Methods for the Treatment of Solid Tumor Cancers Using Illudins and Biomarkers

Abstract

Methods for determining the likelihood that a subject suffering from a solid tumor cancer will benefit from treatment with an illudin are disclosed herein. Further, there are also methods for treatment based on such determination. In several embodiments, markers prostaglandin reductase 1 (PTGR1), Protein Tyrosine Phosphatase Non-Receptor Type 14 (PTPN14), Aspartate Beta-Hydroxylase (ASPH) together with one or more genes or alone may be used to enhance or guide treatment with an illudin. In certain embodiments, the protein or gene may be expressed or methylated.

Claims

1. A method of treating solid tumor cancer in a human subject with a targeted drug therapy comprising: extracting a biological sample from the human subject; measuring the level of expression of PTGR1, PTPN14, ASPH or combination thereof in the biological sample; identifying a patient having cancer sensitive to treatment with an illudin-based anti-cancer agent; treating the human subject with the illudin-based anti-cancer agent having the following structure: ##STR00009## wherein the expression level in the human subject of PTGR1, PTPN14, or ASPH is greater than the level in human without the solid tumor cancer.

2. The method of claim 1, wherein the solid tumor cancer is prostate cancer, ovarian cancer, kidney cancer, and thyroid cancer.

3. The method of claim 1, wherein the solid tumor cancer is colorectal cancer, pancreatic cancer, primary liver cancers, kidney cancer, ovarian cancer, uterine cancer, or breast cancer.

4. The method of claim 1, wherein the ASPH is methylated.

5. A method of treating solid tumor cancer with a targeted drug therapy comprising: identifying a patient having cancer sensitive to treatment with a compound of the formula: ##STR00010## wherein R1, R2 and R3 are independently (C1-C4) alkyl, methyl, or hydroxyl measuring the level of expression of PTGR1 of a combination thereof in the biological sample.

6. The method of claim 5, further comprising the step of measuring the level of expression of PTGR1 of a combination thereof in the biological sample.

7. The method of claim 5, further comprising the step of measuring the level of expression of PTPN14 in the biological sample.

8. The method of claim 5, further comprising e step of measuring the level of expression of ASPH in the biological sample.

9. The method of claim 5, wherein the cancer is newly diagnosed, relapsed, or refractory.

10. The method of claim 5, further comprising modifying a targeted drug therapy based on expression of a gene.

11. The method of claim 9, wherein ASPH is methylated.

12. The method of claim 1, wherein the cancer is colorectal cancer, pancreatic cancer, primary liver cancers, kidney cancer, ovarian cancer, uterine cancer, lung cancer, breast cancer, prostate cancer, sarcomas, or adipose tissue cancer.

13. A method for predicting response lent in a patient having a solid tumor, comprising: obtaining a biological sample from the patient; measuring the level of expression of PTGR1, PTPN 14, ASPH or a combination thereof in the biological sample; and comparing the level of expression in the biological sample to that of a biological sample from a subject not having a solid cancer; wherein an increased level of the expression in the biological sample from the patient relative to that from the subject not having the solid tumor indicates a likelihood of an effective response to the treatment with a compound of the formula: ##STR00011## or a pharmaceutically acceptable salt, solvate or stereoisomer thereof.

14. A kit for determining whether an anti-cancer effect is likely to be produced in a cancer by an illudin, comprising a means for determining the level of PTGR1, PTPN14, ASPH or a combination thereof expression in a cancer relative to a normal value from biological sample from the patient relative to that from the subject having the solid tumor.

15. The method of claim 16, wherein the cancer is colorectal cancer, pancreatic cancer, primary liver cancers, kidney cancer, ovarian cancer, uterine cancer, lung cancer, breast cancer, prostate cancer, sarcomas, or adipose tissue cancer.

