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1.
bioRxiv ; 2024 May 07.
Article in English | MEDLINE | ID: mdl-38766099

ABSTRACT

Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.

2.
J Surg Oncol ; 128(6): 931-937, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37818915

ABSTRACT

Gaps in the cancer care continuum are vast, both in the United States and globally. The American Cancer Society orchestrates an integrated, tripartite approach toward improving the lives of cancer patients and their families through research, advocacy, and patient support. With a focus on eradicating cancer disparities, the American Cancer Society aims to scale and deploy best practices worldwide through partnerships, to ensure everyone has an opportunity to prevent, detect, treat, and survive cancer.


Subject(s)
Neoplasms , Humans , United States , American Cancer Society , Neoplasms/prevention & control , Neoplasms/diagnosis
3.
Cancer Discov ; 13(12): 2584-2609, 2023 12 12.
Article in English | MEDLINE | ID: mdl-37676710

ABSTRACT

Signaling rewiring allows tumors to survive therapy. Here we show that the decrease of the master regulator microphthalmia transcription factor (MITF) in lethal prostate cancer unleashes eukaryotic initiation factor 3B (eIF3B)-dependent translation reprogramming of key mRNAs conferring resistance to androgen deprivation therapy (ADT) and promoting immune evasion. Mechanistically, MITF represses through direct promoter binding eIF3B, which in turn regulates the translation of specific mRNAs. Genome-wide eIF3B enhanced cross-linking immunoprecipitation sequencing (eCLIP-seq) showed specialized binding to a UC-rich motif present in subsets of 5' untranslated regions. Indeed, translation of the androgen receptor and major histocompatibility complex I (MHC-I) through this motif is sensitive to eIF3B amount. Notably, pharmacologic targeting of eIF3B-dependent translation in preclinical models sensitizes prostate cancer to ADT and anti-PD-1 therapy. These findings uncover a hidden connection between transcriptional and translational rewiring promoting therapy-refractory lethal prostate cancer and provide a druggable mechanism that may transcend into effective combined therapeutic strategies. SIGNIFICANCE: Our study shows that specialized eIF3B-dependent translation of specific mRNAs released upon downregulation of the master transcription factor MITF confers castration resistance and immune evasion in lethal prostate cancer. Pharmacologic targeting of this mechanism delays castration resistance and increases immune-checkpoint efficacy. This article is featured in Selected Articles from This Issue, p. 2489.


Subject(s)
Prostatic Neoplasms, Castration-Resistant , Prostatic Neoplasms , Male , Humans , Transcription Factors , Androgen Antagonists/pharmacology , Androgen Antagonists/therapeutic use , Immune Evasion , Receptors, Androgen/genetics , Castration , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology
4.
bioRxiv ; 2023 Mar 23.
Article in English | MEDLINE | ID: mdl-36993449

ABSTRACT

Prostate cancer (PCa) is the second leading cause of cancer death for men in the United States. While organ-confined disease has reasonable expectation of cure, metastatic PCa is universally fatal upon recurrence during hormone therapy, a stage termed castration-resistant prostate cancer (CRPC). Until such time as molecularly defined subtypes can be identified and targeted using precision medicine, it is necessary to investigate new therapies that may apply to the CRPC population as a whole. The administration of ascorbate, more commonly known as ascorbic acid or Vitamin C, has proved lethal to and highly selective for a variety of cancer cell types. There are several mechanisms currently under investigation to explain how ascorbate exerts anti-cancer effects. A simplified model depicts ascorbate as a pro-drug for reactive oxygen species (ROS), which accumulate intracellularly and generate DNA damage. It was therefore hypothesized that poly(ADP-ribose) polymerase (PARP) inhibitors, by inhibiting DNA damage repair, would augment the toxicity of ascorbate. Results: Two distinct CRPC models were found to be sensitive to physiologically relevant doses of ascorbate. Moreover, additional studies indicate that ascorbate inhibits CRPC growth in vitro via multiple mechanisms including disruption of cellular energy dynamics and accumulation of DNA damage. Combination studies were performed in CRPC models with ascorbate in conjunction with escalating doses of three different PARP inhibitors (niraparib, olaparib, and talazoparib). The addition of ascorbate augmented the toxicity of all three PARP inhibitors and proved synergistic with olaparib in both CRPC models. Finally, the combination of olaparib and ascorbate was tested in vivo in both castrated and non-castrated models. In both cohorts, the combination treatment significantly delayed tumor growth compared to monotherapy or untreated control. Conclusions: These data indicate that pharmacological ascorbate is an effective monotherapy at physiological concentrations and kills CRPC cells. Ascorbate-induced tumor cell death was associated with disruption of cellular energy dynamics and accumulation of DNA damage. The addition of PARP inhibition increased the extent of DNA damage and proved effective at slowing CRPC growth both in vitro and in vivo. These findings nominate ascorbate and PARPi as a novel therapeutic regimen that has the potential to improve CRPC patient outcomes.

