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van der Zande K, Tutuhatunewa-Louhanepessy RD, Hamberg P, Ras S, de Feijter JM, Dezentjé VO, Broeks A, Cornelissen S, Beeker A, van der Noort V, Zwart W, Bergman AM. Combined Cabazitaxel and Carboplatin Treatment of Metastatic Castration Resistant Prostate Cancer Patients, With Innate or Acquired Resistance to Cabazitaxel Monotherapy. Clin Genitourin Cancer 2024; 22:445-453.e1. [PMID: 38246830 DOI: 10.1016/j.clgc.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND There is new interest in platinum-based treatment of patients with metastatic castration resistant prostate cancer (mCRPC), to which a subgroup responds. Although platinum sensitivity is suggested to be associated with aggressive disease features and distinct molecular profiles, identification of responders is a clinical challenge. In this study, we selected patients who displayed PSA progression during cabazitaxel monotherapy, for combined cabazitaxel and carboplatin treatment. METHODS In this retrospective study, mCRPC patients received carboplatin and cabazitaxel after biochemical progression following at least 2 cabazitaxel monotherapy cycles. We assessed PSA response, Time to PSA Progression (TTpsa) and Time to Radiographic Progression (TTrad). For a subset of patients, mutational analysis of BRCA-1, BRCA-2, ATM, PTEN, P53 and RB1 was performed. RESULTS Forty-five patients were included, after a median of 4 (3-6) cycles of cabazitaxel monotherapy. Patients received a median of 3 (2-5) cycles of combined cabazitaxel and carboplatin, on which 12 (26.6%) patients had a PSA decline ≥ 50% from baseline. TTpsa was 2 (1-5) months and TTrad 3 (2-6) months. Adverse events were predominantly grade 1-2. Of the 29 (64.4%) patients evaluable for molecular signature, 6 (13.3%) had BRCA1, BRCA2 or ATM mutations and 12 (26.7%) had a PTEN, P53 or RB1 mutations. The occurrence of these mutations was not associated with any clinical outcome measure. CONCLUSIONS In this study we showed that patients with PSA progression during cabazitaxel monotherapy could benefit from the addition of carboplatin to cabazitaxel, while prospective identification of these patients remains a clinical challenge.
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Affiliation(s)
- K van der Zande
- Department of Medical Oncology, Netherlands Cancer Insitute, Amsterdam, The Netherlands; Department of Oncogenomics, Netherlands Cancer Insitute, Amsterdam, The Netherlands
| | - R D Tutuhatunewa-Louhanepessy
- Department of Medical Oncology, Netherlands Cancer Insitute, Amsterdam, The Netherlands; Department of Oncogenomics, Netherlands Cancer Insitute, Amsterdam, The Netherlands
| | - P Hamberg
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland, Schiedam, The Netherlands
| | - S Ras
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland, Schiedam, The Netherlands
| | - J M de Feijter
- Department of Medical Oncology, Netherlands Cancer Insitute, Amsterdam, The Netherlands
| | - V O Dezentjé
- Department of Medical Oncology, Netherlands Cancer Insitute, Amsterdam, The Netherlands
| | - A Broeks
- Core Facility - Molecular Pathology and Biobank. Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - S Cornelissen
- Core Facility - Molecular Pathology and Biobank. Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A Beeker
- Department of Medical Oncology, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - V van der Noort
- Department of Biometrics, Netherlands Cancer Insitute, Amsterdam, The Netherlands
| | - W Zwart
- Department of Oncogenomics, Netherlands Cancer Insitute, Amsterdam, The Netherlands.; Oncode Insitute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - A M Bergman
- Department of Medical Oncology, Netherlands Cancer Insitute, Amsterdam, The Netherlands; Department of Oncogenomics, Netherlands Cancer Insitute, Amsterdam, The Netherlands..
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2
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van Genderen MNG, Kneppers J, Zaalberg A, Bekers EM, Bergman AM, Zwart W, Eduati F. Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties. NPJ Syst Biol Appl 2024; 10:20. [PMID: 38383542 PMCID: PMC10881528 DOI: 10.1038/s41540-024-00344-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024] Open
Abstract
Inhibiting androgen receptor (AR) signaling through androgen deprivation therapy (ADT) reduces prostate cancer (PCa) growth in virtually all patients, but response may be temporary, in which case resistance develops, ultimately leading to lethal castration-resistant prostate cancer (CRPC). The tumor microenvironment (TME) plays an important role in the development and progression of PCa. In addition to tumor cells, TME-resident macrophages and fibroblasts express AR and are therefore also affected by ADT. However, the interplay of different TME cell types in the development of CRPC remains largely unexplored. To understand the complex stochastic nature of cell-cell interactions, we created a PCa-specific agent-based model (PCABM) based on in vitro cell proliferation data. PCa cells, fibroblasts, "pro-inflammatory" M1-like and "pro-tumor" M2-like polarized macrophages are modeled as agents from a simple set of validated base assumptions. PCABM allows us to simulate the effect of ADT on the interplay between various prostate TME cell types. The resulting in vitro growth patterns mimic human PCa. Our PCABM can effectively model hormonal perturbations by ADT, in which PCABM suggests that CRPC arises in clusters of resistant cells, as is observed in multifocal PCa. In addition, fibroblasts compete for cellular space in the TME while simultaneously creating niches for tumor cells to proliferate in. Finally, PCABM predicts that ADT has immunomodulatory effects on macrophages that may enhance tumor survival. Taken together, these results suggest that AR plays a critical role in the cellular interplay and stochastic interactions in the TME that influence tumor cell behavior and CRPC development.
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Affiliation(s)
- Maisa N G van Genderen
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anniek Zaalberg
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Elise M Bekers
- Division of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Wilbert Zwart
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands.
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands.
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands.
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3
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Zaalberg A, Pottendorfer E, Zwart W, Bergman AM. It Takes Two to Tango: The Interplay between Prostate Cancer and Its Microenvironment from an Epigenetic Perspective. Cancers (Basel) 2024; 16:294. [PMID: 38254784 PMCID: PMC10813511 DOI: 10.3390/cancers16020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Prostate cancer is the second most common cancer in men worldwide and is associated with high morbidity and mortality. Consequently, there is an urgent unmet need for novel treatment avenues. In addition to somatic genetic alterations, deviations in the epigenetic landscape of cancer cells and their tumor microenvironment (TME) are critical drivers of prostate cancer initiation and progression. Unlike genomic mutations, epigenetic modifications are potentially reversible. Therefore, the inhibition of aberrant epigenetic modifications represents an attractive and exciting novel treatment strategy for castration-resistant prostate cancer patients. Moreover, drugs targeting the epigenome also exhibit synergistic interactions with conventional therapeutics by directly enhancing their anti-tumorigenic properties by "priming" the tumor and tumor microenvironment to increase drug sensitivity. This review summarizes the major epigenetic alterations in prostate cancer and its TME, and their involvement in prostate tumorigenesis, and discusses the impact of epigenome-targeted therapies.
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Affiliation(s)
- Anniek Zaalberg
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (A.Z.); (E.P.)
| | - Elisabeth Pottendorfer
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (A.Z.); (E.P.)
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (A.Z.); (E.P.)
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Oncode Institute
| | - Andries M. Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (A.Z.); (E.P.)
- Division of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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4
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Mayayo-Peralta I, Debets DO, Prekovic S, Schuurman K, Beerthuijzen S, Almekinders M, Sanders J, Moelans CB, Saleiro S, Wesseling J, van Diest PJ, Henrique R, Jerónimo C, Altelaar M, Zwart W. Proteomics on malignant pleural effusions reveals ERα loss in metastatic breast cancer associates with SGK1-NDRG1 deregulation. Mol Oncol 2024; 18:156-169. [PMID: 37854018 PMCID: PMC10766196 DOI: 10.1002/1878-0261.13540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023] Open
Abstract
Breast cancer (BCa) is a highly heterogeneous disease, with hormone receptor status being a key factor in patient prognostication and treatment decision-making. The majority of primary tumours are positive for oestrogen receptor alpha (ERα), which plays a key role in tumorigenesis and disease progression, and represents the major target for treatment of BCa. However, around one-third of patients with ERα-positive BCa relapse and progress into the metastatic stage, with 20% of metastatic cases characterised by loss of ERα expression after endocrine treatment, known as ERα-conversion. It remains unclear whether ERα-converted cancers are biologically similar to bona fide ERα-negative disease and which signalling cascades compensate for ERα loss and drive tumour progression. To better understand the biological changes that occur in metastatic BCa upon ERα loss, we performed (phospho)proteomics analysis of 47 malignant pleural effusions derived from 37 BCa patients, comparing ERα-positive, ERα-converted and ERα-negative cases. Our data revealed that the loss of ERα-dependency in this metastatic site leads to only a partial switch to an ERα-negative molecular phenotype, with preservation of a luminal-like proteomic landscape. Furthermore, we found evidence for decreased activity of several key kinases, including serum/glucocorticoid regulated kinase 1 (SGK1), in ERα-converted metastases. Loss of SGK1 substrate phosphorylation may compensate for the loss of ERα-dependency in advanced disease and exposes a potential therapeutic vulnerability that may be exploited in treating these patients.
