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Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024; 34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Suzan Stelloo
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
| | - Elif Yapıcı
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Kerim Yavuz
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tunç Morova
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Umut Berkay Altintaş
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Yongsoo Kim
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Gozde Korkmaz
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Nathan A Lack
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Michiel Vermeulen
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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2
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Augello MA, Chen X, Liu D, Lin K, Hakansson A, Sjöström M, Khani F, Deonarine LD, Liu Y, Travascio-Green J, Wu J, Loda M, Feng FY, Robinson BD, Davicioni E, Sboner A, Barbieri CE. Canonical AREs are tumor suppressive regulatory elements in the prostate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581466. [PMID: 38464162 PMCID: PMC10925218 DOI: 10.1101/2024.02.23.581466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The androgen receptor (AR) is the central determinant of prostate tissue identity and differentiation, controlling normal, growth-suppressive prostate-specific gene expression 1 . It is also a key driver of prostate tumorigenesis, becoming "hijacked" to drive oncogenic transcription 2-5 . However, the regulatory elements determining the execution of the growth suppressive AR transcriptional program, and whether this can be reactivated in prostate cancer (PCa) cells remains unclear. Canonical androgen response element (ARE) motifs are the classic DNA binding element for AR 6 . Here, we used a genome-wide strategy to modulate regulatory elements containing AREs to define distinct AR transcriptional programs. We find that activation of these AREs is specifically associated with differentiation and growth suppressive transcription, and this can be reactivated to cause death in AR + PCa cells. In contrast, repression of AREs is well tolerated by PCa cells, but deleterious to normal prostate cells. Finally, gene expression signatures driven by ARE activity are associated with improved prognosis and luminal phenotypes in human PCa patients. This study demonstrates that canonical AREs are responsible for a normal, growth-suppressive, lineage-specific transcriptional program, that this can be reengaged in PCa cells for potential therapeutic benefit, and genes controlled by this mechanism are clinically relevant in human PCa patients.
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Poluben L, Nouri M, Liang J, Varkaris A, Ersoy-Fazlioglu B, Voznesensky O, Lee II, Qiu X, Cato L, Seo JH, Freedman ML, Sowalsky AG, Lack NA, Corey E, Nelson PS, Brown M, Long HW, Balk SP, Russo JW. Increased chromatin accessibility drives transition to androgen receptor splice variant dependence in castration-resistant prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575110. [PMID: 38260576 PMCID: PMC10802579 DOI: 10.1101/2024.01.10.575110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Androgen receptor (AR) splice variants, of which ARv7 is the most common, are increased in prostate cancer (PC) that develops resistance to androgen signaling inhibitor drugs, but the extent to which these variants drive AR activity, and whether they have novel functions or dependencies, remain to be determined. We generated a subline of VCaP PC cells (VCaP16) that is resistant to the AR inhibitor enzalutamide (ENZ) and found that AR activity was independent of the full-length AR (ARfl), despite its continued high-level expression, and was instead driven by ARv7. The ARv7 cistrome and transcriptome in VCaP16 cells mirrored that of the ARfl in VCaP cells, although ARv7 chromatin binding was weaker, and strong ARv7 binding sites correlated with higher affinity ARfl binding sites across multiple models and clinical samples. Notably, although ARv7 expression in VCaP cells increased rapidly in response to ENZ, there was a long lag before it gained chromatin binding and transcriptional activity. This lag was associated with an increase in chromatin accessibility, with the AR and nuclear factor I (NFI) motifs being most enriched at these more accessible sites. Moreover, the transcriptional effects of combined NFIB and NFIX knockdown versus ARv7 knockdown were highly correlated. These findings indicate that ARv7 can drive the AR program, but that its activity is dependent on adaptations that increase chromatin accessibility to enhance its intrinsically weak chromatin binding.
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Senapati D, Sharma V, Rath SK, Rai U, Panigrahi N. Functional implications and therapeutic targeting of androgen response elements in prostate cancer. Biochimie 2023; 214:188-198. [PMID: 37460038 DOI: 10.1016/j.biochi.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/12/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
The androgen receptor (AR) plays an essential role in the growth and progression of prostate cancer (CaP). Ligand-activated AR inside the nucleus binds to the androgen response element (ARE) of the target genes in dimeric form and recruits transcriptional machinery to facilitate gene transcription. Pharmacological compounds that inhibit the AR action either bind to the ligand binding domain (LBD) or interfere with the interactions of AR with other co-regulatory proteins, slowing the progression of the disease. However, the emergence of resistance to conventional treatment makes clinical management of CaP difficult. Resistance has been associated with activation of androgen/AR axis that restores AR transcriptional activity. Activated AR signaling in resistance cases can be mediated by several mechanisms including AR amplification, gain-of-function AR mutations, androgen receptor variant (ARVs), intracrine androgen production, and overexpression of AR coactivators. Importantly, in castration resistant prostate cancer, ARVs lacking the LBD become constitutively active and promote hormone-independent development, underlining the need to concentrate on the other domain or the AR-DNA interface for the identification of novel actionable targets. In this review, we highlight the plasticity of AR-DNA binding and explain how fine-tuning AR's cooperative interactions with DNA translate into developing an alternative strategy to antagonize AR activity.
