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1.
Nat Genet ; 56(3): 371-376, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38424461

ABSTRACT

Available genetically defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Here, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant bladder and prostate cancer models. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.


Subject(s)
Neoplasms , Male , Humans , Genotype , Phenotype , Neoplasms/genetics , Genetic Association Studies
2.
bioRxiv ; 2023 Apr 14.
Article in English | MEDLINE | ID: mdl-37609344

ABSTRACT

Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant bladder and prostate cancer models. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.

3.
Mol Oncol ; 17(12): 2709-2727, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37533407

ABSTRACT

Most patients with muscle-invasive bladder cancer (MIBC) are not cured with platinum chemotherapy. Up-regulation of nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) is a major mechanism underlying chemoresistance, suggesting that its pharmacological inhibition may increase platinum efficacy. NF-κB signaling was investigated in two patient cohorts. The Cancer Genome Atlas (TCGA) was used to correlate NF-κB signaling and patient survival. The efficacy of cisplatin plus the NF-κB inhibitor dimethylaminoparthenolide (DMAPT) versus cisplatin or DMAPT alone was tested in vitro. Xenografted and immunocompetent MIBC mouse models were studied in vivo. Platinum-naive claudin-low MIBC showed constitutive NF-κB signaling and this was associated with reduced disease-specific survival in TCGA patients. Chemotherapy up-regulated NF-κB signaling and chemoresistance-associated genes, including SPHK1, PLAUR, and SERPINE1. In mice, DMAPT significantly improved the efficacy of cisplatin in both models. The combination preserved body weight, renal function, and morphology, reduced muscle fatigue and IL-6 serum levels, and did not aggravate immuno-hematological toxicity compared with cisplatin alone. These data provide a rationale for combining NF-κB inhibition with platinum-based chemotherapy and conducting a clinical trial in MIBC patients.


Subject(s)
Antineoplastic Agents , Urinary Bladder Neoplasms , Humans , Mice , Animals , NF-kappa B/genetics , Cisplatin/pharmacology , Cisplatin/therapeutic use , Drug Resistance, Neoplasm , Urinary Bladder Neoplasms/drug therapy , Urinary Bladder Neoplasms/genetics , Muscles , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use
4.
Clin Genitourin Cancer ; 21(6): 669-678, 2023 12.
Article in English | MEDLINE | ID: mdl-37344281

ABSTRACT

BACKGROUND: Nectin-4 and Trop-2 are transmembrane targets of FDA-approved antibody-drug conjugates (ADC) Enfortumab-vedotin (EV) and Sacituzumab govitecan (SG), respectively, for the treatment of metastatic urothelial carcinoma (mUC). The expression and role of Nectin-4 and Trop-2 in mUC variant histology is poorly described. MATERIALS AND METHODS: We evaluate membranous and cytoplasmic protein expression, and mRNA levels of Nectin-4 and Trop-2 within matched primary and metastatic mUC samples to determine heterogeneity of ADC targets in mUC variants. RESULTS: Patients with mUC were consented for rapid autopsy immediately after death. Tissues from matched primary and metastatic lesions were collected. A total of 67 specimens from 20 patients were analyzed: 27 were UC, 17 plasmacytoid (PUC), 18 UC with squamous differentiation (UCSD), and 5 neuroendocrine (NE); 10 from primary and 57 from metastatic sites. All histology except NE expressed moderate-high levels of Nectin-4 and Trop-2 by both immunohistochemistry and RNAseq. Nectin-4 demonstrated prominent cytoplasmic staining in metastatic PUC and UCSD. Trop-2 demonstrated strong cytoplasmic and membrane staining in primary and metastatic tumors. Interestingly, Nectin-4 and Trop-2 expression are positively correlated at both mRNA and protein levels. CONCLUSION: UC and non-NE variants express notable level of Nectin-4 and Trop-2 in both primary and metastatic lesions. Membrane staining of Nectin-4 and Trop-2 is present but cytoplasmic staining is a more common event in both mUC and mUC variant histology. These findings support evaluation of EV and SG in heavily treated variant histology BC and urge attention on the clinical relevance of cytoplasmic localization of ADC targets.


