Xie, Fang

Most patients with metastatic prostate cancer eventually develop resistance to primary androgen deprivation therapy. To identify predictive biomarker for Abiraterone acetate/prednisone resistance, we screened alternative splice variants between responders and non-responders from the PROMOTE clinical study and pinned down the most significant variant, CENPK–delta8. Through preclinical patient-derived mouse xenograft (PDX) and 3D organoids obtained from responders and non-responders, as well as in vitro models, aberrant CENPK–delta8 expression was determined to link to drug resistance via enhanced migration and proliferation. The FLNA and FLOT1 were observed to specifically bind to CENK–delta8 rather than wild-type CENPK, underscoring the role of CENPK–delta8 in cytoskeleton organization and cell migration. Our study, leveraging data from the PROMOTE study, TCGA, and TCGA SpliceReq databases, highlights the important function of alternative splice variants in drug response and their potential to be prognostic biomarkers for improving individual therapeutic outcomes in precision medicine.

Approximately one‐third of patients with metastatic castration‐resistant prostate cancer (CRPC) exhibited primary abiraterone resistance. To identify alternative treatment for abiraterone nonresponders, we performed drug discovery analyses using the L1000 database using differentially expressed genes identified in tumor biopsies and patient‐derived xenograft (PDX) tumors between abiraterone responders and nonresponders enrolled in PROMOTE trial. This approach identified 3 drugs, including topoisomerase II (TOP2) inhibitor mitoxantrone, CDK4/6 inhibitor palbociclib, and pan‐CDK inhibitor PHA‐793887. These drugs significantly suppressed the growth of abiraterone‐resistant cell lines and PDX models. Moreover, we identified 11 genes targeted by all 3 drugs that were associated with worse outcomes in both the PROMOTE and Stand Up To Cancer cohorts. This 11‐gene panel might also function as biomarkers to select the 3 alternative therapies for this subgroup of patients with CRPC, warranting further clinical investigation.

Abstract Castration resistant prostate cancer (CRPC) is a deadly disease with a poor prognosis. Treatment options for CRPC patients involve taxanes or newly developed drugs targeting the androgen pathway or androgen synthesis, including CYP17 inhibitors. However, response to therapy varies dramatically among patients, which might be due, in part, to tumor heterogeneity. Therefore, understanding of the genomic landscape of CRPC would be important to help achieve better outcomes by developing personalized therapies. One challenge contributing to our lack of therapies for CRPC is a paucity of clinically relevant animal models predictive of response to therapy in human patients. The Prostate Cancer Medically Optimized Genome Enhanced Therapy (PROMOTE) study is a Mayo Clinic prospective trial designed for patients with metastatic CRPC who are treated with abiraterone acetate, a CYP17 inhibitor, over a 12 week period. Fresh tissue from metastatic lesions, primarily bone metastases, was obtained by needle core biopsy before and 12 weeks after initiating abiraterone acetate treatment. The samples were submitted for DNA and RNA sequencing and were also used to generate patient-derived xenograft (PDX) models. PDX models were developed by injecting biopsy samples subcutaneously or under the renal capsule in male non-obese diabetic (NOD)/severe combined immunodeficient (SCID) or NOD/SCID/IL-2γ-receptor null (NSG) mice implanted with 25mg testosterone pellets at the time of tissue implantation and 2 months later. Baseline samples from 103 unique patients as well as second samples from 61 patients post abiraterone acetate treatment were injected into approximately 600 mice. Of the samples for which pathology is currently available, 31% of the biopsies injected into mice were confirmed to include tumor tissue, which may be compared with a figure of 37.5% of samples sent for sequencing. Thus far, we have established 8 PDX models, four from baseline and four from post treatment samples. Seven models were derived from metastatic bone lesions, and one model from a liver metastasis. The tumor tissue in each model was expanded into a second of generation of mice and harvested when the tumors grew. No tumor was expanded more than four times. Genomic and transcriptomic analysis of xenograft tissue from different “generations” of xenograft expansion is ongoing and will be compared with similar data for the original biopsy. The evaluation of treatment response after exposure of these PDX models to different therapies including CYP19 inhibitors, AR blockers and taxanes is ongoing. These PDX models provide a tool for future drug testing and for studying mechanisms of resistance to therapy in CRPC. Citation Format: Fang Xie, Manish Kohli, Yin Ping, Rafael E. Jimenez, Richard M. Weinshilboum, Liewei Wang. Developing patient derived xenograft (PDX) models for metastatic castration resistant prostate cancer (CRPC) during CYP17 inhibitor therapy. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A05.