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Affiliation(s)
- Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Donna O Debets
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Suzanne Beerthuijzen
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mathilde Almekinders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, The Netherlands
| | - Sandra Saleiro
- Lung Cancer Clinics, Portuguese Oncology Institute of Porto, Portugal
| | - Jelle Wesseling
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, The Netherlands
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of the Portuguese Oncology Institute-Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of the Portuguese Oncology Institute-Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
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5
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Prekovic S, Chalkiadakis T, Roest M, Roden D, Lutz C, Schuurman K, Opdam M, Hoekman L, Abbott N, Tesselaar T, Wajahat M, Dwyer AR, Mayayo‐Peralta I, Gomez G, Altelaar M, Beijersbergen R, Győrffy B, Young L, Linn S, Jonkers J, Tilley W, Hickey T, Vareslija D, Swarbrick A, Zwart W. Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Mol Med 2023; 15:e17737. [PMID: 37902007 PMCID: PMC10701603 DOI: 10.15252/emmm.202317737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.
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Affiliation(s)
- Stefan Prekovic
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Center for Molecular MedicineUMC UtrechtUtrechtThe Netherlands
| | | | - Merel Roest
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Daniel Roden
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tanja Tesselaar
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Maliha Wajahat
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Isabel Mayayo‐Peralta
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Gabriela Gomez
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
| | - Maarten Altelaar
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening CentreNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Balázs Győrffy
- TTK Cancer Biomarker Research GroupInstitute of EnzymologyBudapestHungary
- Department of Bioinformatics and 2nd Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Leonie Young
- Endocrine Oncology Research Group, Department of SurgeryThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Sabine Linn
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
- Freemasons Centre for Male Health and WellbeingUniversity of AdelaideAdelaideSAAustralia
| | - Theresa Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Damir Vareslija
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Alexander Swarbrick
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands
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6
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Elabd S, Pauletto E, Solozobova V, Eickhoff N, Padrao N, Zwart W, Blattner C. TRIM25 targets p300 for degradation. Life Sci Alliance 2023; 6:e202301980. [PMID: 37770115 PMCID: PMC10539465 DOI: 10.26508/lsa.202301980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023] Open
Abstract
p300 is an important transcriptional co-factor. By stimulating the transfer of acetyl residues onto histones and several key transcription factors, p300 enhances transcriptional initiation and impacts cellular processes including cell proliferation and cell division. Despite its importance for cellular homeostasis, its regulation is poorly understood. We show that TRIM25, a member of the TRIM protein family, targets p300 for proteasomal degradation. However, despite TRIM25's RING domain and E3 activity, degradation of p300 by TRIM25 is independent of TRIM25-mediated p300 ubiquitination. Instead, TRIM25 promotes the interaction of p300 with dynein, which ensures a microtubule-dependent transport of p300 to cellular proteasomes. Through mediating p300 degradation, TRIM25 affects p300-dependent gene expression.
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Affiliation(s)
- Seham Elabd
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe, Germany
- https://ror.org/00mzz1w90 Human Physiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Eleonora Pauletto
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe, Germany
| | - Valeria Solozobova
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe, Germany
| | - Nils Eickhoff
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nuno Padrao
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christine Blattner
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe, Germany
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7
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Yavuz S, Kabbech H, van Staalduinen J, Linder S, van Cappellen W, Nigg A, Abraham T, Slotman J, Quevedo M, Poot R, Zwart W, van Royen M, Grosveld F, Smal I, Houtsmuller A. Compartmentalization of androgen receptors at endogenous genes in living cells. Nucleic Acids Res 2023; 51:10992-11009. [PMID: 37791849 PMCID: PMC10639085 DOI: 10.1093/nar/gkad803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/06/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, multiple androgen receptors (ARs) accumulate in microscopically discernable foci which are irregularly distributed in the nucleus. Here, we investigated the formation and physical nature of these foci, by combining novel fluorescent labeling techniques to visualize a defined chromatin locus of AR-regulated genes-PTPRN2 or BANP-simultaneously with either AR foci or individual AR molecules. Quantitative colocalization analysis showed evidence of AR foci formation induced by R1881 at both PTPRN2 and BANP loci. Furthermore, single-particle tracking (SPT) revealed three distinct subdiffusive fractional Brownian motion (fBm) states: immobilized ARs were observed near the labeled genes likely as a consequence of DNA-binding, while the intermediate confined state showed a similar spatial behavior but with larger displacements, suggesting compartmentalization by liquid-liquid phase separation (LLPS), while freely mobile ARs were diffusing in the nuclear environment. All together, we show for the first time in living cells the presence of AR-regulated genes in AR foci.
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Affiliation(s)
- Selçuk Yavuz
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hélène Kabbech
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jente van Staalduinen
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Simon Linder
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex L Nigg
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tsion E Abraham
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan A Slotman
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marti Quevedo
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ihor Smal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
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8
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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 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] [What about the content of this article? (0)] [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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9
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Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer. Cancer Discov 2023; 13:2470-2487. [PMID: 37694973 PMCID: PMC10618745 DOI: 10.1158/2159-8290.cd-23-0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023]
Abstract
Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state-specific "regulatory transposable elements." Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements. SIGNIFICANCE We show that oncogenesis relies on co-opting transposable elements from pluripotent stem cells as regulatory elements altering the recruitment of lineage-specific transcription factors. We further discover how co-option is dependent on active chromatin states with important implications for developing treatment options against drivers of oncogenesis across the repetitive DNA. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
- Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tina Keshavarzian
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisanne Mout
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ankita Nand
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mona Teng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aditi Qamra
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ken J. Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James R. Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Theodorus H. van der Kwast
- Laboratory Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ganesh V. Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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10
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Linder S, Severson TM, van der Mijn KJC, Nevedomskaya E, Siefert JC, Stelloo S, Pomerantz MM, Freedman ML, van der Poel H, Jerónimo C, Henrique R, Bergman AM, Zwart W. Grade Group 1 Prostate Cancers Exhibit Tumor-defining Androgen Receptor-driven Programs. Eur Urol 2023; 84:455-460. [PMID: 37271632 DOI: 10.1016/j.eururo.2023.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/30/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Grade group 1 (GG1) primary prostate cancers with a pathologic Gleason score of 6 are considered indolent and generally not associated with fatal outcomes, so treatment is not indicated for most cases. These low-grade cancers have an overall negligible risk of locoregional progression and metastasis to distant organs, which is why there is an ongoing debate about whether these lesions should be reclassified as "noncancerous". However, the underlying molecular activity of key disease drivers, such as the androgen receptor (AR), have thus far not been thoroughly characterized in low-grade tumors. Therefore, we set out to delineate the AR chromatin-binding landscape in low-grade GG1 prostate cancers to gain insights into whether these AR-driven programs are actually tumor-specific or are normal prostate epithelium-like. These analyses showed that GG1 tumors do not harbor a distinct AR cistrome and, similar to higher-grade cancers, AR preferentially binds to tumor-defining cis-regulatory elements. Furthermore, the enhancer activity of these regions and the expression of their respective target genes were not significantly different in GG1 tumors. From an epigenetic perspective, this finding supports the cancer designation currently given to these low-grade tumors and clearly distinguishes them from noncancerous benign tissue. PATIENT SUMMARY: We characterized the molecular activity of the androgen receptor protein, which drives prostate cancer disease, in low-grade tumors. Our results show that these tumors are true cancers and are clearly separate from benign prostate tissue despite their low clinical aggressiveness.