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Affiliation(s)
- Dhirodatta Senapati
- GITAM School of Pharmacy, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, India.
| | - Vikas Sharma
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Santosh Kumar Rath
- School of Pharmaceuticals and Population Health Informatics, DIT University, Dehradun, Uttarakhand, India
| | - Uddipak Rai
- School of Pharmaceuticals and Population Health Informatics, DIT University, Dehradun, Uttarakhand, India
| | - Naresh Panigrahi
- GITAM School of Pharmacy, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, India
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Janaththani P, Tevz G, Fernando A, Malik A, Rockstroh A, Kryza T, Walpole C, Moya L, Lehman M, Nelson C, Srinivasan S, Clements J, Batra J. Unravelling the Role of Iroquois Homeobox 4 and its Interplay with Androgen Receptor in Prostate Cancer. RESEARCH SQUARE 2023:rs.3.rs-3295914. [PMID: 38076926 PMCID: PMC10705702 DOI: 10.21203/rs.3.rs-3295914/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Genome-wide association studies have linked Iroquois-Homeobox 4 (IRX4) as a robust expression quantitative-trait locus associated with prostate cancer (PCa) risk. However, the intricate mechanism and regulatory factors governing IRX4 expression in PCa remain poorly understood. Here, we unveil enrichment of androgen-responsive gene signatures in metastatic prostate tumors exhibiting heightened IRX4 expression. Furthermore, we uncover a novel interaction between IRX4 and the androgen receptor (AR) co-factor, FOXA1, suggesting that IRX4 modulates PCa cell behavior through AR cistrome alteration. Remarkably, we identified a distinctive short insertion-deletion polymorphism (INDEL), upstream of the IRX4 gene that differentially regulates IRX4 expression through the disruption of AR binding. This INDEL emerges as the most significant PCa risk-associated variant within the 5p15 locus, in a genetic analysis involving 82,591 PCa cases and 61,213 controls and was associated with PCa survival in patients undergoing androgen-deprivation therapy. These studies suggest the potential of this INDEL as a prognostic biomarker for androgen therapy in PCa and IRX4 as a potential therapeutic target in combination with current clinical management.
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Affiliation(s)
- Panchadsaram Janaththani
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Melbourne, Victoria
| | - Gregor Tevz
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Achala Fernando
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Adil Malik
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Anja Rockstroh
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Thomas Kryza
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Mater Research UQ, Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Carina Walpole
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Mater Research UQ, Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Leire Moya
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Melanie Lehman
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada
| | - Colleen Nelson
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - The Australian Prostate Cancer BioResource
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | | | - Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
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7
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Logotheti S, Papadaki E, Zolota V, Logothetis C, Vrahatis AG, Soundararajan R, Tzelepi V. Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics. Cancers (Basel) 2023; 15:4357. [PMID: 37686633 PMCID: PMC10486655 DOI: 10.3390/cancers15174357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer (PCa), the most frequent and second most lethal cancer type in men in developed countries, is a highly heterogeneous disease. PCa heterogeneity, therapy resistance, stemness, and lethal progression have been attributed to lineage plasticity, which refers to the ability of neoplastic cells to undergo phenotypic changes under microenvironmental pressures by switching between developmental cell states. What remains to be elucidated is how to identify measurements of lineage plasticity, how to implement them to inform preclinical and clinical research, and, further, how to classify patients and inform therapeutic strategies in the clinic. Recent research has highlighted the crucial role of next-generation sequencing technologies in identifying potential biomarkers associated with lineage plasticity. Here, we review the genomic, transcriptomic, and epigenetic events that have been described in PCa and highlight those with significance for lineage plasticity. We further focus on their relevance in PCa research and their benefits in PCa patient classification. Finally, we explore ways in which bioinformatic analyses can be used to determine lineage plasticity based on large omics analyses and algorithms that can shed light on upstream and downstream events. Most importantly, an integrated multiomics approach may soon allow for the identification of a lineage plasticity signature, which would revolutionize the molecular classification of PCa patients.