5.
Eur Urol ; 84(1): 117-126, 2023 07.
Article in English | MEDLINE | ID: mdl-36566154

ABSTRACT

BACKGROUND: Previous studies have reported on incidence and mortality patterns for individual genitourinary cancers in the USA. However, these studies addressed individual cancer types rather than genitourinary cancers overall. OBJECTIVE: To comprehensively examine disparities and trends in the incidence and mortality for the four major genitourinary cancers (bladder, kidney, prostate, and testis) in the USA. DESIGN, SETTING, AND PARTICIPANTS: We obtained incidence data from the National Cancer Institute 22-registry Surveillance, Epidemiology and End Results (SEER) database and the US Cancer Statistics database (Centers for Disease Control and Prevention) and mortality data from the National Center for Health Statistics to examine cross-sectional and temporal trends in incidence and death rates stratified by sex, race/ethnicity, and county. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Age-adjusted incidence and death rates were calculated using SEER*Stat software. Temporal trends were analyzed using Joinpoint regression for a two-sided significance level of p < 0.05. RESULTS AND LIMITATIONS: Incidence and mortality rates for bladder and kidney cancers were two to four times higher for men than for women. Among non-Hispanic White individuals, the highest incidence rates were found in the Northeast for bladder cancer and in Appalachia for kidney cancer, whereas the highest death rates for prostate cancer were found in the West. Incidence rates increased for cancers of the kidney and testis and for advanced-stage prostate cancer in almost all racial/ethnic populations and for bladder cancer in the American Indian/Alaska Native population. Death rates increased for testicular cancer in the Hispanic population and stabilized for prostate cancer among White and Asian American/Pacific Islander men after a steady decline since the early 1990s. Study limitations include misclassification of race/ethnicity on medical records and death certificates. CONCLUSIONS: We found persistent sociodemographic disparities and unfavorable trends in incidence or mortality for all four major genitourinary cancers. Future studies should elucidate the reasons for these patterns. PATIENT SUMMARY: In the USA, rates of cancer cases are increasing for kidney, testis, and advanced-stage prostate cancers in the overall population, and for bladder cancer in the American Indian/Alaska Native population. Differences in the rates by sex and race/ethnicity remain.


Subject(s)
Kidney Neoplasms , Prostatic Neoplasms , Testicular Neoplasms , Urinary Bladder Neoplasms , Male , Humans , United States/epidemiology , Testicular Neoplasms/epidemiology , Incidence , Cross-Sectional Studies , Kidney Neoplasms/epidemiology , SEER Program
6.
Front Oncol ; 13: 1251297, 2023.
Article in English | MEDLINE | ID: mdl-38188290