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Affiliation(s)
- Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Koen J C van der Mijn
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ekaterina Nevedomskaya
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joseph C Siefert
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew L Freedman
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA; Division of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henk van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Urology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of the Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of the Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Andries M Bergman
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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11
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Manjón AG, Manzo SG, Prekovic S, Potgeter L, van Schaik T, Liu NQ, Flach K, Peric-Hupkes D, Joosten S, Teunissen H, Friskes A, Ilic M, Hintzen D, Franceschini-Santos VH, Zwart W, de Wit E, van Steensel B, Medema RH. Perturbations in 3D genome organization can promote acquired drug resistance. Cell Rep 2023; 42:113124. [PMID: 37733591 DOI: 10.1016/j.celrep.2023.113124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/05/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
Acquired drug resistance is a major problem in the treatment of cancer. hTERT-immortalized, untransformed RPE-1 cells can acquire resistance to Taxol by derepressing the ABCB1 gene, encoding for the multidrug transporter P-gP. Here, we investigate how the ABCB1 gene is derepressed. ABCB1 activation is associated with reduced H3K9 trimethylation, increased H3K27 acetylation, and ABCB1 displacement from the nuclear lamina. While altering DNA methylation and H3K27 methylation had no major impact on ABCB1 expression, nor did it promote resistance, disrupting the nuclear lamina component Lamin B Receptor did promote the acquisition of a Taxol-resistant phenotype in a subset of cells. CRISPRa-mediated gene activation supported the notion that lamina dissociation influences ABCB1 derepression. We propose a model in which nuclear lamina dissociation of a repressed gene allows for its activation, implying that deregulation of the 3D genome topology could play an important role in tumor evolution and the acquisition of drug resistance.
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Affiliation(s)
- Anna G Manjón
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Stefano Giustino Manzo
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Stefan Prekovic
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Leon Potgeter
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Tom van Schaik
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Ning Qing Liu
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Koen Flach
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Daniel Peric-Hupkes
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Stacey Joosten
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Anoek Friskes
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Mila Ilic
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Dorine Hintzen
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Vinícius H Franceschini-Santos
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Wilbert Zwart
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Bas van Steensel
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
| | - René H Medema
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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12
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Prekovic S, Zwart W. Inhibiting the Glucocorticoid Receptor to Enhance Chemotherapy Response. J Clin Oncol 2023; 41:4790-4793. [PMID: 37535891 DOI: 10.1200/jco.23.01195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 08/05/2023] Open
Abstract
Explaining the biology of how glucocorticoid receptor blockade boosts chemotherapy in ovarian cancer.
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Affiliation(s)
- Stefan Prekovic
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Netherlands Cancer Institute and Oncode Institute, Amsterdam, the Netherlands
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13
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Mayayo-Peralta I, Gregoricchio S, Schuurman K, Yavuz S, Zaalberg A, Kojic A, Abbott N, Geverts B, Beerthuijzen S, Siefert J, Severson TM, van Baalen M, Hoekman L, Lieftink C, Altelaar M, Beijersbergen RL, Houtsmuller A, Prekovic S, Zwart W. PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription. Nucleic Acids Res 2023; 51:9576-9593. [PMID: 37070193 PMCID: PMC10570044 DOI: 10.1093/nar/gkad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
How steroid hormone receptors (SHRs) regulate transcriptional activity remains partly understood. Upon activation, SHRs bind the genome together with a co-regulator repertoire, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited co-regulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we functionally dissected the Glucocorticoid Receptor (GR) complex. We describe a functional cross-talk between PAXIP1 and the cohesin subunit STAG2, critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on chromatin, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. In lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.
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Affiliation(s)
- Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Selçuk Yavuz
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
| | - Anniek Zaalberg
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aleksandar Kojic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Suzanne Beerthuijzen
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joseph Siefert
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martijn van Baalen
- Flow Cytometry Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
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14
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Clarisse D, Prekovic S, Vlummens P, Staessens E, Van Wesemael K, Thommis J, Fijalkowska D, Acke G, Zwart W, Beck IM, Offner F, De Bosscher K. Crosstalk between glucocorticoid and mineralocorticoid receptors boosts glucocorticoid-induced killing of multiple myeloma cells. Cell Mol Life Sci 2023; 80:249. [PMID: 37578563 PMCID: PMC10425521 DOI: 10.1007/s00018-023-04900-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/11/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
The glucocorticoid receptor (GR) is a crucial drug target in multiple myeloma as its activation with glucocorticoids effectively triggers myeloma cell death. However, as high-dose glucocorticoids are also associated with deleterious side effects, novel approaches are urgently needed to improve GR action in myeloma. Here, we reveal a functional crosstalk between GR and the mineralocorticoid receptor (MR) that plays a role in improved myeloma cell killing. We show that the GR agonist dexamethasone (Dex) downregulates MR levels in a GR-dependent way in myeloma cells. Co-treatment of Dex with the MR antagonist spironolactone (Spi) enhances Dex-induced cell killing in primary, newly diagnosed GC-sensitive myeloma cells. In a relapsed GC-resistant setting, Spi alone induces distinct myeloma cell killing. On a mechanistic level, we find that a GR-MR crosstalk likely arises from an endogenous interaction between GR and MR in myeloma cells. Quantitative dimerization assays show that Spi reduces Dex-induced GR-MR heterodimerization and completely abolishes Dex-induced MR-MR homodimerization, while leaving GR-GR homodimerization intact. Unbiased transcriptomics analyses reveal that c-myc and many of its target genes are downregulated most by combined Dex-Spi treatment. Proteomics analyses further identify that several metabolic hallmarks are modulated most by this combination treatment. Finally, we identified a subset of Dex-Spi downregulated genes and proteins that may predict prognosis in the CoMMpass myeloma patient cohort. Our study demonstrates that GR-MR crosstalk is therapeutically relevant in myeloma as it provides novel strategies for glucocorticoid-based dose-reduction.
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Affiliation(s)
- Dorien Clarisse
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Stefan Prekovic
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Philip Vlummens
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Eleni Staessens
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Karlien Van Wesemael
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Jonathan Thommis
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Guillaume Acke
- Department of Chemistry, Ghent University, Ghent, Belgium
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ilse M Beck
- Department of Health Sciences, Odisee University of Applied Sciences, Ghent, Belgium
| | - Fritz Offner
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Karolien De Bosscher
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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15
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Passier M, van Genderen MN, Zaalberg A, Kneppers J, Bekers EM, Bergman AM, Zwart W, Eduati F. Exploring the Onset and Progression of Prostate Cancer through a Multicellular Agent-based Model. Cancer Res Commun 2023; 3:1473-1485. [PMID: 37554550 PMCID: PMC10405859 DOI: 10.1158/2767-9764.crc-23-0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/15/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
Over 10% of men will be diagnosed with prostate cancer during their lifetime. Arising from luminal cells of the prostatic acinus, prostate cancer is influenced by multiple cells in its microenvironment. To expand our knowledge and explore means to prevent and treat the disease, it is important to understand what drives the onset and early stages of prostate cancer. In this study, we developed an agent-based model of a prostatic acinus including its microenvironment, to allow for in silico studying of prostate cancer development. The model was based on prior reports and in-house data of tumor cells cocultured with cancer-associated fibroblasts (CAF) and protumor and/or antitumor macrophages. Growth patterns depicted by the model were pathologically validated on hematoxylin and eosin slide images of human prostate cancer specimens. We identified that stochasticity of interactions between macrophages and tumor cells at early stages strongly affect tumor development. In addition, we discovered that more systematic deviations in tumor development result from a combinatorial effect of the probability of acquiring mutations and the tumor-promoting abilities of CAFs and macrophages. In silico modeled tumors were then compared with 494 patients with cancer with matching characteristics, showing strong association between predicted tumor load and patients' clinical outcome. Our findings suggest that the likelihood of tumor formation depends on a combination of stochastic events and systematic characteristics. While stochasticity cannot be controlled, information on systematic effects may aid the development of prevention strategies tailored to the molecular characteristics of an individual patient. Significance We developed a computational model to study which factors of the tumor microenvironment drive prostate cancer development, with potential to aid the development of new prevention strategies.