Subject(s)
Carcinoma, Transitional Cell , Immunoconjugates , Urinary Bladder Neoplasms , Humans , Nectins , Carcinoma, Transitional Cell/drug therapy , Autopsy , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/drug therapy , Immunoconjugates/therapeutic use , RNA, Messenger/genetics
5.
Cancer Cell ; 41(5): 853-870.e13, 2023 05 08.
Article in English | MEDLINE | ID: mdl-37084735

ABSTRACT

We uncover a tumor-suppressive process in urothelium called transcriptional-translational conflict caused by deregulation of the central chromatin remodeling component ARID1A. Loss of Arid1a triggers an increase in a nexus of pro-proliferation transcripts, but a simultaneous inhibition of the eukaryotic elongation factor 2 (eEF2), which results in tumor suppression. Resolution of this conflict through enhancing translation elongation speed enables the efficient and precise synthesis of a network of poised mRNAs resulting in uncontrolled proliferation, clonogenic growth, and bladder cancer progression. We observe a similar phenomenon in patients with ARID1A-low tumors, which also exhibit increased translation elongation activity through eEF2. These findings have important clinical implications because ARID1A-deficient, but not ARID1A-proficient, tumors are sensitive to pharmacologic inhibition of protein synthesis. These discoveries reveal an oncogenic stress created by transcriptional-translational conflict and provide a unified gene expression model that unveils the importance of the crosstalk between transcription and translation in promoting cancer.


Subject(s)
Chromatin , Urinary Bladder Neoplasms , Humans , Urinary Bladder Neoplasms/genetics
6.
Clin Genitourin Cancer ; 21(2): 265-272, 2023 04.
Article in English | MEDLINE | ID: mdl-36710146

ABSTRACT

INTRODUCTION: Cisplatin-based neoadjuvant chemotherapy (NAC) followed by cystectomy is the standard for muscle-invasive bladder cancer (MIBC), however, NAC confers only a small survival benefit and new strategies are needed to increase its efficacy. Pre-clinical data suggest that in response to DNA damage the tumor microenvironment (TME) adopts a paracrine secretory phenotype dependent on mTOR signaling which may provide an escape mechanism for tumor resistance, thus offering an opportunity to increase NAC effectiveness with mTOR blockade. PATIENTS & METHODS: We conducted a phase I/II clinical trial to assess the safety and efficacy of gemcitabine-cisplatin-rapamycin combination. Grapefruit juice was administered to enhance rapamycin pharmacokinetics by inhibiting intestinal enzymatic degradation. Phase I was a dose determination/safety study followed by a single arm Phase II study of NAC prior to radical cystectomy evaluating pathologic response with a 26% pCR rate target. RESULTS: In phase I, 6 patients enrolled, and the phase 2 dose of 35 mg rapamycin established. Fifteen patients enrolled in phase II; 13 were evaluable. Rapamycin was tolerated without serious adverse events. At the preplanned analysis, the complete response rate (23%) did not meet the prespecified level for continuing and the study was stopped due to futility. With immunohistochemistry, successful suppression of the mTOR signaling pathway in the tumor was achieved while limited mTOR activity was seen in the TME. CONCLUSION: Adding rapamycin to gemcitabine-cisplatin therapy for patients with MIBC was well tolerated but failed to improve therapeutic efficacy despite evidence of mTOR blockade in tumor cells. Further efforts to understand the role of the tumor microenvironment in chemotherapy resistance is needed.


Subject(s)
Cisplatin , Urinary Bladder Neoplasms , Humans , Cisplatin/therapeutic use , Gemcitabine , Sirolimus/adverse effects , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Urinary Bladder Neoplasms/pathology , Deoxycytidine , Neoadjuvant Therapy/adverse effects , Cystectomy , Muscles/pathology , TOR Serine-Threonine Kinases , Neoplasm Invasiveness , Tumor Microenvironment
7.
Eur Urol Focus ; 8(3): 657-659, 2022 05.
Article in English | MEDLINE | ID: mdl-35915037

ABSTRACT

Prediction of treatment response has attracted growing attention in cancer research to improve clinical outcomes via individualized treatment regimens. Patient-derived organoids and xenografts are novel preclinical model systems that recapitulate the genetic and phenotypic features of parental tumors for this purpose. Organoid culture has been successfully established in multiple cancers and used for assessment of drug and immunotherapy responses. Patient-derived xenograft (PDX) models provide insights into in vivo tumor growth and metastatic potential. Continued improvements in these model systems to better maintain tumor architecture and microenvironment will advance patient-specific targeted therapies. PATIENT SUMMARY: This mini review describes up-to-date organoid and xenograft models of bladder cancer created using patient-derived tissue. These models are important for research and may provide information on mutations and expression patterns for cancer-related genes that are unique to each patient, and could facilitate personalized therapy for individual patients.