ABSTRACT

Introduction: We previously reported that cholesterol homeostasis in prostate cancer (PC) is regulated by 27-hydroxycholesterol (27HC) and that CYP27A1, the enzyme that converts cholesterol to 27HC, is frequently lost in PCs. We observed that restoring the CYP27A1/27HC axis inhibited PC growth. In this study, we investigated the mechanism of 27HC-mediated anti-PC effects. Methods: We employed in vitro models and human transcriptomics data to investigate 27HC mechanism of action in PC. LNCaP (AR+) and DU145 (AR-) cells were treated with 27HC or vehicle. Transcriptome profiling was performed using the Affymetrix GeneChip™ microarray system. Differential expression was determined, and gene set enrichment analysis was done using the GSEA software with hallmark gene sets from MSigDB. Key changes were validated at mRNA and protein levels. Human PC transcriptomes from six datasets were analyzed to determine the correlation between CYP27A1 and DNA repair gene expression signatures. DNA damage was assessed via comet assays. Results: Transcriptome analysis revealed 27HC treatment downregulated Hallmark pathways related to DNA damage repair, decreased expression of FEN1 and RAD51, and induced "BRCAness" by downregulating genes involved in homologous recombination regulation in LNCaP cells. Consistently, we found a correlation between higher CYP27A1 expression (i.e., higher intracellular 27HC) and decreased expression of DNA repair gene signatures in castration-sensitive PC (CSPC) in human PC datasets. However, such correlation was less clear in metastatic castration-resistant PC (mCRPC). 27HC increased expression of DNA damage repair markers in PC cells, notably in AR+ cells, but no consistent effects in AR- cells and decreased expression in non-neoplastic prostate epithelial cells. While testing the clinical implications of this, we noted that 27HC treatment increased DNA damage in LNCaP cells via comet assays. Effects were reversible by adding back cholesterol, but not androgens. Finally, in combination with olaparib, a PARP inhibitor, we showed additive DNA damage effects. Discussion: These results suggest 27HC induces "BRCAness", a functional state thought to increase sensitivity to PARP inhibitors, and leads to increased DNA damage, especially in CSPC. Given the emerging appreciation that defective DNA damage repair can drive PC growth, future studies are needed to test whether 27HC creates a synthetic lethality to PARP inhibitors and DNA damaging agents in CSPC.

7.
Cancer ; 128 Suppl 13: 2673-2677, 2022 07 01.
Article in English | MEDLINE | ID: mdl-35699608

ABSTRACT

Over the past 30 years, the American Cancer Society (ACS) has played a key role in shaping the field of patient navigation as a means to address cancer disparities. Through collaborations with organizations like the National Navigation Roundtable and the ACS Cancer Action Network, the ACS is uniquely positioned to help develop sustainable navigation models that directly address disparities in access to quality cancer care. As health systems continue to adapt and change in response to various factors, including an aging population and rapid advances in screening and treatment, it is important to evaluate existing navigation-delivery models and promote those that are sustainable while maximizing reach and impact and providing the greatest return on investment (ROI). In this report, the term ROI is used to describe the potential financial gain resulting from the navigation service (ROI = net gains/total program cost). Calculating net gains requires assigning a monetary value to key outcomes and subtracting this amount from the total program cost. ROI is a measure often used by health care executives to show the savings or financial benefit from a program or service. Other measures of financial impact exist that may be of greater or lesser value to program leadership, including cost effectiveness (if financial information for outcomes is not available) and cost-benefit analysis. Here, the current and future commitment of the ACS to advancing the field of patient navigation is outlined as an organizational priority and a key building block in their health equity strategy. By working with partners like the National Navigation Roundtable, the ACS can help guide efforts to evaluate these approaches, with the goal of identifying the most effective and potentially sustainable models of delivery while also increasing equitable access to care.


Subject(s)
Neoplasms , Patient Navigation , Aged , American Cancer Society , Cost-Benefit Analysis , Delivery of Health Care , Humans , Neoplasms/therapy
8.
Cancer J ; 28(2): 107-110, 2022.
Article in English | MEDLINE | ID: mdl-35333494