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Affiliation(s)
- Margot Passier
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Maisa N.G. van Genderen
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Anniek Zaalberg
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Elise M. Bekers
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Andries M. Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Wilbert Zwart
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
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16
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Gregoricchio S, Zwart W. snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis. Bioinform Adv 2023; 3:vbad080. [PMID: 37397353 PMCID: PMC10307938 DOI: 10.1093/bioadv/vbad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Summary Genome-wide chromosome conformation capture (Hi-C) is a technique that allows the study of 3D genome organization. Despite being widely used, analysis of Hi-C data is technically challenging and involves several time-consuming steps that often require manual involvement making it error prone, potentially affecting data reproducibility. In order to facilitate and simplify these analyses we implemented snHiC, a snakemake-based pipeline that allows for the generation of contact matrices at multiple resolutions in one single run, aggregation of individual samples into user-specified groups, detection of domains, compartments, loops and stripes and performance of differential compartment and chromatin interaction analyses. Availability and implementation Source code is freely available at https://github.com/sebastian-gregoricchio/snHiC. A yaml-formatted file (snHiC/workflow/envs/snHiC_conda_env_stable.yaml) is available to build a compatible conda environment. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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17
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Zaalberg A, Minnee E, Mayayo-Peralta I, Schuurman K, Gregoricchio S, van Schaik TA, Hoekman L, Li D, Corey E, Janssen H, Lieftink C, Prekovic S, Altelaar M, Nelson PS, Beijersbergen RL, Zwart W, Bergman A. A genome-wide CRISPR screen in human prostate cancer cells reveals drivers of macrophage-mediated cell killing and positions AR as a tumor-intrinsic immunomodulator. bioRxiv 2023:2023.06.06.543873. [PMID: 37333335 PMCID: PMC10274642 DOI: 10.1101/2023.06.06.543873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The crosstalk between prostate cancer (PCa) cells and the tumor microenvironment plays a pivotal role in disease progression and metastasis and could provide novel opportunities for patient treatment. Macrophages are the most abundant immune cells in the prostate tumor microenvironment (TME) and are capable of killing tumor cells. To identify genes in the tumor cells that are critical for macrophage-mediated killing, we performed a genome-wide co-culture CRISPR screen and identified AR, PRKCD, and multiple components of the NF-κB pathway as hits, whose expression in the tumor cell are essential for being targeted and killed by macrophages. These data position AR signaling as an immunomodulator, and confirmed by androgen-deprivation experiments, that rendered hormone-deprived tumor cells resistant to macrophage-mediated killing. Proteomic analyses showed a downregulation of oxidative phosphorylation in the PRKCD- and IKBKG-KO cells compared to the control, suggesting impaired mitochondrial function, which was confirmed by electron microscopy analyses. Furthermore, phosphoproteomic analyses revealed that all hits impaired ferroptosis signaling, which was validated transcriptionally using samples from a neoadjuvant clinical trial with the AR-inhibitor enzalutamide. Collectively, our data demonstrate that AR functions together with the PRKCD and the NF-κB pathway to evade macrophage-mediated killing. As hormonal intervention represents the mainstay therapy for treatment of prostate cancer patients, our findings may have direct implications and provide a plausible explanation for the clinically observed persistence of tumor cells despite androgen deprivation therapy.
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18
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Dinis Fernandes C, Schaap A, Kant J, van Houdt P, Wijkstra H, Bekers E, Linder S, Bergman AM, van der Heide U, Mischi M, Zwart W, Eduati F, Turco S. Radiogenomics Analysis Linking Multiparametric MRI and Transcriptomics in Prostate Cancer. Cancers (Basel) 2023; 15:3074. [PMID: 37370685 DOI: 10.3390/cancers15123074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Prostate cancer (PCa) is a highly prevalent cancer type with a heterogeneous prognosis. An accurate assessment of tumor aggressiveness can pave the way for tailored treatment strategies, potentially leading to better outcomes. While tumor aggressiveness is typically assessed based on invasive methods (e.g., biopsy), radiogenomics, combining diagnostic imaging with genomic information can help uncover aggressive (imaging) phenotypes, which in turn can provide non-invasive advice on individualized treatment regimens. In this study, we carried out a parallel analysis on both imaging and transcriptomics data in order to identify features associated with clinically significant PCa (defined as an ISUP grade ≥ 3), subsequently evaluating the correlation between them. Textural imaging features were extracted from multi-parametric MRI sequences (T2W, DWI, and DCE) and combined with DCE-derived parametric pharmacokinetic maps obtained using magnetic resonance dispersion imaging (MRDI). A transcriptomic analysis was performed to derive functional features on transcription factors (TFs), and pathway activity from RNA sequencing data, here referred to as transcriptomic features. For both the imaging and transcriptomic features, different machine learning models were separately trained and optimized to classify tumors in either clinically insignificant or significant PCa. These models were validated in an independent cohort and model performance was used to isolate a subset of relevant imaging and transcriptomic features to be further investigated. A final set of 31 imaging features was correlated to 33 transcriptomic features obtained on the same tumors. Five significant correlations (p < 0.05) were found, of which, three had moderate strength (|r| ≥ 0.5). The strongest significant correlations were seen between a perfusion-based imaging feature-MRDI A median-and the activities of the TFs STAT6 (-0.64) and TFAP2A (-0.50). A higher-order T2W textural feature was also significantly correlated to the activity of the TF STAT6 (-0.58). STAT6 plays an important role in controlling cell proliferation and migration. Loss of the AP2alpha protein expression, quantified by TFAP2A, has been strongly associated with aggressiveness and progression in PCa. According to our findings, a combination of texture features extracted from T2W and DCE, as well as perfusion-based pharmacokinetic features, can be considered for the prediction of clinically significant PCa, with the pharmacokinetic MRDI A feature being the most correlated with the underlying transcriptomic information. These results highlight a link between quantitative imaging features and the underlying transcriptomic landscape of prostate tumors.
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Affiliation(s)
- Catarina Dinis Fernandes
- Electrical Engineering Department, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Annekoos Schaap
- Electrical Engineering Department, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Joan Kant
- Biomedical Engineering-Computational Biology Department, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Petra van Houdt
- Department of Radiation Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Hessel Wijkstra
- Electrical Engineering Department, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Department of Urology, Amsterdam University Medical Centers, 1100 DD Amsterdam, The Netherlands
| | - Elise Bekers
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Simon Linder
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Uulke van der Heide
- Department of Radiation Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Massimo Mischi
- Electrical Engineering Department, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Wilbert Zwart
- Biomedical Engineering-Computational Biology Department, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Federica Eduati
- Biomedical Engineering-Computational Biology Department, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Simona Turco
- Electrical Engineering Department, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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19
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Severson TM, Zhu Y, Prekovic S, Schuurman K, Nguyen HM, Brown LG, Hakkola S, Kim Y, Kneppers J, Linder S, Stelloo S, Lieftink C, van der Heijden M, Nykter M, van der Noort V, Sanders J, Morris B, Jenster G, van Leenders GJLH, Pomerantz M, Freedman ML, Beijersbergen RL, Urbanucci A, Wessels L, Corey E, Zwart W, Bergman AM. Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients. medRxiv 2023:2023.02.24.23286403. [PMID: 36865297 PMCID: PMC9980263 DOI: 10.1101/2023.02.24.23286403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Androgen Receptor (AR) signaling inhibitors, including enzalutamide, are treatment options for patients with metastatic castration-resistant prostate cancer (mCRPC), but resistance inevitably develops. Using metastatic samples from a prospective phase II clinical trial, we epigenetically profiled enhancer/promoter activities with H3K27ac chromatin immunoprecipitation followed by sequencing, before and after AR-targeted therapy. We identified a distinct subset of H3K27ac-differentially marked regions that associated with treatment responsiveness. These data were successfully validated in mCRPC patient-derived xenograft models (PDX). In silico analyses revealed HDAC3 as a critical factor that can drive resistance to hormonal interventions, which we validated in vitro . Using cell lines and mCRPC PDX tumors in vitro , we identified drug-drug synergy between enzalutamide and the pan-HDAC inhibitor vorinostat, providing therapeutic proof-of-concept. These findings demonstrate rationale for new therapeutic strategies using a combination of AR and HDAC inhibitors to improve patient outcome in advanced stages of mCRPC.
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20
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Buoninfante OA, Pilzecker B, Spanjaard A, de Groot D, Prekovic S, Song JY, Lieftink C, Ayidah M, Pritchard CEJ, Vivié J, Mcgrath KE, Huijbers IJ, Philipsen S, von Lindern M, Zwart W, Beijersbergen R, Palis J, van den Berk PCM, Jacobs H. Mammalian life depends on two distinct pathways of DNA damage tolerance. Proc Natl Acad Sci U S A 2023; 120:e2216055120. [PMID: 36669105 PMCID: PMC9942833 DOI: 10.1073/pnas.2216055120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA damage threatens genomic integrity and instigates stem cell failure. To bypass genotoxic lesions during replication, cells employ DNA damage tolerance (DDT), which is regulated via PCNA ubiquitination and REV1. DDT is conserved in all domains of life, yet its relevance in mammals remains unclear. Here, we show that inactivation of both PCNA-ubiquitination and REV1 results in embryonic and adult lethality, and the accumulation of DNA damage in hematopoietic stem and progenitor cells (HSPCs) that ultimately resulted in their depletion. Our results reveal the crucial relevance of DDT in the maintenance of stem cell compartments and mammalian life in unperturbed conditions.