Subject(s)
Organoids , Urinary Bladder Neoplasms , Animals , Disease Models, Animal , Heterografts , Humans , Immunotherapy , Rare Diseases/pathology , Tumor Microenvironment , Urinary Bladder/pathology , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology
8.
Nat Rev Urol ; 19(9): 515-533, 2022 09.
Article in English | MEDLINE | ID: mdl-35764795

ABSTRACT

Bladder cancer is a prevalent but currently understudied cancer type and patient outcomes are poor when it progresses to the muscle-invasive stage. Current research in bladder cancer focuses on the genetic and epigenetic alterations occurring within the urothelial cell compartment; however, the stromal compartment receives less attention. Dynamic changes and intercellular communications occur in the tumour microenvironment (TME) of the bladder - a new concept and niche that we designate as the bladder TME (bTME) - during tumour evolution, metastatic progression and in the context of therapeutic response. Collagens and their cognate receptors, the discoidin domain receptors, have a role in various steps of the metastatic cascade and in immune checkpoint resistance. Furthermore, the presence of another TME niche, the metastatic TME (met-TME), is a novel concept that could support divergent progression of metastatic colonization in different organs, resulting in distant metastases with distinct characteristics and genetics from the primary tumour. The stroma has divergent roles in mediating therapeutic response to BCG immunotherapy and immune checkpoint inhibitors, as well as conventional chemotherapy or trimodality therapy (that is, maximal transurethral resection of bladder tumour, chemotherapy and radiotherapy). The local bTME and distant met-TME are currently conceptually and therapeutically unexploited niches that should be actively investigated. New biological insights from these TMEs will enable rational design of strategies that co-target the tumour and stroma, which are expected to improve the outcomes of patients with advanced bladder cancer.


Subject(s)
Tumor Microenvironment , Urinary Bladder Neoplasms , Humans , Immunotherapy/methods , Urinary Bladder/pathology , Urinary Bladder Neoplasms/pathology
10.
Mol Ther ; 30(4): 1628-1644, 2022 04 06.
Article in English | MEDLINE | ID: mdl-35121110

ABSTRACT

The androgen receptor (AR) plays a pivotal role in driving prostate cancer (PCa) development. However, when stimulated by high levels of androgens, AR can also function as a tumor suppressor in PCa cells. While the high-dose testosterone (high-T) treatment is currently being tested in clinical trials of castration-resistant prostate cancer (CRPC), there is still a pressing need to fully understand the underlying mechanism and thus develop treatment strategies to exploit this tumor-suppressive activity of AR. In this study, we demonstrate that retinoblastoma (Rb) family proteins play a central role in maintaining the global chromatin binding and transcriptional repression program of AR and that Rb inactivation desensitizes CRPC to the high-dose testosterone treatment in vitro and in vivo. Using a series of patient-derived xenograft (PDX) CRPC models, we further show that the efficacy of high-T treatment can be fully exploited by a CDK4/6 inhibitor, which strengthens the chromatin binding of the Rb-E2F repressor complex by blocking the hyperphosphorylation of Rb proteins. Overall, our study provides strong mechanistic and preclinical evidence on further developing clinical trials to combine high-T with CDK4/6 inhibitors in treating CRPC.