16. The kit of claim 18, wherein the illudin has ##STR00012##

Description

DETAILED DESCRIPTION

[0025] One member of the anti-cancer agent sensitivity determination marker includes gene markers prostaglandin reductase 1 (PTGR1), Protein Tyrosine Phosphatase Non-Receptor Type 14 (PTPN14), Aspartate Beta-Hydroxylase (ASPH) together with one or more genes or alone. In certain embodiments, the protein gene may be expressed or methylated. Prostaglandin reductase 1 (PTGR1) is a highly inducible enzyme with enone reductase activity. The marker PTGRI was correlated with sensitivity to illudin-based treatments or correlated with true responders to illudin-based treatments. The use of the marker, alone or with others, can reduce the gaps in the treatment of cancers (e.g., prostate cancers) by developing predictive biomarker-based screening tests enabling precision medicine-based therapies to patients. The inventors have discovered that detection of solid tumor-associated mutated nucleic acid or protein sequences circulating in subjects with a solid tumor cancer that can accurately determine whether the subject is sensitive to a treatment with an illudin.

[0026] In specific embodiments, the DNA of the PTGR1, PTPN14, ASPH genes are methylated. DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts to repress gene transcription.

[0027] A method of treating or managing solid tumor cancer (e.g., prostate cancer, ovarian cancer, liver cancer, kidney cancer, and thyroid cancer) includes

[0028] identifying a patient having cancer sensitive to treatment with an illudin of the formula:

##STR00005##

[0029] illudin or a pharmaceutically acceptable salt, solvate or stereoisomer thereof; and

[0030] administering to the patient a therapeutically effective amount of the illudin.

[0031] A method of treating or managing solid tumor treatment includes

[0032] identifying a patient having solid tumor cancer sensitive to treatment with an illudin having the formula:

##STR00006##

or a pharmaceutically acceptable salt, solvate or stereoisomer thereof; and

[0033] administering to the patient a therapeutically effective amount of the compound.

[0034] A method for predicting response to treatment in a patient having a solid tumor, comprising:

[0035] obtaining a biological sample from the patient;

[0036] measuring the level of expression of PTGR1, PTPN14, ASPH or a combination thereof in the biological sample; and

[0037] comparing the level of expression in the biological sample to that of a biological sample from a subject not having a solid cancer;

[0038] wherein an increased level of the expression in the biological sample from the patient relative to that from the subject not having the solid tumor indicates a likelihood of an effective response to the treatment with a compound of the formula:

##STR00007##

or a pharmaceutically acceptable salt, solvate or stereoisomer thereof.

[0039] A method for predicting response to treatment in a patient having a solid tumor, comprising: obtaining a biological sample from the patient;

[0040] measuring the level of expression of PTGR1, PTPN14, ASPH or a combination thereof in the biological sample; and

[0041] comparing the level of the expression of PTGR1, PTPN14, ASPH or a combination thereof in the biological sample to that of a biological sample from a subject not having a solid tumor;

[0042] wherein a decreased level of expression of PTGR1, PTPN14, ASPH or a combination thereof in the biological sample from the patient relative to that from the subject not having a solid tumor indicates a likelihood of an effective response to the treatment with a compound of the formula:

##STR00008##

or a pharmaceutically acceptable salt, solvate or stereoisomer thereof.

[0043] In one embodiment provided herein is a method of treating or managing solid tumor cancer, comprising: identifying a patient having solid tumor cancer sensitive to treatment with an illudin, or a pharmaceutically acceptable salt; and administering to the patient a therapeutically effective amount of the compound. In certain embodiments, methods provided herein further comprise administering a therapeutically effective amount of an additional active agent, which is illudin.

[0044] In one embodiment, the illudin is administered once on day 1 of a 21 day cycle or another cycle.

[0045] In another embodiment, the illudin may be administered with one or more second active ingredients. Such active ingredients may be other anti-cancer agents or agents used to treat cancer patients.

[0046] As set out above, the solid tumor cancer may be selected from the group consisting of colorectal cancer, pancreatic cancer, primary liver cancers, kidney cancer, ovarian cancer, uterine cancer, lung cancer, breast cancer, prostate cancer, sarcomas, and adipose tissue cancer.