ABSTRACT

PURPOSE: A multidisciplinary panel of experts convened to review the early effects of the COVID-19 pandemic on cancer care in the United States as part of a symposium convened by the National Cancer Policy Forum in July 2021. METHODS: Representatives from the cancer care community, patients, infection prevention, and a government agency provided insight into key elements of the response to and impact of the COVID-19 pandemic on cancer care in the United States in 2020. RESULTS: Multiple stakeholders worked quickly to adapt to provide seamless care to cancer patients with considerable success despite the profound uncertainties that faced us in the early days of the pandemic. DISCUSSION: The experiences of the early days of COVID-19 in the cancer community led to key recommendations toward the goal of preparing for the next major disruption to cancer care. These include increasing competency in emergent technologies, rapid communication, engagement of all key stakeholders in policy decisions, ensuring emergency preparedness, and advocating for permanent regulatory changes to minimize barriers to enable a unified cancer community to provide effective and readily accessible cancer care.


Subject(s)
COVID-19 , Influenza, Human , Neoplasms , COVID-19/prevention & control , Humans , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Neoplasms/therapy , Pandemics/prevention & control , United States/epidemiology
9.
Cancer Epidemiol Biomarkers Prev ; 31(5): 955-964, 2022 05 04.
Article in English | MEDLINE | ID: mdl-35064067

ABSTRACT

BACKGROUND: Cancer centers are expected to engage communities and reduce the burden of cancer in their catchment areas. However, the extent to which cancer centers adequately reach the entire US population is unknown. METHODS: We surveyed all members of the Association of American Cancer Institutes (N = 102 cancer centers) to document and map each cancer center's primary catchment area. Catchment area descriptions were aggregated to the county level. Catchment area coverage scores were calculated for each county and choropleths generated representing coverage across the US. Similar analyses were used to overlay US population density, cancer incidence, and cancer-related mortality compared with each county's cancer center catchment area coverage. RESULTS: Roughly 85% of US counties were included in at least one cancer center's primary catchment area. However, 15% of US counties, or roughly 25 million Americans, do not reside in a catchment area. When catchment area coverage was integrated with population density, cancer incidence, and cancer-related mortality metrics, geographical trends in both over- and undercoverage were apparent. CONCLUSIONS: Geographic gaps in cancer center catchment area coverage exist and may be propagating cancer disparities. Efforts to ensure coverage to all Americans should be a priority of cancer center leadership. IMPACT: This is the first known geographic analysis and interpretation of the primary catchment areas of all US-based cancer centers and identifies key geographic gaps important to target for disparities reduction. See related commentary by Lieberman-Cribbin and Taioli, p. 949.


Subject(s)
Neoplasms , Public Health , Catchment Area, Health , Humans , Neoplasms/epidemiology , Neoplasms/prevention & control , Research Design , Surveys and Questionnaires , United States/epidemiology
10.
Clin Cancer Res ; 28(7): 1446-1459, 2022 04 01.
Article in English | MEDLINE | ID: mdl-35078861

ABSTRACT

PURPOSE: DNA-dependent protein kinase catalytic subunit (DNA-PKcs, herein referred as DNA-PK) is a multifunctional kinase of high cancer relevance. DNA-PK is deregulated in multiple tumor types, including prostate cancer, and is associated with poor outcomes. DNA-PK was previously nominated as a therapeutic target and DNA-PK inhibitors are currently undergoing clinical investigation. Although DNA-PK is well studied in DNA repair and transcriptional regulation, much remains to be understood about the way by which DNA-PK drives aggressive disease phenotypes. EXPERIMENTAL DESIGN: Here, unbiased proteomic and metabolomic approaches in clinically relevant tumor models uncovered a novel role of DNA-PK in metabolic regulation of cancer progression. DNA-PK regulation of metabolism was interrogated using pharmacologic and genetic perturbation using in vitro cell models, in vivo xenografts, and ex vivo in patient-derived explants (PDE). RESULTS: Key findings reveal: (i) the first-in-field DNA-PK protein interactome; (ii) numerous DNA-PK novel partners involved in glycolysis; (iii) DNA-PK interacts with, phosphorylates (in vitro), and increases the enzymatic activity of glycolytic enzymes ALDOA and PKM2; (iv) DNA-PK drives synthesis of glucose-derived pyruvate and lactate; (v) DNA-PK regulates glycolysis in vitro, in vivo, and ex vivo; and (vi) combination of DNA-PK inhibitor with glycolytic inhibitor 2-deoxyglucose leads to additive anti-proliferative effects in aggressive disease. CONCLUSIONS: Findings herein unveil novel DNA-PK partners, substrates, and function in prostate cancer. DNA-PK impacts glycolysis through direct interaction with glycolytic enzymes and modulation of enzymatic activity. These events support energy production that may contribute to generation and/or maintenance of DNA-PK-mediated aggressive disease phenotypes.