Subject(s)
Prostatic Neoplasms, Castration-Resistant , Receptors, Androgen , Cell Line, Tumor , Chromatin , Cyclin-Dependent Kinase 4/antagonists & inhibitors , Cyclin-Dependent Kinase 4/therapeutic use , Cyclin-Dependent Kinase 6/antagonists & inhibitors , Cyclin-Dependent Kinase 6/therapeutic use , Genes, Tumor Suppressor , Humans , Male , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology , Receptors, Androgen/genetics , Receptors, Androgen/metabolism , Retinoblastoma Protein/genetics , Testosterone/therapeutic use
11.
Cancer Res ; 81(18): 4736-4750, 2021 09 15.
Article in English | MEDLINE | ID: mdl-34312180

ABSTRACT

Neuroendocrine (NE) differentiation in metastatic castration-resistant prostate cancer (mCRPC) is an increasingly common clinical feature arising from cellular plasticity. We recently characterized two mCRPC phenotypes with NE features: androgen receptor (AR)-positive NE-positive amphicrine prostate cancer (AMPC) and AR-negative small cell or neuroendocrine prostate cancer (SCNPC). Here, we interrogated the regulation of RE1-silencing transcription factor (REST), a transcriptional repressor of neuronal genes, and elucidated molecular programs driving AMPC and SCNPC biology. Analysis of prostate cancer cell lines, mCRPC specimens, and LuCaP patient-derived xenograft models detected alternative splicing of REST to REST4 and attenuated REST repressor activity in AMPC and SCNPC. The REST locus was also hypermethylated and REST expression was reduced in SCNPC. While serine/arginine repetitive matrix protein 4 (SRRM4) was previously implicated in alternative splicing of REST in mCRPC, we detected SRRM3 expression in REST4-positive, SRRM4-negative AMPC, and SCNPC. In CRPC cell lines, SRRM3 induced alternative splicing of REST to REST4 and exacerbated the expression of REST-repressed genes. Furthermore, SRRM3 and SRRM4 expression defined molecular subsets of AMPC and SCNPC across species and tumor types. Two AMPC phenotypes and three SCNPC phenotypes were characterized, denoted either by REST attenuation and ASCL1 activity or by progressive activation of neuronal transcription factor programs, respectively. These results nominate SRRM3 as the principal REST splicing factor expressed in early NE differentiation and provide a framework to molecularly classify diverse NE phenotypes in mCRPC. SIGNIFICANCE: This study identifies SRRM3 as a key inducer of cellular plasticity in prostate cancer with neuroendocrine features and delineates distinct neuroendocrine phenotypes to inform therapeutic development and precision medicine applications.


Subject(s)
Alternative Splicing , Carcinoma, Neuroendocrine/genetics , Carcinoma, Neuroendocrine/metabolism , Nerve Tissue Proteins/metabolism , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/metabolism , Proteins/metabolism , Biomarkers, Tumor , Carcinoma, Neuroendocrine/pathology , Cell Line, Tumor , Ectopic Gene Expression , Gene Expression Regulation, Neoplastic , Humans , Immunohistochemistry , Male , Nerve Tissue Proteins/genetics , Prostatic Neoplasms, Castration-Resistant/pathology , Proteins/genetics , RNA Splicing Factors/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism
12.
Sci Adv ; 7(31)2021 Jul.
Article in English | MEDLINE | ID: mdl-34321211

ABSTRACT

The role of RNA methylation on N 6-adenosine (m6A) in cancer has been acknowledged, but the underlying mechanisms remain obscure. Here, we identified homeobox containing 1 (HMBOX1) as an authentic target mRNA of m6A machinery, which is highly methylated in malignant cells compared to the normal counterparts and subject to expedited degradation upon the modification. m6A-mediated down-regulation of HMBOX1 causes telomere dysfunction and inactivation of p53 signaling, which leads to chromosome abnormalities and aggressive phenotypes. CRISPR-based, m6A-editing tools further prove that the methyl groups on HMBOX1 per se contribute to the generation of altered cancer genome. In multiple types of human cancers, expression of the RNA methyltransferase METTL3 is negatively correlated with the telomere length but favorably with fractions of altered cancer genome, whereas HMBOX1 mRNA levels show the opposite patterns. Our work suggests that the cancer-driving genomic alterations may potentially be fixed by rectifying particular epitranscriptomic program.