[0047] In one embodiment, one or more of the following genes may be used as a marker with PTGR1 to determine sensitivity to an illudin-based anticancer agent: TNFRSF1B, LCK, TAL1, GNG12, S100A10, CD247, ATP1B1, LAMC1, PTPRC, PTPN7, PTPN14, CAPN2, ENAH, LCT, CXCR4, ITGA4, CASP10, HDAC4, NUP210, WWTR1, PFN2, MLF1, CD38, RHOH, ITK, LCP2, HIST1H3B, MYB, IKZF1, PIK3CG, MET, NRF1, TRBC1, PTPRN2, PTK2B, ASPH, NFIB, CNTRL, PRKCQ, MYOF, CTBP2, LMO2, CD3D, TWF1, NCKAP1L, CKAP4, LCP1, CFL2, TJP1, ALDH1A2, TLE3, TNFRSF12A, PRKCB, NFATC3, WWOX, CBFA2T3, ATP2A3, GIPC1, HAUS5, MAP4K1, SDC4, APP, SLC38A5, WAS, and IL2RG.

[0048] In another embodiment, one or more of the following gene markers may be used WWTR1, HIST1H3B, ASPH, MYOF, CTBP2, CBFA2T3 and SDC4. In another embodiment, one or more markers were combined with PTGR1 with one, more or all of the following genes with PTGR1: PTPN14, ITGA4, HDAC4, ITK, IKZF1, PIK3CG, NRF1, ASPH, and PRKCQ. In some instances, the sensitivity can approach 100%.

[0049] In yet another embodiment, the two markers PTGR1 and SDC4 may be used as the markers.

[0050] In the instance where a PTGR1 combination of genes is used, screening of an anti-cancer agent sensitivity enhancer can be performed through employment, as an index, of variation in expression of a PTGR1 combination of genes after exposure to the illudin-based anti-cancer agent. That is, a substance which decreases the PTGR1 combination of genes level before exposure to the illudin-based anti-cancer agent or which promotes variation in the expression or elevates the level after exposure to the illudin-based anti-cancer agent, in vitro or in vivo, enhances the sensitivity to the anti-cancer agent. In addition, in an in vitro case, a substance which promotes variation in the expression or elevates the level after exposure to the anti-cancer agent corresponding to the target cancer cells can serve as a substance which enhances the sensitivity to the illudin-based anti-cancer agent (i.e., anti-cancer agent sensitivity enhancer).

[0051] In order to carry out the method for determining sensitivity of a specimen to an anti-cancer agent, a kit containing a protocol for measuring any of the substances present in the specimen is employed. The kit contains a reagent for measuring any of these substances, an indication of an instruction manual for use of the reagent, standards for determining the presence or absence of sensitivity to the illudin-based anti-cancer agent, etc. The standards include (relative) standard levels of these metabolism-related substances, a (relative) high threshold level, a (relative) low threshold level, factors affecting the measurements, the degree of the effects, etc. These substance levels may be set so as to suit the illudin-based anti-cancer agent selected. The sensitivity determination may be performed in the same manner on the basis of the standards.

[0052] Screening of an illudin-based anti-cancer agent can be performed by means of the illudin-based anti-cancer agent sensitivity determination marker as an index. That is, a substance which can vary the level of the anti-cancer agent sensitivity determination marker in vitro or in vivo is evaluated as an anti-cancer agent. For example, in an in vitro case, a substance which varies the anti-cancer agent sensitivity determination marker level in various cancer cells after exposure to the substance can serve as an anti-cancer agent. Also, when the anti-cancer agent sensitivity determination marker level in a cancer-bearing animal is varied after administration of a substance thereto, the substance can serve as an anti-cancer agent. If the anti-cancer agent is expected to exhibit a pharmacological effect, the increase in anti-cancer agent sensitivity determination marker level is observed before occurrence of tumor shrinkage or attaining cytocidal effect. Therefore, screening based on the anti-cancer agent sensitivity determination marker level as an index can realize, for a shorter period of time, determination whether or not the test substance serves as a useful anti-cancer agent, whereby efforts and cost involved in the development of anti-cancer agents are greatly expected to be reduced.