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Affiliation(s)
| | - Bas Pilzecker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Daniël de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, 3584 CXUtrecht, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Matilda Ayidah
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Colin E. J. Pritchard
- Mouse Clinic for Cancer and Aging Research, Transgenic Facility, The Netherlands Cancer Institute, 1066 CXAmsterdam, The Netherlands
| | - Judith Vivié
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, 3584 CTUtrecht, The Netherlands
| | - Kathleen E. Mcgrath
- Department of Pediatrics, University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY14642
| | - Ivo J. Huijbers
- Mouse Clinic for Cancer and Aging Research, Transgenic Facility, The Netherlands Cancer Institute, 1066 CXAmsterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus Medical Center, 3015CNRotterdam, The Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratories, 1066CXAmsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY14642
| | - Paul C. M. van den Berk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
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21
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Kneppers J, Severson TM, Siefert JC, Schol P, Joosten SEP, Yu IPL, Huang CCF, Morova T, Altıntaş UB, Giambartolomei C, Seo JH, Baca SC, Carneiro I, Emberly E, Pasaniuc B, Jerónimo C, Henrique R, Freedman ML, Wessels LFA, Lack NA, Bergman AM, Zwart W. Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential. Nat Commun 2022; 13:7367. [PMID: 36450752 PMCID: PMC9712620 DOI: 10.1038/s41467-022-35135-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Androgen receptor (AR) drives prostate cancer (PCa) development and progression. AR chromatin binding profiles are highly plastic and form recurrent programmatic changes that differentiate disease stages, subtypes and patient outcomes. While prior studies focused on concordance between patient subgroups, inter-tumor heterogeneity of AR enhancer selectivity remains unexplored. Here we report high levels of AR chromatin binding heterogeneity in human primary prostate tumors, that overlap with heterogeneity observed in healthy prostate epithelium. Such heterogeneity has functional consequences, as somatic mutations converge on commonly-shared AR sites in primary over metastatic tissues. In contrast, less-frequently shared AR sites associate strongly with AR-driven gene expression, while such heterogeneous AR enhancer usage also distinguishes patients' outcome. These findings indicate that epigenetic heterogeneity in primary disease is directly informative for risk of biochemical relapse. Cumulatively, our results illustrate a high level of AR enhancer heterogeneity in primary PCa driving differential expression and clinical impact.
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Affiliation(s)
- Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joseph C Siefert
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pieter Schol
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivan Pak Lok Yu
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | | | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Ji-Heui Seo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Sylvan C Baca
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Isa Carneiro
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Carmen Jerónimo
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Matthew L Freedman
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, USA
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
- School of Medicine, Koç University, Istanbul, Turkey
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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22
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Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
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Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
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23
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Eickhoff N, Bergman AM, Zwart W. Homing in on a Moving Target: Androgen Receptor Cistromic Plasticity in Prostate Cancer. Endocrinology 2022; 163:6705578. [PMID: 36125208 DOI: 10.1210/endocr/bqac153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Indexed: 11/19/2022]
Abstract
The androgen receptor (AR) is the critical driver in prostate cancer and exerts its function mainly through transcriptional control. Recent advances in clinical studies and cell line models have illustrated that AR chromatin binding features are not static; rather they are highly variable yet reproducibly altered between clinical stages. Extensive genomic analyses of AR chromatin binding features in different disease stages have revealed a high degree of plasticity of AR chromatin interactions in clinical samples. Mechanistically, AR chromatin binding patterns are associated with specific somatic mutations on AR and other permutations, including mutations of AR-interacting proteins. Here we summarize the most recent studies on how the AR cistrome is dynamically altered in prostate cancer models and patient samples, and what implications this has for the identification of therapeutic targets to avoid the emergence of treatment resistance.
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Affiliation(s)
- Nils Eickhoff
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
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24
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Friskes A, Koob L, Krenning L, Severson TM, Koeleman E, Vergara X, Schubert M, van den Berg J, Evers B, Manjón AG, Joosten S, Kim Y, Zwart W, Medema R. Double-strand break toxicity is chromatin context independent. Nucleic Acids Res 2022; 50:9930-9947. [PMID: 36107780 PMCID: PMC9508844 DOI: 10.1093/nar/gkac758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022] Open
Abstract
Cells respond to double-strand breaks (DSBs) by activating DNA damage response pathways, including cell cycle arrest. We have previously shown that a single double-strand break generated via CRISPR/Cas9 is sufficient to delay cell cycle progression and compromise cell viability. However, we also found that the cellular response to DSBs can vary, independent of the number of lesions. This implies that not all DSBs are equally toxic, and raises the question if the location of a single double-strand break could influence its toxicity. To systematically investigate if DSB-location is a determinant of toxicity we performed a CRISPR/Cas9 screen targeting 6237 single sites in the human genome. Next, we developed a data-driven framework to design CRISPR/Cas9 sgRNA (crRNA) pools targeting specific chromatin features. The chromatin context was defined using ChromHMM states, Lamin-B1 DAM-iD, DNAseI hypersensitivity, and RNA-sequencing data. We computationally designed 6 distinct crRNA pools, each containing 10 crRNAs targeting the same chromatin state. We show that the toxicity of a DSB is highly similar across the different ChromHMM states. Rather, we find that the major determinants of toxicity of a sgRNA are cutting efficiency and off-target effects. Thus, chromatin features have little to no effect on the toxicity of a single CRISPR/Cas9-induced DSB.
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Affiliation(s)
- Anoek Friskes
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lisa Koob
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lenno Krenning
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Tesa M Severson
- Oncode Institute, Division of Oncogenomics, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Emma S Koeleman
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Xabier Vergara
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Division of Gene Regulation, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Michael Schubert
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jeroen van den Berg
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis and NKI Robotics and Screening Center, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anna G Manjón
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Stacey Joosten
- Oncode Institute, Division of Oncogenomics, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Yongsoo Kim
- Oncode Institute, Division of Oncogenomics, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Oncode Institute, Division of Oncogenomics, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - René H Medema
- Oncode Institute, Division of Cell Biology, the Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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25
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Baca SC, Singler C, Zacharia S, Seo JH, Morova T, Hach F, Ding Y, Schwarz T, Huang CCF, Anderson J, Fay AP, Kalita C, Groha S, Pomerantz MM, Wang V, Linder S, Sweeney CJ, Zwart W, Lack NA, Pasaniuc B, Takeda DY, Gusev A, Freedman ML. Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation. Nat Genet 2022; 54:1364-1375. [PMID: 36071171 PMCID: PMC9784646 DOI: 10.1038/s41588-022-01168-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/19/2022] [Indexed: 12/25/2022]
Abstract
Many genetic variants affect disease risk by altering context-dependent gene regulation. Such variants are difficult to study mechanistically using current methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs). To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for identifying genotypic and allele-specific effects on chromatin that are also associated with disease. In prostate cancer, CWAS identified regulatory elements and androgen receptor-binding sites that explained the association at 52 of 98 known prostate cancer risk loci and discovered 17 additional risk loci. CWAS implicated key developmental transcription factors in prostate cancer risk that are overlooked by eQTL-based approaches due to context-dependent gene regulation. We experimentally validated associations and demonstrated the extensibility of CWAS to additional epigenomic datasets and phenotypes, including response to prostate cancer treatment. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting transcriptional regulation.
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Affiliation(s)
- Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Cassandra Singler
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Soumya Zacharia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tunc Morova
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada
| | - Faraz Hach
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada
| | - Yi Ding
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA
| | | | - Jacob Anderson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - André P. Fay
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cynthia Kalita
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA
| | - Stefan Groha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Mark M. Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Victoria Wang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | | | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Nathan A. Lack
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada,School of Medicine, Koç University, Istanbul, Turkey
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA,Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Y. Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA,These authors jointly supervised this work. Correspondence should be directed to M.L.F or A.G. ()
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA,These authors jointly supervised this work. Correspondence should be directed to M.L.F or A.G. ()
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26
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Gregoricchio S, Polit L, Esposito M, Berthelet J, Delestré L, Evanno E, Diop M, Gallais I, Aleth H, Poplineau M, Zwart W, Rosenbauer F, Rodrigues-Lima F, Duprez E, Boeva V, Guillouf C. HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia. Nucleic Acids Res 2022; 50:7938-7958. [PMID: 35871293 PMCID: PMC9371914 DOI: 10.1093/nar/gkac613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.