13.
JCI Insight ; 6(11)2021 06 08.
Article in English | MEDLINE | ID: mdl-34032633

ABSTRACT

Using genetically engineered mouse models, this work demonstrates that protein synthesis is essential for efficient urothelial cancer formation and growth but dispensable for bladder homeostasis. Through a candidate gene analysis for translation regulators implicated in this dependency, we discovered that phosphorylation of the translation initiation factor eIF4E at serine 209 is increased in both murine and human bladder cancer, and this phosphorylation corresponds with an increase in de novo protein synthesis. Employing an eIF4E serine 209 to alanine knock-in mutant mouse model, we show that this single posttranslational modification is critical for bladder cancer initiation and progression, despite having no impact on normal bladder tissue maintenance. Using murine and human models of advanced bladder cancer, we demonstrate that only tumors with high levels of eIF4E phosphorylation are therapeutically vulnerable to eFT508, the first clinical-grade inhibitor of MNK1 and MNK2, the upstream kinases of eIF4E. Our results show that phospho-eIF4E plays an important role in bladder cancer pathogenesis, and targeting its upstream kinases could be an effective therapeutic option for bladder cancer patients with high levels of eIF4E phosphorylation.


Subject(s)
Carcinoma, Transitional Cell/genetics , Cell Transformation, Neoplastic/genetics , Eukaryotic Initiation Factor-4E/metabolism , Protein Biosynthesis/genetics , RNA, Messenger/metabolism , Urinary Bladder Neoplasms/genetics , Urothelium/metabolism , Animals , Butylhydroxybutylnitrosamine/toxicity , Carcinoma, Transitional Cell/chemically induced , Carcinoma, Transitional Cell/metabolism , Cell Transformation, Neoplastic/metabolism , Drug Screening Assays, Antitumor , Gene Knock-In Techniques , Homeostasis , Humans , Mice , Neoplasm Transplantation , Protein Kinase Inhibitors/pharmacology , Pyridines/pharmacology , Pyrimidines/pharmacology , Ribosomal Proteins/genetics , Urinary Bladder Neoplasms/chemically induced , Urinary Bladder Neoplasms/metabolism
14.
Sci Rep ; 11(1): 4609, 2021 02 25.
Article in English | MEDLINE | ID: mdl-33633154

ABSTRACT

Bladder cancer is among the most prevalent cancers worldwide. Currently, few bladder cancer models have undergone thorough characterization to assess their fidelity to patient tumors, especially upon propagation in the laboratory. Here, we establish and molecularly characterize CoCaB 1, an aggressive cisplatin-resistant muscle-invasive bladder cancer patient-derived xenograft (PDX) and companion organoid system. CoCaB 1 was a subcutaneous PDX model reliably transplanted in vivo and demonstrated an acceleration in growth upon serial transplantation, which was reflected in organoid and 2D cell culture systems. Transcriptome analysis revealed progression towards an increasingly proliferative and stem-like expression profile. Gene expression differences between organoid and PDX models reflected expected differences in cellular composition, with organoids enriched in lipid biosynthesis and metabolism genes and deprived of extracellular components observed in PDXs. Both PDX and organoid models maintained the histological fidelity and mutational heterogeneity of their parental tumor. This study establishes the CoCaB 1 PDX and organoid system as companion representative tumor models for the development of novel bladder cancer therapies.


Subject(s)
Organoids/metabolism , Urinary Bladder Neoplasms/pathology , Animals , Antineoplastic Agents/therapeutic use , Cisplatin/therapeutic use , Deoxycytidine/analogs & derivatives , Deoxycytidine/therapeutic use , Drug Resistance, Neoplasm , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Heterografts , Humans , Male , Mice, SCID , Neoplasm Invasiveness , Neoplasm Transplantation , Gemcitabine
16.
Eur Urol ; 77(2): 144-155, 2020 02.
Article in English | MEDLINE | ID: mdl-31227306