Subject(s)
DNA-Activated Protein Kinase , Prostatic Neoplasms, Castration-Resistant , DNA , DNA-Activated Protein Kinase/genetics , DNA-Activated Protein Kinase/metabolism , Glycolysis , Humans , Male , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Proteomics , Pyruvate Kinase/metabolism
11.
Cancer Res ; 82(2): 221-234, 2022 01 15.
Article in English | MEDLINE | ID: mdl-34625422

ABSTRACT

The retinoblastoma tumor suppressor (RB) is a critical regulator of E2F-dependent transcription, controlling a multitude of protumorigenic networks including but not limited to cell-cycle control. Here, genome-wide assessment of E2F1 function after RB loss in isogenic models of prostate cancer revealed unexpected repositioning and cooperation with oncogenic transcription factors, including the major driver of disease progression, the androgen receptor (AR). Further investigation revealed that observed AR/E2F1 cooperation elicited novel transcriptional networks that promote cancer phenotypes, especially as related to evasion of cell death. These observations were reflected in assessment of human disease, indicating the clinical relevance of the AR/E2F1 cooperome in prostate cancer. Together, these studies reveal new mechanisms by which RB loss induces cancer progression and highlight the importance of understanding the targets of E2F1 function. SIGNIFICANCE: This study identifies that RB loss in prostate cancer drives cooperation between AR and E2F1 as coregulators of transcription, which is linked to the progression of advanced disease.


Subject(s)
Carcinogenesis/genetics , E2F1 Transcription Factor/metabolism , Oncogene Proteins/metabolism , Prostatic Neoplasms/metabolism , Receptors, Androgen/metabolism , Retinoblastoma Binding Proteins/metabolism , Signal Transduction/genetics , Ubiquitin-Protein Ligases/metabolism , Apoptosis/genetics , Binding Sites , Cell Line, Tumor , Cell Survival/genetics , Cohort Studies , E2F1 Transcription Factor/genetics , Gene Expression Regulation, Neoplastic , Gene Knockdown Techniques , Humans , Male , Oncogene Proteins/genetics , Oncogenes , Prostatic Neoplasms/pathology , Protein Binding/genetics , Retinoblastoma Binding Proteins/genetics , Transfection , Ubiquitin-Protein Ligases/genetics
12.
Clin Cancer Res ; 28(2): 255-264, 2022 01 15.
Article in English | MEDLINE | ID: mdl-34407969

ABSTRACT

The retinoblastoma tumor suppressor protein (pRB) is a known regulator of cell-cycle control; however, recent studies identified critical functions for pRB in regulating cancer-associated gene networks that influence the DNA damage response, apoptosis, and cell metabolism. Understanding the impact of these pRB functions on cancer development and progression in the clinical setting will be essential, given the prevalence of pRB loss of function across disease types. Moreover, the current state of evidence supports the concept that pRB loss results in pleiotropic effects distinct from tumor proliferation. Here, the implications of pRB loss (and resultant pathway deregulation) on disease progression and therapeutic response will be reviewed, based on clinical observation. Developing a better understanding of the pRB-regulated pathways that underpin the aggressive features of pRB-deficient tumors will be essential for further developing pRB as a biomarker of disease progression and for stratifying pRB-deficient tumors into more effective treatment regimens.