Abstract Genetic risks in breast cancer remain only partly understood. Here, we report the results of a genome-wide association study of germline DNA from 4,658 women, including 252 women experiencing a breast cancer recurrence, who were entered on the MA.27 adjuvant trial comparing the aromatase inhibitors (AI) anastrozole and exemestane. Single-nucleotide polymorphisms (SNP) of top significance were identified in the gene encoding MIR2052HG, a long noncoding RNA of unknown function. Heterozygous or homozygous individuals for variant alleles exhibited a ∼40% or ∼63% decrease, respectively, in the hazard of breast cancer recurrence relative to homozygous wild-type individuals. Functional genomic studies in lymphoblastoid cell lines and ERα-positive breast cancer cell lines showed that expression from MIR2052HG and the ESR1 gene encoding estrogen receptor-α (ERα) was induced by estrogen and AI in a SNP-dependent manner. Variant SNP genotypes exhibited increased ERα binding to estrogen response elements, relative to wild-type genotypes, a pattern that was reversed by AI treatment. Further, variant SNPs were associated with lower expression of MIR2052HG and ERα. RNAi-mediated silencing of MIR2052HG in breast cancer cell lines decreased ERα expression, cell proliferation, and anchorage-independent colony formation. Mechanistic investigations revealed that MIR2052HG sustained ERα levels both by promoting AKT/FOXO3-mediated ESR1 transcription and by limiting ubiquitin-mediated, proteasome-dependent degradation of ERα. Taken together, our results define MIR2052HS as a functionally polymorphic gene that affects risks of breast cancer recurrence in women treated with AI. More broadly, our results offer a pharmacogenomic basis to understand differences in the response of breast cancer patients to AI therapy. Cancer Res; 76(23); 7012–23. ©2016 AACR.

Abstract Elucidating mechanisms of chemoresistance is critical to improve cancer therapy, especially for the treatment of pancreatic ductal adenocarcinoma (PDAC). Genome-wide association studies have suggested the less studied gene HEAT repeat-containing protein 1 (HEATR1) as a possible determinant of cellular sensitivity to different chemotherapeutic drugs. In this study, we assessed this hypothesized link in PDAC, where HEATR1 expression is downregulated significantly. HEATR1 silencing in PDAC cells increased resistance to gemcitabine and other chemotherapeutics, where this effect was associated with increased AKT kinase phosphorylation at the Thr308 regulatory site. Mechanistically, HEATR1 enhanced cell responsiveness to gemcitabine by acting as a scaffold to facilitate interactions between AKT and the protein phosphatase PP2A, thereby promoting Thr308 dephosphorylation. Consistent with these findings, treatment with the AKT inhibitor triciribine sensitized HEATR1-depleted PDAC cells to gemcitabine, suggesting that this therapeutic combination may overcome gemcitabine resistance in patients with low HEATR1 expression. Clinically, we found that HEATR1 downregulation in PDAC patients was associated with increased AKT phosphorylation, poor response to tumor resection plus gemcitabine standard-of-care treatment, and shorter overall survival. Collectively, our findings establish HEATR1 as a novel regulator of AKT and a candidate predictive and prognostic indicator of drug responsiveness and outcome in PDAC patients. Cancer Res; 76(3); 572–81. ©2015 AACR.