ABSTRACT

BACKGROUND: Androgen deprivation therapy improves the survival of castration-resistant prostate cancer (CRPC) patients, yet ultimately fails with debilitating side effects. Supraphysiological testosterone (SPT)-based therapy produces clinical responses with improved quality of life in a subset of patients. Currently, no information defines a durable response to SPT. OBJECTIVE: To identify key molecular phenotypes underlying SPT response to improve patient selection and guide combination treatment to achieve a durable response. DESIGN, SETTING, AND PARTICIPANTS: A patient-derived xenograft (PDX) preclinical trial was performed with 13 CRPC PDXs to identify molecular features associated with SPT response. Comprehensive intratumoral androgen, tumor growth, and integrated transcriptomic and protein analyses were performed in three PDXs resistant to the newer androgen receptor (AR) pathway inhibitor enzalutamide (ENZ) to define SPT response and resistance. INTERVENTION: Testosterone cypionate. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: SPT efficacy was evaluated by PDX growth, prostate-specific antigen (PSA) change, and survival. Intratumoral androgens were analyzed using mass spectrometry. Global transcriptome analysis was performed using RNA sequencing, and confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry. Log-rank and Mann-Whitney tests were used for survival and molecular analyses, respectively. RESULTS AND LIMITATIONS: A durable SPT responder was identified, presenting robust repressions of ARv7 and E2F transcriptional outputs, and a DNA damage response (DDR) transcriptomic program that were altogether restored upon SPT resistance in the transient responder. ENZ rechallenge of SPT-relapsed PDXs resulted in PSA decreases but tumor progression. CONCLUSIONS: SPT produces a durable response in AR-pathway inhibitor ENZ CRPC that is associated with sustained suppression of ARv7 and E2F transcriptional outputs, and the DDR transcriptome, highlighting the potential of combination treatments that maintain suppression of these programs to drive a durable response to SPT. PATIENT SUMMARY: Patients with ENZ-resistant prostate cancer have very limited treatment options. Supraphysiological testosterone presents a prominent option for improved quality of life and a potential durable response in patients with sustained suppression on ARv7/E2F transcriptional outputs and DNA repair program.


Subject(s)
Prostatic Neoplasms, Castration-Resistant/drug therapy , Testosterone/administration & dosage , Animals , Benzamides , DNA Repair , Drug Resistance, Neoplasm , Humans , Male , Mice , Mice, Inbred C57BL , Nitriles , Phenylthiohydantoin/analogs & derivatives , Phenylthiohydantoin/therapeutic use , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology , Time Factors , Transcriptome , Treatment Failure , Xenograft Model Antitumor Assays
17.
J Clin Invest ; 129(10): 4245-4260, 2019 07 16.
Article in English | MEDLINE | ID: mdl-31310591

ABSTRACT

Prostate cancer (PC) is initially dependent on androgen receptor (AR) signaling for survival and growth. Therapeutics designed to suppress AR activity serve as the primary intervention for advanced disease. However, supraphysiological androgen (SPA) concentrations can produce paradoxical responses leading to PC growth inhibition. We sought to discern the mechanisms by which SPA inhibits PC and to determine if molecular context associates with anti-tumor activity. SPA produced an AR-mediated, dose-dependent induction of DNA double-strand breaks (DSBs), G0/G1 cell cycle arrest and cellular senescence. SPA repressed genes involved in DNA repair and delayed the restoration of damaged DNA which was augmented by PARP1 inhibition. SPA-induced DSBs were accentuated in BRCA2-deficient PCs, and combining SPA with PARP or DNA-PKcs inhibition further repressed growth. Next-generation sequencing was performed on biospecimens from PC patients receiving SPA as part of ongoing Phase II clinical trials. Patients with mutations in genes mediating homology-directed DNA repair were more likely to exhibit clinical responses to SPA. These results provide a mechanistic rationale for directing SPA therapy to PCs with AR amplification or DNA repair deficiency, and for combining SPA therapy with PARP inhibition.


Subject(s)
Androgens/pharmacology , DNA Damage , G1 Phase Cell Cycle Checkpoints/drug effects , Prostatic Neoplasms/drug therapy , Receptors, Androgen/metabolism , Resting Phase, Cell Cycle/drug effects , BRCA2 Protein/deficiency , BRCA2 Protein/metabolism , Cellular Senescence/drug effects , Cellular Senescence/genetics , G1 Phase Cell Cycle Checkpoints/genetics , Gene Amplification , Humans , Male , PC-3 Cells , Poly(ADP-ribose) Polymerases/genetics , Poly(ADP-ribose) Polymerases/metabolism , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/pathology , Receptors, Androgen/genetics , Resting Phase, Cell Cycle/genetics
18.
JCI Insight ; 52019 05 30.
Article in English | MEDLINE | ID: mdl-31145100