[0053] When the cancer has no sensitivity to an anti-cancer agent, no pharmacological effect can be expected from the anti-cancer agent. If such a pharmaceutically impotent anti-cancer agent is continuously administered to the patient, the cancer may progress, and side effects may be aggravated. Thus, the anti-cancer agent sensitivity determination marker may be employed not only to determine therapeutic response to the anti-cancer agent, but also to greatly contribute to prevention of aggravation of side effects, which would otherwise be caused by continuous administration of a pharmaceutically inactive anti-cancer agent.

[0054] Through employment, in combination, of the thus-obtained anti-cancer agent sensitivity enhancer and an illudin-based anti-cancer agent which is a sensitivity enhancement target of the enhancer, the therapeutic effect of the illudin-based anti-cancer agent is drastically enhanced. The combination of the illudin-based anti-cancer agent sensitivity enhancer and the anti-cancer agent which is a sensitivity enhancement target of the enhancer may be a composition containing both ingredients, or a combined drug of preparations containing individual ingredients.

[0055] To assist with monitoring of subjects, it is particularly if the reference value is obtained from the subject, as part of an on-going screening program. Alternatively, the reference value may be obtained from a population of subjects who have no solid tumor cancer.

[0056] Cells for testing may be obtained by any method known in the art, including but not limited to as a surgical resection, as a biopsy for example but not limited to a needle biopsy, core biopsy, or aspirate, or collection from a fluid sample, such as blood, urine, cerebral spinal fluid, cystic fluid, etc. Methods of measuring DNA/mRNA include but are not limited to polymerase chain reaction, in situ hybridization, gel electrophoresis, sequence analysis, and microarray analysis or a combination thereof. Methods of measuring protein include but are not limited to mass spectrometry techniques, 1-D or 2-D gel-based analysis systems, chromatography, enzyme linked immunosorbent assays (ELISAs), radioimmunoassays (RIA), enzyme immunoassays (EIA), Western Blotting, immunoprecipitation, and immunohistochemistry. Antibody arrays or protein chips may also be employed. That an anticancer effect is “likely” to be produced by an agent in a subject means that the subject, in the parameter or parameters being tested (e.g., level of PTGR1, PTPN14 and ASPH mRNA, methylated DNA and/or protein, expression of genes or exons listed in Example 1), is more similar to other subjects in which the agent produces a significant anticancer effect than to other subjects in which the agent does not produce a significant anticancer effect. That an anticancer effect is “unlikely” to be produced by an agent in a subject means that the subject, in the parameter or parameters being tested, is more similar to other subjects in which the agent does not produce a significant anticancer effect than to other subjects in which the agent does produce a significant anticancer effect.

[0057] Pharmaceutical compositions can be used in the preparation of individual, single unit dosage forms. Pharmaceutical compositions and dosage forms provided herein comprise an immunomodulatory compound provided herein, or a pharmaceutically acceptable salt, solvate, hydrate, stereoisomer, or prodrug thereof. Pharmaceutical compositions and dosage forms provided herein can further comprise one or more excipients.

[0058] Pharmaceutical compositions and dosage forms provided herein can also comprise one or more second active ingredients. Consequently, pharmaceutical compositions and dosage forms provided herein comprise the active ingredients disclosed herein (e.g., an immunomodulatory compound). Examples of optional second, or additional, active ingredients are disclosed herein.

