 1 to 3, 5, and 7, wherein the cancer is breast cancer, colon cancer, renal cell carcinoma, lung cancer, hepatocellular carcinoma, gastric cancer, ovarian cancer, pancreatic cancer, esophageal cancer, prostate cancer, sarcoma, bladder cancer, head and neck cancer, glioblastoma, diffuse large B-cell lymphoma, leukemia, or melanoma.

10. 9. The method of any one of claims 4, 6 and 8, wherein the cancer is breast cancer, colon cancer, renal cell carcinoma, lung cancer, hepatocellular carcinoma, gastric cancer, ovarian cancer, pancreatic cancer, esophageal cancer, prostate cancer, sarcoma, bladder cancer, head and neck cancer, glioblastoma, diffuse large B-cell lymphoma, leukemia, or melanoma.

11. The cancer therapeutic agent according to claim 9 , wherein the cancer is melanoma, small cell lung cancer, or non-small cell lung cancer.

12. 11. The method of claim 10, wherein the cancer is melanoma, small cell lung cancer, or non-small cell lung cancer.

13. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9 and 11, wherein the cancer is metastatic and / or locally advanced.

14. 13. The method of any one of claims 4, 6, 8, 10 and 12, wherein the cancer is metastatic and / or locally advanced.

15. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11 and 13, wherein the cancer is unresectable.

16. 15. The method of any one of claims 4, 6, 8, 10, 12 and 14, wherein the cancer is unresectable.

17. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11, 13 and 15, wherein the effective amount comprises an amount effective to inhibit metastatic colony formation of the cancer.

18. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11, 13, 15 and 17, wherein the cancer is resistant to platinum-containing chemotherapy, PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, mitotic inhibitors, topoisomerase inhibitors, antimetabolites, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents.

19. 17. The method of any one of claims 4, 6, 8, 10, 12, 14 and 16, wherein the cancer is resistant to platinum-containing chemotherapy, PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, mitotic inhibitors, topoisomerase inhibitors, antimetabolites, angiogenesis inhibitors, kinase inhibitors, and / or alkylating agents.

20. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11, 13, 15, 17 and 18, wherein the cancer has progressed during or after treatment with platinum-containing chemotherapy, a PD-1 inhibitor, a PD-L1 inhibitor, an angiogenesis inhibitor, a kinase inhibitor, and / or an alkylating agent.

21. 20. The method of any one of claims 4, 6, 8, 10, 12, 14, 16 and 19, wherein the cancer has progressed during or after treatment with platinum-containing chemotherapy, a PD-1 inhibitor, a PD-L1 inhibitor, an angiogenesis inhibitor, a kinase inhibitor, and / or an alkylating agent.

22. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11, 13, 15, 17, 18 and 20, wherein the cancer has been determined or is predicted to be resistant to a PD-1 inhibitor, a PD-L1 inhibitor, a CTLA-4 inhibitor, a topoisomerase inhibitor, an antimetabolite, an angiogenesis inhibitor, a kinase inhibitor, and / or an alkylating agent.

23. 22. The method of any one of claims 4, 6, 8, 10, 12, 14, 16, 19 and 21, wherein the cancer is determined or predicted to be resistant to a PD-1 inhibitor, a PD-L1 inhibitor, a CTLA-4 inhibitor, a topoisomerase inhibitor, an antimetabolite, an angiogenesis inhibitor, a kinase inhibitor, and / or an alkylating agent.

24. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11, 13, 15, 17, 18, 20 and 22, wherein the subject is a subject receiving additional anticancer therapy.

25. 24. The method of any one of claims 4, 6, 8, 10, 12, 14, 16, 19, 21 and 23, wherein the subject is receiving an additional anti-cancer therapy.

26. The method of claim 24 , wherein the additional anti-cancer therapy comprises surgery, radiation therapy, chemotherapy, and / or immunotherapy.

27. 26. The method of claim 25, wherein the additional anti-cancer therapy comprises surgery, radiation therapy, chemotherapy, and / or immunotherapy.

28. The method of claim 26, wherein the additional anti-cancer therapy comprises chemotherapy and / or immunotherapy.

29. 28. The method of claim 27, wherein the additional anti-cancer therapy comprises chemotherapy and / or immunotherapy.

30. The method of claim 28, wherein the chemotherapy comprises docetaxel, carboplatin or cisplatin, pemetrexed, and / or pembrolizumab.

31. 30. The method of claim 29, wherein the chemotherapy comprises docetaxel, carboplatin or cisplatin, pemetrexed, and / or pembrolizumab.

32. The cancer therapeutic agent according to any one of claims 1 to 3, 5, 7, 9, 11, 13, 15, 17, 18, 20, 22, 24, 26, 28 and 30, wherein the subject is administered an effective amount of folic acid, vitamin B12, corticosteroid, statin, antiemetic, antidiarrheal, appetite stimulant, general stimulant, bisphosphonate, gonadotropin releasing hormone agonist, growth factor, and / or LHRH agonist.

33. 32. The method of any one of claims 4, 6, 8, 10, 12, 14, 16, 19, 21, 23, 25, 27, 29, and 31, wherein the subject is administered an effective amount of folic acid, vitamin B12, a corticosteroid, a statin, an antiemetic, an antidiarrheal, an appetite stimulant, a general stimulant, a bisphosphonate, a gonadotropin releasing hormone agonist, a growth factor, and / or an LHRH agonist.

34. The method of claim 1, wherein the subject has an ε4 allele defined by the rs7412 and rs429358 polymorphisms, an ε3 allele and an ε4 allele defined by the rs7412 and rs429358 polymorphisms, or an ε2 allele and an ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene.

35. 5. The method of claim 4, wherein the subject has an ε4 allele defined by the rs7412 and rs429358 polymorphisms, an ε3 allele and an ε4 allele defined by the rs7412 and rs429358 polymorphisms, or an ε2 allele and an ε4 allele defined by the rs7412 and rs429358 polymorphisms in the ApoE gene.

36. The method of claim 34, wherein the subject has the ε4 allele in the ApoE gene, the allele being defined by the rs7412 and rs429358 polymorphisms.

37. 36. The method of claim 35, wherein the subject has the ε4 allele in the ApoE gene defined by the rs7412 and rs429358 polymorphisms.

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