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Affiliation(s)
- Sebastian Gregoricchio
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Lélia Polit
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
| | - Michela Esposito
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Laure Delestré
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Emilie Evanno
- Curie Institute , Inserm U830, F- 75005 Paris, France
| | - M’Boyba Diop
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Hanna Aleth
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | - Mathilde Poplineau
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | | | - Estelle Duprez
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Valentina Boeva
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
- Department of Computer Science and Department of Biology , ETH Zurich, 8092 Zurich , Switzerland
| | - Christel Guillouf
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
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27
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Linder S, Hoogstraat M, Stelloo S, Eickhoff N, Schuurman K, de Barros H, Alkemade M, Bekers EM, Severson TM, Sanders J, Huang CCF, Morova T, Altintas UB, Hoekman L, Kim Y, Baca SC, Sjostrom M, Zaalberg A, Hintzen DC, de Jong J, Kluin RJC, de Rink I, Giambartolomei C, Seo JH, Pasaniuc B, Altelaar M, Medema RH, Feng FY, Zoubeidi A, Freedman ML, Wessels LFA, Butler LM, Lack NA, van der Poel H, Bergman AM, Zwart W. Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence. Cancer Discov 2022; 12:2074-2097. [PMID: 35754340 PMCID: PMC7613567 DOI: 10.1158/2159-8290.cd-21-0576] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022]
Abstract
In prostate cancer, androgen receptor (AR)-targeting agents are very effective in various disease stages. However, therapy resistance inevitably occurs and little is known about how tumor cells adapt to bypass AR suppression. Here, we performed integrative multi-omics analyses on tissues isolated before and after 3 months of AR-targeting enzalutamide monotherapy from high-risk prostate cancer patients enrolled in a neoadjuvant clinical trial. Transcriptomic analyses demonstrated that AR inhibition drove tumors towards a neuroendocrine-like disease state. Additionally, epigenomic profiling revealed massive enzalutamide-induced reprogramming of pioneer factor FOXA1 - from inactive chromatin sites towards active cis-regulatory elements that dictate pro-survival signals. Notably, treatment-induced FOXA1 sites were enriched for circadian clock component ARNTL. Post-treatment ARNTL levels associated with poor outcome, and ARNTL knockout strongly decreased prostate cancer cell growth. Our data highlight a remarkable cistromic plasticity of FOXA1 following AR-targeted therapy, and revealed an acquired dependency on circadian regulator ARNTL, a novel candidate therapeutic target.
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Affiliation(s)
- Simon Linder
- The Netherlands Cancer Institute, Amsterdam, North Holland, Netherlands
| | | | - Suzan Stelloo
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Nils Eickhoff
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | - Elise M Bekers
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Joyce Sanders
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Tunc Morova
- University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Sylvan C Baca
- Hungarian Academy of Sciences, Boston, United States
| | - Martin Sjostrom
- University of California, San Francisco, San Francisco, United States
| | | | | | | | - Roelof J C Kluin
- The Netherlands Cancer Institute, Amsterdam, Noord-Holland, Netherlands
| | | | | | - Ji-Heui Seo
- Dana-Farber Cancer Institute, BOSTON, Massachusetts, United States
| | - Bogdan Pasaniuc
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | | | - Rene H Medema
- University Medical Center Utrecht, Amsterdam, Netherlands
| | - Felix Y Feng
- University of California, San Francisco, San Francisco, CA, United States
| | - Amina Zoubeidi
- University of British Columbia, Vancouver, British Colombia, Canada
| | | | | | - Lisa M Butler
- University of Adelaide, School of Medicine and Freemasons Foundation Centre for Men's Health, Adelaide, SA, Australia
| | - Nathan A Lack
- University of British Columbia, Vancouver, BC, Canada
| | | | | | - Wilbert Zwart
- Netherlands Cancer Institute, Amsterdam, Netherlands
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28
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Zaalberg A, Minnee E, Zwart W, Bergman AM. Abstract 1570: Macrophage mediated cell-kill evasion by human prostate cancer cells. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Macrophages can adopt a cytotoxic M1 phenotype which can eliminate cancer cells. However, despite the presence of macrophages in the prostate, prostate cancer (PCa) is a prevalent cancer in men. This suggests that PCa cells can evade M1 macrophage mediated cell-kill. We have shown that human THP-1 derived M1-like macrophages readily kill human prostate cancer LNCap cells, while in testosterone proficient conditions (Fraction Growth over Mono-culture (FGM): 0.1). However, in testosterone deprived conditions LNCap cells survive (FGM: 1.1). In addition, when exposed to M1-like macrophage conditioned medium, LNCap cells are killed in testosterone proficient conditions and not in depleted conditions (FGM: 0.2 and 0.7, respectively). This suggests that M1 macrophage mediated PCa cell-kill depends on Androgen Receptor (AR) signaling and the release of soluble factors by macrophages. This is supported by cell-kill of castration-resistant LNCap-abl cells with an AR amplification (FGM: 0.1) in testosterone deprived conditions and no cell-kill in both testosterone deprived and proficient conditions of castration resistant PC3 cells without AR expression when co-cultured with M1-like macrophages (FGM: 0.7 and 0.7. respectively). To dissect the mechanism of M1 macrophage mediated cell-kill evasion, a genome wide CRISPR knock-out screen was performed in LNCap cells in co-culture with M1-like macrophages. LNCap cells were transfected with the Brunello library and cultured in testosterone proficient conditions. After 72 hours of co-culture, cells were harvested and DNA was isolated and submitted for sequencing. After quality check analysis, five gene knock-outs with a significant (log2FcMedian >1.5) survival advantage were identified, AR, PRKCD (Protein Kinase C Delta), IKBKA (Inhibitor of nuclear factor kappa-B kinase subunit α:), IKBKB (Inhibitor of nuclear factor kappa-B kinase subunit β) and IKBKG (Inhibitor of nuclear factor kappa-B kinase subunit γ). The latter three genes are components of the IkB kinase (IKK) complex, which is essential for activation of members of the nuclear factor-kB (NFkB) family of transcription factors. The hits as identified in the CRISPR knock-out screen, were validated in single guide knock-out LNCap cells in co-culture with M1-like macrophages. Additionally, we have shown that AR signaling enhances PRKCD expression, both at the RNA and protein level. Moreover, expression of PRKCD is significantly lower in prostatectomy specimen of 56 patients treated for 3 months with the AR signalling inhibitor enzalutamide prior to surgery, than untreated matched controls. Furthermore, LNCap cells lacking PRKCD, IKBKB and IKBKG were significantly less affected in their growth by reactive oxygen species (H2O2) than non-targeting LNCap cells. Ongoing studies are aimed to dissect how these critical factors are interconnected in LNCap cells, M1 macrophage mediated cell-kill evasion as a result.
Citation Format: Anniek Zaalberg, Emma Minnee, Wilbert Zwart, Andries M. Bergman. Macrophage mediated cell-kill evasion by human prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1570.
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Affiliation(s)
| | - Emma Minnee
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Wilbert Zwart
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
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29
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Severson T, Qiu X, Alshalalfa M, Sjöström M, Quigley D, Bergman A, Long H, Feng F, Freedman ML, Zwart W, Pomerantz MM. Androgen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer. Clin Epigenetics 2022; 14:60. [PMID: 35509021 PMCID: PMC9069737 DOI: 10.1186/s13148-022-01278-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
The androgen receptor (AR) is a prostate master transcription factor. It binds to genetic enhancers, where it regulates gene activity and plays a fundamental role in prostate pathophysiology. Previous work has demonstrated that AR-DNA binding is systematically and consistently reprogrammed during prostate tumorigenesis and disease progression. We charted these reprogrammed AR sites and identified genes proximal to them. We were able to devise gene lists based on AR status within specific histological contexts: normal prostate epithelium, primary prostate tumor, and metastatic prostate cancer. We evaluated expression of the genes in these gene sets in subjects from two distinct clinical cohorts-men treated with surgery for localized prostate cancer and men with metastatic prostate cancer. Among men with localized prostate cancer, expression of genes proximal to AR sites lost in the transition from normal prostate to prostate tumor was associated with clinical outcome. Among men with metastatic disease, expression of genes proximal to AR sites gained in metastatic tumors was associated with clinical outcome. These results are consistent with the notion that AR is fundamental to both maintaining differentiation in normal prostate tissue and driving de-differentiation in advanced prostate cancer. More broadly, the study demonstrates the power of incorporating context-dependent epigenetic data into genetic analyses.