Subject(s)
Retinal Neoplasms , Retinoblastoma , Apoptosis/genetics , Humans , Retinoblastoma/genetics , Retinoblastoma/therapy , Retinoblastoma Protein/genetics , Retinoblastoma Protein/metabolism
13.
Oncogene ; 41(3): 444-458, 2022 01.
Article in English | MEDLINE | ID: mdl-34773073

ABSTRACT

The tumor suppressor gene TP53 is the most frequently mutated gene in numerous cancer types, including prostate cancer (PCa). Specifically, missense mutations in TP53 are selectively enriched in PCa, and cluster to particular "hot spots" in the p53 DNA binding domain with mutation at the R273 residue occurring most frequently. While this residue is similarly mutated to R273C-p53 or R273H-p53 in all cancer types examined, in PCa selective enrichment of R273C-p53 is observed. Importantly, examination of clinical datasets indicated that TP53 heterozygosity can either be maintained or loss of heterozygosity (LOH) occurs. Thus, to mimic tumor-associated mutant p53, R273C-p53 and R273H-p53 isogenic PCa models were developed in the presence or absence of wild-type p53. In the absence of wild-type p53, both R273C-p53 and R273H-p53 exhibited similar loss of DNA binding, transcriptional profiles, and loss of canonical tumor suppressor functions associated with wild-type p53. In the presence of wild-type p53 expression, both R273C-p53 and R273H-p53 supported canonical p53 target gene expression yet elicited distinct cistromic and transcriptional profiles when compared to each other. Moreover, heterozygous modeling of R273C-p53 or R273H-p53 expression resulted in distinct phenotypic outcomes in vitro and in vivo. Thus, mutant p53 acts in a context-dependent manner to elicit pro-tumorigenic transcriptional profiles, providing critical insight into mutant p53-mediated prostate cancer progression.


Subject(s)
Carcinogenesis/genetics , Prostatic Neoplasms/genetics , Tumor Suppressor Protein p53/metabolism , Humans , Male , Phenotype
14.
Cancer Res ; 82(4): 523-533, 2022 02 15.
Article in English | MEDLINE | ID: mdl-34893509

ABSTRACT

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a pleiotropic protein kinase that plays critical roles in cellular processes fundamental to cancer. DNA-PKcs expression and activity are frequently deregulated in multiple hematologic and solid tumors and have been tightly linked to poor outcome. Given the potentially influential role of DNA-PKcs in cancer development and progression, therapeutic targeting of this kinase is being tested in preclinical and clinical settings. This review summarizes the latest advances in the field, providing a comprehensive discussion of DNA-PKcs functions in cancer and an update on the clinical assessment of DNA-PK inhibitors in cancer therapy.


Subject(s)
DNA-Activated Protein Kinase/genetics , Energy Metabolism/genetics , Gene Expression Regulation, Neoplastic , Immunity/genetics , Neoplasms/genetics , Protein Biosynthesis/genetics , Animals , Clinical Trials as Topic , DNA-Activated Protein Kinase/antagonists & inhibitors , DNA-Activated Protein Kinase/metabolism , Humans , Neoplasms/drug therapy , Neoplasms/enzymology , Protein Kinase Inhibitors/therapeutic use , Substrate Specificity , Tumor Microenvironment/drug effects , Tumor Microenvironment/genetics
15.
Cancer Commun (Lond) ; 41(12): 1387-1397, 2021 12.
Article in English | MEDLINE | ID: mdl-34520132

ABSTRACT

BACKGROUND: DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer (PCa). However, it has not yet been possible to incorporate information of DNA methylation and gene expression into polygenic risk scores (PRSs). Here, we aimed to develop and validate an improved PRS for PCa risk by incorporating genetically predicted gene expression and DNA methylation, and other genomic information using an integrative method. METHODS: Using data from the PRACTICAL consortium, we derived multiple sets of genetic scores, including those based on available single-nucleotide polymorphisms through widely used methods of pruning and thresholding, LDpred, LDpred-funt, AnnoPred, and EBPRS, as well as PRS constructed using the genetically predicted gene expression and DNA methylation through a revised pruning and thresholding strategy. In the tuning step, using the UK Biobank data (1458 prevalent cases and 1467 controls), we selected PRSs with the best performance. Using an independent set of data from the UK Biobank, we developed an integrative PRS combining information from individual scores. Furthermore, in the testing step, we tested the performance of the integrative PRS in another independent set of UK Biobank data of incident cases and controls. RESULTS: Our constructed PRS had improved performance (C statistics: 76.1%) over PRSs constructed by individual benchmark methods (from 69.6% to 74.7%). Furthermore, our new PRS had much higher risk assessment power than family history. The overall net reclassification improvement was 69.0% by adding PRS to the baseline model compared with 12.5% by adding family history. CONCLUSIONS: We developed and validated a new PRS which may improve the utility in predicting the risk of developing PCa. Our innovative method can also be applied to other human diseases to improve risk prediction across multiple outcomes.