[0059] Kits and compositions for carrying out the methods provided herein are also contemplated. In certain embodiments, provided herein are kits useful for determining the efficacy of an anti-cancer compound. In certain embodiments, provided herein are kits useful for assessing the efficacy of a compound in treating a patient. In some embodiments, provided herein are kits useful for determining the effect of an immunomodulatory compound. The kit comprises a solid support, and a means for detecting the gene, protein, or glycoprotein expression of at least one biomarker in a biological sample. Such a kit may employ, for example, a dipstick, a membrane, a chip, a disk, a test strip, a filter, a microsphere, a slide, a multiwell plate, or an optical fiber. The solid support of the kit can be, for example, a plastic, silicon, a metal, a resin, glass, a membrane, a particle, a precipitate, a gel, a polymer, a sheet, a sphere, a polysaccharide, a capillary, a film, a plate, or a slide. The biological sample can be, for example, a cell culture, a cell line, a tissue, an oral tissue, gastrointestinal tissue, an organ, an organelle, a biological fluid, a blood sample, a urine sample, or a skin sample.

[0060] In one embodiment a kit provided herein comprises an illudin compound provided herein, or a pharmaceutically acceptable salt, solvate or hydrate thereof. Kits may further comprise additional active agents, including but not limited to those disclosed herein.

EXAMPLES

[0061] Certain embodiments provided herein are illustrated by the following non-limiting example. As shown in Example 1, analyses of in vitro Illudin (LP-184) sensitivity data from a panel of cancer cell lines with known multi-omic molecular profiles yielded a signature of 10 genes (ASPH, HDAC4, IKZF1, ITGA4, ITK, NRF1, PIK3CG, PRKCQ, PTGR1, and PTPN14) capable of predicting illudin sensitivity with up to or including 100% accuracy on blind testing. The gene expression, DNA mutation, DNA methylation and protein expression status of these 10 genes was further computed as a correlation with Illudin (LP-184) sensitivity. Out of these 10 genes, 3 genes emerged as having highly significant correlations with Illudin bioactivity at the multiomic level, as represented in table 1. These gene identities are PTGR1, PTPN14 and ASPH. These 3 genes also carry the highest gene weightage in terms of relative importance while determining Illudin (LP-184) sensitivity according to FIG. 1. They were revealed to be the most prominent genes in classifying a sample as an illudin responder or non-responder as shown in FIG. 2. Overall, a novel gene set that determines sensitivity to and predicts responses to Illudins (LP-184) in cancer has been established.

Example 1

[0062] Genes Correlated With LP-184 (Illudin Family) Sensitivity in Cancer

TABLE-US-00001 Gene name Parameter Correlation coefficient p value PTGR1 Gene expression 0.868 0 DNA methylation −0.728 0 Protein expression 0.561 0.000004 PTPN14 Gene expression 0.709 0 DNA methylation −0.639 0 ASPH Gene expression 0.536 0.000012 DNA mutation −0.343 0.007733 Protein expression 0.579 0.000002

[0063] FIG. 1 shows the relative importance of an exemplary gene signature for hydroxyureamethylacylfulvene. In this relative variable importance graph, gene weightage analysis was performed to analyze the relative ranking of the top 10 genes in the hydroxyureamethylacylfulvene signature in cancer. The data shows that PTGR1 (Prostaglandin Reductase 1) followed by PTPN14 and ASPH are gene signatures for hydroxyureamethylacylfulvene sensitivity.

[0064] FIG. 2. shows PTGR1 and PTPN14 association with positive response to hydroxyureamethylacylfulvene. In this sensitivity analysis graph, the effect of gene expression on the response variable is studied across LP-184 gene signatures using the lekprofile function. High expression of PTGR1 (Prostaglandin Reductase 1) was correlated to positive response to LP-184) with PTPN14 being the next most highly correlated gene. This experiment was conducted on a panel of cancer cells.

[0065] The embodiments described above are intended to be merely exemplary, and those skilled in the art will recognize, or will be able to ascertain using no more than routine experimentation, numerous equivalents of specific compounds, materials, and procedures. All such equivalents are considered to be within the scope of the embodiments and are encompassed by the appended claims.