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Affiliation(s)
- Tesa Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.,Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - David Quigley
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Andries Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Felix Feng
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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30
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Kubler K, Nardone A, Anand S, Gorvich D, Droog M, Hermida-Prado F, Akshi T, Feit AS, Cohen G, Dackus G, Pun M, Kuang Y, Cha J, Miller M, Gibson WJ, Paweletz CP, Van Allen EM, van Leeuwen FE, Nederlof P, Hollema H, Nguyen QD, Mourits MJE, Leshchiner I, Stewart C, Matulonis UA, Zwart W, Maruvka YE, Getz G, Jeselsohn R. Abstract GS2-09: Tamoxifen instigates uterine cancer development by activating PI3K signaling and supersedes PIK3CA driver mutations. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-gs2-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tamoxifen is widely used in the adjuvant treatment of estrogen receptor–positive (ER+) breast cancer and is an important drug for pre-menopausal women and post-menopausal patients who cannot tolerate aromatase inhibitors. Despite the clear clinical benefit in improving relapse-free and overall survival in these patients, an adverse effect of tamoxifen is a 2- to 7-fold increased risk of uterine cancer (UC) after 2-5 years of treatment. To date, the mechanism of tamoxifen-driven tumorigenesis is not well understood, and preventive approaches are lacking. Here, to molecularly characterize tamoxifen-associated uterine cancers (TA-UCs) and gain insights into their unique evolution, we performed whole-exome sequencing of 21 TA-UCs (discovery cohort) and droplet digital PCR (ddPCR) of an additional 40 TA-UCs (validation cohort) obtained from the ‘Tamoxifen Associated Malignancies: Aspects of Risk’ (TAMARISK) study. In addition, we used in vivo mouse models to: (i) further investigate tamoxifen-activated molecular pathways that may be involved in TA-UC tumorigenesis; and (ii) offer mechanistic insights. Overall, we discovered that TA-UCs were genomically similar to non–TA-UCs from The Cancer Genome Atlas (TCGA) project, with one profound exception: TA-UCs are characterized by a lower-than-expected frequency of mutations in two highly prevalent UC driver genes in the PI3K pathway: PIK3CA (14% [3/21] vs 48% [265/554] in non–TA-UC; P=0.003, Fisher’s exact test; Q=0.02, Benjamini-Hochberg FDR) and PIK3R1 (0%, [0/21] vs 31% [174/554]; P=0.001; Q=0.01). We used ddPCR in the independent TA-UC validation cohort and confirmed the low frequency of mutations in PIK3CA (7.5% [3/40] vs 21% [144/685] in control UCs from the Dana-Farber contribution to the AACR GENIE project; P=0.04). We next performed mouse in vivo studies and demonstrated that tamoxifen activated the PI3K pathway and increased cell proliferation in normal mouse uterine tissue through paracrine and autocrine effects, both of which were abrogated by the PI3K inhibitor alpelisib. Taken together, we describe a distinct and novel pathway of carcinogenesis in which tamoxifen acts as a driver event in the uterus and promotes tumor development in a mutation-independent manner. Indeed, tamoxifen may increase the risk of UC by activating the PI3K pathway, which can substitute for the early acquisition of oncogenic PIK3CA or PIK3R1 mutations observed in non–TA-UC tumors. Furthermore, the ability of a PI3K inhibitor to reduce cell proliferation in our mouse model raises the possibility that downregulating the PI3K pathway may prevent or significantly reduce TA-UC development, offering a potential future therapeutic and prevention strategy for specific high-risk patients undergoing tamoxifen therapy.
Citation Format: Kirsten Kubler, Agostina Nardone, Shankara Anand, Daniel Gorvich, Marjolein Droog, Francisco Hermida-Prado, Tara Akshi, Avery S Feit, Gabriella Cohen, Gwen Dackus, Matthew Pun, Yanan Kuang, Justin Cha, Mendy Miller, William J Gibson, Cloud P Paweletz, Eliezer M Van Allen, Flora E van Leeuwen, Petra Nederlof, Harry Hollema, Quang-Dé Nguyen, Marian JE Mourits, Ignaty Leshchiner, Chip Stewart, Ursula A Matulonis, Wilbert Zwart, Yosef E Maruvka, Gad Getz, Rinath Jeselsohn. Tamoxifen instigates uterine cancer development by activating PI3K signaling and supersedes PIK3CA driver mutations [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS2-09.
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Affiliation(s)
| | | | | | | | | | | | - Tara Akshi
- Dana Farber Cancer Institute, Boston, MA
| | | | | | - Gwen Dackus
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wilbert Zwart
- Netherlands Cancer Institute, Amsterdam, Netherlands
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31
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Chen P, Turco S, Wijkstra H, Zwart W, Huang P, Mischi M. Biopsy-region-based multiparametric ultrasound imaging for prostate cancer localization. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00830-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Kneppers J, Bergman AM, Zwart W. Prostate Cancer Epigenetic Plasticity and Enhancer Heterogeneity: Molecular Causes, Consequences and Clinical Implications. Advances in Experimental Medicine and Biology 2022; 1390:255-275. [DOI: 10.1007/978-3-031-11836-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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33
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Manjón AG, Linder S, Teunissen H, Friskes A, Zwart W, de Wit E, Medema RH. Unexpected gene activation following CRISPR-Cas9-mediated genome editing. EMBO Rep 2021; 23:e53902. [PMID: 34927791 PMCID: PMC8811649 DOI: 10.15252/embr.202153902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
The discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its development as a genome editing tool has revolutionized the field of molecular biology. In the DNA damage field, CRISPR has brought an alternative to induce endogenous double-strand breaks (DSBs) at desired genomic locations and study the DNA damage response and its consequences. Many systems for sgRNA delivery have been reported in order to efficiently generate this DSB, including lentiviral vectors. However, some of the consequences of these systems are not yet well understood. Here, we report that lentiviral-based sgRNA vectors can integrate into the endogenous genomic target location, leading to undesired activation of the target gene. By generating a DSB in the regulatory region of the ABCB1 gene using a lentiviral sgRNA vector, we can induce the formation of Taxol-resistant colonies. We show that these colonies upregulate ABCB1 via integration of the EEF1A1 and the U6 promoters from the sgRNA vector. We believe that this is an unreported CRISPR/Cas9 on-target effect that researchers need to be aware of when using lentiviral vectors for genome editing.