Subject(s)
DNA Methylation , Prostatic Neoplasms , DNA Methylation/genetics , Gene Expression , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Multifactorial Inheritance , Prostatic Neoplasms/genetics , Risk Factors
16.
Urol Clin North Am ; 48(3): 339-347, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34210489

ABSTRACT

Androgen receptor function, tumor cell plasticity, loss of tumor suppressors, and defects in DNA repair genes affect aggressive features of prostate cancer. Prostate cancer development, progression, and aggressive behavior are often attributable to function of the androgen receptor. Tumor cell plasticity, neuroendocrine features, and loss of tumor suppressors lend aggressive behavior to prostate cancer cells. DNA repair defects have ramifications for prostate cancer cell behavior.


Subject(s)
Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , Receptors, Androgen/genetics , Androgen Antagonists/therapeutic use , Biomarkers, Tumor/genetics , Cell Plasticity , DNA Repair , Disease Progression , Gene Expression Regulation, Neoplastic , Genetic Testing , Germ-Line Mutation , Humans , Male , Precision Medicine , Prostate-Specific Antigen/blood , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology
17.
EMBO J ; 40(16): e102509, 2021 08 16.
Article in English | MEDLINE | ID: mdl-34155658

ABSTRACT

The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.


Subject(s)
Ubiquitin Thiolesterase/genetics , Apoptosis , Endoplasmic Reticulum Stress/genetics , HCT116 Cells , Humans , Mediator Complex/genetics , Promoter Regions, Genetic , RNA Polymerase II , Transcription, Genetic
18.
J Pers Med ; 11(5)2021 Apr 22.
Article in English | MEDLINE | ID: mdl-33922147

ABSTRACT

Guidelines for genetic testing have been established for multiple tumor types, frequently indicating the most confident molecularly targeted treatment options. However, considering the often-complex presentation of individual cancer patients, in addition to the combinatorial complexity and inherent uncertainties of molecular findings, deriving optimal treatment strategies frequently becomes very challenging. Here, we report a comprehensive analysis of a 68-year-old male with metastatic prostate cancer, encompassing pathology and MRI findings, transcriptomic results, and key genomics findings from whole-exome sequencing, both somatic aberrations and germline variants. We identify multiple somatic aberrations that are known to be enriched in prostate cancer, including a deletion of PTEN and a fusion transcript involving BRCA2. The gene expression patterns in the tumor biopsy were also strikingly similar to prostate tumor samples from TCGA. Furthermore, we detected multiple lines of evidence for homologous recombination repair deficiency (HRD), including a dominant contribution by mutational signature SBS3, which is specifically attributed to HRD. On the basis of the genomic and transcriptomic findings, and in light of the clinical case presentation, we discussed the personalized treatment options that exist for this patient and the various challenges that one faces in the process of translating high-throughput sequencing data towards treatment regimens.