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Affiliation(s)
- Souzana Logotheti
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Eugenia Papadaki
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
- Department of Informatics, Ionian University, 49100 Corfu, Greece;
| | - Vasiliki Zolota
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | | | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vasiliki Tzelepi
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
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Siddappa M, Hussain S, Wani SA, White J, Tang H, Gray JS, Jafari H, Wu HC, Long MD, Elhussin I, Karanam B, Wang H, Morgan R, Hardiman G, Adelani IB, Rotimi SO, Murphy AR, Nonn L, Davis MB, Kittles RA, Hughes Halbert C, Sucheston-Campbell LE, Yates C, Campbell MJ. African American Prostate Cancer Displays Quantitatively Distinct Vitamin D Receptor Cistrome-transcriptome Relationships Regulated by BAZ1A. CANCER RESEARCH COMMUNICATIONS 2023; 3:621-639. [PMID: 37082578 PMCID: PMC10112383 DOI: 10.1158/2767-9764.crc-22-0389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/12/2023] [Accepted: 03/07/2023] [Indexed: 04/22/2023]
Abstract
African American (AA) prostate cancer associates with vitamin D3 deficiency, but vitamin D receptor (VDR) genomic actions have not been investigated in this context. We undertook VDR proteogenomic analyses in European American (EA) and AA prostate cell lines and four clinical cohorts. Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) analyses revealed that nonmalignant AA RC43N prostate cells displayed the greatest dynamic protein content in the VDR complex. Likewise, in AA cells, Assay for Transposase-Accessible Chromatin using sequencing established greater 1α,25(OH)2D3-regulated chromatin accessibility, chromatin immunoprecipitation sequencing revealed significant enhancer-enriched VDR cistrome, and RNA sequencing identified the largest 1α,25(OH)2D3-dependent transcriptome. These VDR functions were significantly corrupted in the isogenic AA RC43T prostate cancer cells, and significantly distinct from EA cell models. We identified reduced expression of the chromatin remodeler, BAZ1A, in three AA prostate cancer cohorts as well as RC43T compared with RC43N. Restored BAZ1A expression significantly increased 1α,25(OH)2D3-regulated VDR-dependent gene expression in RC43T, but not HPr1AR or LNCaP cells. The clinical impact of VDR cistrome-transcriptome relationships were tested in three different clinical prostate cancer cohorts. Strikingly, only in AA patients with prostate cancer, the genes bound by VDR and/or associated with 1α,25(OH)2D3-dependent open chromatin (i) predicted progression from high-grade prostatic intraepithelial neoplasia to prostate cancer; (ii) responded to vitamin D3 supplementation in prostate cancer tumors; (iii) differentially responded to 25(OH)D3 serum levels. Finally, partial correlation analyses established that BAZ1A and components of the VDR complex identified by RIME significantly strengthened the correlation between VDR and target genes in AA prostate cancer only. Therefore, VDR transcriptional control is most potent in AA prostate cells and distorted through a BAZ1A-dependent control of VDR function. Significance Our study identified that genomic ancestry drives the VDR complex composition, genomic distribution, and transcriptional function, and is disrupted by BAZ1A and illustrates a novel driver for AA prostate cancer.
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Affiliation(s)
- Manjunath Siddappa
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Shahid Hussain
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Sajad A. Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jason White
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Hancong Tang
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jaimie S. Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Hedieh Jafari
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Hsu-Chang Wu
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Mark D. Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Isra Elhussin
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Balasubramanyam Karanam
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Honghe Wang
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Rebecca Morgan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Gary Hardiman
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | | | - Solomon O. Rotimi
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Adam R. Murphy
- Department of Urology, Northwestern Medicine, Chicago, Illinois
| | - Larisa Nonn
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois
| | - Melissa B. Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California
| | - Chanita Hughes Halbert
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Lara E. Sucheston-Campbell
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Clayton Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Moray J. Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
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Let’s Go 3D! New Generation of Models for Evaluating Drug Response and Resistance in Prostate Cancer. Int J Mol Sci 2023; 24:ijms24065293. [PMID: 36982368 PMCID: PMC10049142 DOI: 10.3390/ijms24065293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Prostate cancer (PC) is the third most frequently diagnosed cancer worldwide and the second most frequent in men. Several risk factors can contribute to the development of PC, and those include age, family history, and specific genetic mutations. So far, drug testing in PC, as well as in cancer research in general, has been performed on 2D cell cultures. This is mainly because of the vast benefits these models provide, including simplicity and cost effectiveness. However, it is now known that these models are exposed to much higher stiffness; lose physiological extracellular matrix on artificial plastic surfaces; and show changes in differentiation, polarization, and cell–cell communication. This leads to the loss of crucial cellular signaling pathways and changes in cell responses to stimuli when compared to in vivo conditions. Here, we emphasize the importance of a diverse collection of 3D PC models and their benefits over 2D models in drug discovery and screening from the studies done so far, outlining their benefits and limitations. We highlight the differences between the diverse types of 3D models, with the focus on tumor–stroma interactions, cell populations, and extracellular matrix composition, and we summarize various standard and novel therapies tested on 3D models of PC for the purpose of raising awareness of the possibilities for a personalized approach in PC therapy.
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10
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Masone MC. ARBS heterogeneity in prostate cancer progression. Nat Rev Urol 2023; 20:65. [PMID: 36600089 DOI: 10.1038/s41585-022-00716-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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