ABSTRACT

BACKGROUND: Little is known about the genomic differences between metastatic urothelial carcinoma (LTUC) and upper tract urothelial carcinoma (UTUC). We compare genomic features of primary and metastatic UTUC and LTUC tumors in a cohort of patients with end stage disease. METHODS: We performed whole exome sequencing on matched primary and metastatic tumor samples (N=37) from 7 patients with metastatic UC collected via rapid autopsy. Inter- and intra-patient mutational burden, mutational signatures, predicted deleterious mutations, and somatic copy alterations (sCNV) were analyzed. RESULTS: We investigated 3 patients with UTUC (3 primary samples, 13 metastases) and 4 patients with LTUC (4 primary samples, 17 metastases). We found that sSNV burden was higher in metastatic LTUC compared to UTUC. Moreover, the APOBEC mutational signature was pervasive in metastatic LTUC and less so in UTUC. Despite a lower overall sSNV burden, UTUC displayed greater inter- and intra-individual genomic distances at the copy number level between primary and metastatic tumors than LTUC. Our data also indicate that metastatic UTUC lesions can arise from small clonal populations present in the primary cancer. Importantly, putative druggable mutations were found across patients with the majority shared across all metastases within a patient. CONCLUSIONS: Metastatic UTUC demonstrated a lower overall mutational burden but greater structural variability compared to LTUC. Our findings suggest that metastatic UTUC displays a greater spectrum of copy number divergence from LTUC. Importantly, we identified druggable lesions shared across metastatic samples, which demonstrate a level of targetable homogeneity within individual patients.


Subject(s)
Carcinoma, Transitional Cell/genetics , Genomics , Urologic Neoplasms/genetics , Aged , Autopsy , Female , Humans , Male , Middle Aged , Mutation , Sequence Analysis , Exome Sequencing
19.
Clin Cancer Res ; 25(16): 5082-5093, 2019 08 15.
Article in English | MEDLINE | ID: mdl-30224344

ABSTRACT

PURPOSE: After cisplatin-based neoadjuvant chemotherapy (NAC), 60% of patients with muscle-invasive bladder cancer (MIBC) still have residual invasive disease at radical cystectomy. The NAC-induced biological alterations in these cisplatin-resistant tumors remain largely unstudied. EXPERIMENTAL DESIGN: Radical cystectomy samples were available for gene expression analysis from 133 patients with residual invasive disease after cisplatin-based NAC, of whom 116 had matched pre-NAC samples. Unsupervised consensus clustering (CC) was performed and the consensus clusters were investigated for their biological and clinical characteristics. Hematoxylin & Eosin and IHC on tissue microarrays were used to confirm tissue sampling and gene expression analysis. RESULTS: Established molecular subtyping models proved to be inconsistent in their classification of the post-NAC samples. Unsupervised CC revealed four distinct consensus clusters. The CC1-Basal and CC2-Luminal subtypes expressed genes consistent with a basal and a luminal phenotype, respectively, and were similar to the corresponding established pretreatment molecular subtypes. The CC3-Immune subtype had the highest immune activity, including T-cell infiltration and checkpoint molecule expression, but lacked both basal and luminal markers. The CC4-Scar-like subtype expressed genes associated with wound healing/scarring, although the proportion of tumor cell content in this subtype did not differ from the other subtypes. Patients with CC4-Scar-like tumors had the most favorable prognosis. CONCLUSIONS: This study expands our knowledge on MIBC not responding to cisplatin by suggesting molecular subtypes to understand the biology of these tumors. Although these molecular subtypes imply consequences for adjuvant treatments, this ultimately needs to be tested in clinical trials.


Subject(s)
Biomarkers, Tumor/genetics , Cisplatin/adverse effects , Neoadjuvant Therapy/adverse effects , Urinary Bladder Neoplasms/drug therapy , Aged , Cisplatin/administration & dosage , Cystectomy , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Male , Middle Aged , Neoplasm Proteins/genetics , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology , Urinary Bladder Neoplasms/surgery
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