19.
Cancer Discov ; 11(9): 2334-2353, 2021 09.
Article in English | MEDLINE | ID: mdl-33879449

ABSTRACT

Loss of the retinoblastoma (RB) tumor suppressor protein is a critical step in reprogramming biological networks that drive cancer progression, although mechanistic insight has been largely limited to the impact of RB loss on cell-cycle regulation. Here, isogenic modeling of RB loss identified disease stage-specific rewiring of E2F1 function, providing the first-in-field mapping of the E2F1 cistrome and transcriptome after RB loss across disease progression. Biochemical and functional assessment using both in vitro and in vivo models identified an unexpected, prominent role for E2F1 in regulation of redox metabolism after RB loss, driving an increase in the synthesis of the antioxidant glutathione, specific to advanced disease. These E2F1-dependent events resulted in protection from reactive oxygen species in response to therapeutic intervention. On balance, these findings reveal novel pathways through which RB loss promotes cancer progression and highlight potentially new nodes of intervention for treating RB-deficient cancers. SIGNIFICANCE: This study identifies stage-specific consequences of RB loss across cancer progression that have a direct impact on tumor response to clinically utilized therapeutics. The study herein is the first to investigate the effect of RB loss on global metabolic regulation and link RB/E2F1 to redox control in multiple advanced diseases.This article is highlighted in the In This Issue feature, p. 2113.


Subject(s)
E2F1 Transcription Factor/genetics , Retinal Neoplasms/genetics , Retinoblastoma Protein/genetics , Retinoblastoma/genetics , Animals , Cell Line, Tumor , Humans , Mice , Neoplasm Metastasis , Retinal Neoplasms/pathology , Retinoblastoma/secondary , Signal Transduction , Xenograft Model Antitumor Assays
20.
Clin Cancer Res ; 27(11): 3017-3027, 2021 06 01.
Article in English | MEDLINE | ID: mdl-33727260

ABSTRACT

PURPOSE: Palbociclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, blocks proliferation in a RB and cyclin D-dependent manner in preclinical prostate cancer models. We hypothesized that cotargeting androgen receptor and cell cycle with palbociclib would improve outcomes in patients with metastatic hormone-sensitive prostate cancer (mHSPC). PATIENTS AND METHODS: A total of 60 patients with RB-intact mHSPC were randomized (1:2) to Arm 1: androgen deprivation (AD) or Arm 2: AD + palbociclib. Primary endpoint was PSA response rate (RR) after 28 weeks of therapy. Secondary endpoints included safety, PSA, and clinical progression-free survival (PFS), as well as PSA and radiographic RR. Tumors underwent exome sequencing when available. Circulating tumor cells (CTC) were enumerated at various timepoints. RESULTS: A total of 72 patients with mHSPC underwent metastatic disease biopsy and 64 had adequate tissue for RB assessment. A total of 62 of 64 (97%) retained RB expression. A total of 60 patients initiated therapy (Arm 1: 20; Arm 2: 40). Neutropenia was the most common grade 3/4 adverse event in Arm 2. Eighty percent of patients (Arm 1: 16/20, Arm 2: 32/40; P = 0.87) met primary PSA endpoint ≤4 ng/mL at 28 weeks. PSA undetectable rate at 28 weeks was 50% and 43% in Arms 1 and 2, respectively (P = 0.5). Radiographic RR was 89% in both arms. Twelve-month biochemical PFS was 69% and 74% in Arms 1 and 2, respectively (P = 0.72). TP53 and PIK3 pathway mutations, 8q gains, and pretreatment CTCs were associated with reduced PSA PFS. CONCLUSIONS: Palbociclib did not impact outcome in RB-intact mHSPC. Pretreatment CTC, TP53 and PIK3 pathway mutations, and 8q gain were associated with poor outcome.


Subject(s)
Androgen Antagonists/administration & dosage , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Piperazines/administration & dosage , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/genetics , Pyridines/administration & dosage , Retinoblastoma Protein/metabolism , Adult , Aged , Aged, 80 and over , Bone Neoplasms/secondary , Disease-Free Survival , Humans , Male , Middle Aged , Mutation , Neoplastic Cells, Circulating , Phosphatidylinositol 3-Kinases/metabolism , Prostatic Neoplasms/mortality , Prostatic Neoplasms/pathology , Signal Transduction/genetics , Soft Tissue Neoplasms/secondary , Treatment Outcome , Tumor Suppressor Protein p53/metabolism
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