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Affiliation(s)
- Anna G Manjón
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simon Linder
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Teunissen
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anoek Friskes
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elzo de Wit
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René H Medema
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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34
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Joosten SEP, Wellenstein M, Koornstra R, van Rossum A, Sanders J, van der Noort V, Ferrandez MC, Harkes R, Mandjes IAM, Rosing H, Huitema A, Beijnen JH, Wesseling J, van Diest PJ, Horlings HM, Linn SC, Zwart W. IHC-based Ki67 as response biomarker to tamoxifen in breast cancer window trials enrolling premenopausal women. NPJ Breast Cancer 2021; 7:138. [PMID: 34671036 PMCID: PMC8528844 DOI: 10.1038/s41523-021-00344-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 09/21/2021] [Indexed: 11/24/2022] Open
Abstract
Window studies are gaining traction to assess (molecular) changes in short timeframes. Decreased tumor cell positivity for the proliferation marker Ki67 is often used as a proxy for treatment response. Immunohistochemistry (IHC)-based Ki67 on tissue from neo-adjuvant trials was previously reported to be predictive for long-term response to endocrine therapy for breast cancer in postmenopausal women, but none of these trials enrolled premenopausal women. Nonetheless, the marker is being used on this subpopulation. We compared pathologist assessed IHC-based Ki67 in samples from pre- and postmenopausal women in a neo-adjuvant, endocrine therapy focused trial (NCT00738777), randomized between tamoxifen, anastrozole, or fulvestrant. These results were compared with (1) IHC-based Ki67 scoring by AI, (2) mitotic figures, (3) mRNA-based Ki67, (4) five independent gene expression signatures capturing proliferation, and (5) blood levels for tamoxifen and its metabolites as well as estradiol. Upon tamoxifen, IHC-based Ki67 levels were decreased in both pre- and postmenopausal breast cancer patients, which was confirmed using mRNA-based cell proliferation markers. The magnitude of decrease of Ki67 IHC was smaller in pre- versus postmenopausal women. We found a direct relationship between post-treatment estradiol levels and the magnitude of the Ki67 decrease in tumors. These data suggest IHC-based Ki67 may be an appropriate biomarker for tamoxifen response in premenopausal breast cancer patients, but anti-proliferative effect size depends on estradiol levels.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Rutger Koornstra
- Department of Internal Medicine and Medical Oncology, Rijnstate hospital, Arnhem, The Netherlands
| | - Annelot van Rossum
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vincent van der Noort
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maria C Ferrandez
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rolf Harkes
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ingrid A M Mandjes
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hilde Rosing
- Department of Pharmacy and Pharmacology, Antoni van Leeuwenhoek-The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alwin Huitema
- Department of Pharmacy and Pharmacology, Antoni van Leeuwenhoek-The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Clinical Pharmacy, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jos H Beijnen
- Department of Pharmacy and Pharmacology, Antoni van Leeuwenhoek-The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jelle Wesseling
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Centre, Utrecht, The Netherlands
| | - Hugo M Horlings
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Department of Pathology, University Medical Centre, Utrecht, The Netherlands. .,Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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Siefert JC, Cioni B, Muraro MJ, Alshalalfa M, Vivié J, van der Poel HG, Schoots IG, Bekers E, Feng FY, Wessels LFA, Zwart W, Bergman AM. The Prognostic Potential of Human Prostate Cancer-Associated Macrophage Subtypes as Revealed by Single-Cell Transcriptomics. Mol Cancer Res 2021; 19:1778-1791. [PMID: 34131070 PMCID: PMC9398107 DOI: 10.1158/1541-7786.mcr-20-0740] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/18/2020] [Accepted: 06/07/2021] [Indexed: 01/07/2023]
Abstract
Macrophages in the tumor microenvironment are causally linked with prostate cancer development and progression, yet little is known about their composition in neoplastic human tissue. By performing single cell transcriptomic analysis of human prostate cancer resident macrophages, three distinct populations were identified in the diseased prostate. Unexpectedly, no differences were observed between macrophages isolated from the tumorous and nontumorous portions of the prostatectomy specimens. Markers associated with canonical M1 and M2 macrophage phenotypes were identifiable, however these were not the main factors defining unique subtypes. The genes selectively associated with each macrophage cluster were used to develop a gene signature which was highly associated with both recurrence-free and metastasis-free survival. These results highlight the relevance of tissue-specific macrophage subtypes in the tumor microenvironment for prostate cancer progression and demonstrates the utility of profiling single-cell transcriptomics in human tumor samples as a strategy to design gene classifiers for patient prognostication. IMPLICATIONS: The specific macrophage subtypes present in a diseased human prostate have prognostic value, suggesting that the relative proportions of these populations are related to patient outcome. Understanding the relative contributions of these subtypes will not only inform patient prognostication, but will enable personalized immunotherapeutic strategies to increase beneficial populations or reduce detrimental populations.
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Affiliation(s)
- Joseph C Siefert
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bianca Cioni
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mauro J Muraro
- Single Cell Discoveries B.V., the Netherlands.,Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Judith Vivié
- Single Cell Discoveries B.V., the Netherlands.,Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands
| | - Henk G van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ivo G Schoots
- Department of Radiology and Nuclear Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elise Bekers
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Felix Y Feng
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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36
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van der Zande K, Oyen WJG, Zwart W, Bergman AM. Radium-223 Treatment of Patients with Metastatic Castration Resistant Prostate Cancer: Biomarkers for Stratification and Response Evaluation. Cancers (Basel) 2021; 13:cancers13174346. [PMID: 34503156 PMCID: PMC8431634 DOI: 10.3390/cancers13174346] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Radium-223 dichloride ([223Ra]RaCl2; Ra-223) is an alpha-emitting radiopharmaceutical treatment for patients with metastatic castration resistant prostate cancer (mCRPC) with predominantly bone metastases. While responses to chemotherapeutic and antihormonal mCRPC treatments can be assessed by serum PSA levels, a decrease of serum PSA levels is not expected during Ra-223 therapy. Moreover, radiographic evaluation of bone metastases response is challenging. Therefore, novel biomarkers to select patients for Ra-223 treatment and monitoring response are urgently needed. In this review, we discuss the currently used and exploratory biomarkers for this purpose, including soluble and cellular factors detected in the peripheral blood, genetic defects and radiographic assessments. We conclude that some biomarkers, including metabolic products of collagen degradation and novel PET scan techniques, might hold promise as predictors of response to Ra-223 treatment. However, these biomarkers have not been extensively studied. Consequently, currently, no biomarker has established a place in patient stratification and response evaluation. Abstract Radium-223 dichloride ([223Ra]RaCl2; Ra-223) is a targeted alpha-emitting radiopharmaceutical which results in an overall survival and health related quality of life (HRQoL) benefit in symptomatic patients with metastatic castration resistant prostate cancer (mCRPC) and predominantly bone metastasis. Although effective, options to select patients who will derive treatment benefit and to monitor and predict treatment outcomes are limited. PSA response and radiographic evaluation are commonly used in mCRPC treatment assessment but are not informative in Ra-223 treated patients. Consequently, there is a clear need for predictive and prognostic tools. In this review, we discuss the physiology of bone metastases and the mechanism of action and efficacy of Ra-223 treatment, as well as offering an outline of current innovative prognostic and predictive biomarkers.
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Affiliation(s)
- Kim van der Zande
- Department of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands;
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Wim J. G. Oyen
- Department of Nuclear Medicine, Rijnstate Hospital, Wagnerlaan 55, 6815 AD Arnhem, The Netherlands;
| | - Wilbert Zwart
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Correspondence: (W.Z.); (A.M.B.); Tel.: +31-2051-28156 (W.Z.); +31-2051-22569 (A.M.B.)
| | - Andries M. Bergman
- Department of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands;
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Correspondence: (W.Z.); (A.M.B.); Tel.: +31-2051-28156 (W.Z.); +31-2051-22569 (A.M.B.)
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37
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Prekovic S, Schuurman K, Mayayo-Peralta I, Manjón AG, Buijs M, Yavuz S, Wellenstein MD, Barrera A, Monkhorst K, Huber A, Morris B, Lieftink C, Chalkiadakis T, Alkan F, Silva J, Győrffy B, Hoekman L, van den Broek B, Teunissen H, Debets DO, Severson T, Jonkers J, Reddy T, de Visser KE, Faller W, Beijersbergen R, Altelaar M, de Wit E, Medema R, Zwart W. Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer. Nat Commun 2021; 12:4360. [PMID: 34272384 PMCID: PMC8285479 DOI: 10.1038/s41467-021-24537-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The glucocorticoid receptor (GR) regulates gene expression, governing aspects of homeostasis, but is also involved in cancer. Pharmacological GR activation is frequently used to alleviate therapy-related side-effects. While prior studies have shown GR activation might also have anti-proliferative action on tumours, the underpinnings of glucocorticoid action and its direct effectors in non-lymphoid solid cancers remain elusive. Here, we study the mechanisms of glucocorticoid response, focusing on lung cancer. We show that GR activation induces reversible cancer cell dormancy characterised by anticancer drug tolerance, and activation of growth factor survival signalling accompanied by vulnerability to inhibitors. GR-induced dormancy is dependent on a single GR-target gene, CDKN1C, regulated through chromatin looping of a GR-occupied upstream distal enhancer in a SWI/SNF-dependent fashion. These insights illustrate the importance of GR signalling in non-lymphoid solid cancer biology, particularly in lung cancer, and warrant caution for use of glucocorticoids in treatment of anticancer therapy related side-effects.
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Affiliation(s)
- Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna G Manjón
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark Buijs
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Selçuk Yavuz
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Max D Wellenstein
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alejandro Barrera
- Department of Biostatistics & Bioinformatics, and Centre for Genomic & Computational Biology, Duke University Medical Centre, Durham, NC, USA
| | - Kim Monkhorst
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne Huber
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Ben Morris
- Division of Molecular Carcinogenesis and Robotics and Screening Centre, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Robotics and Screening Centre, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Theofilos Chalkiadakis
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Balázs Győrffy
- Semmelweis University Department of Bioinformatics and 2nd Department of Pediatrics, Budapest, Hungary.,TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Liesbeth Hoekman
- Mass spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram van den Broek
- Division of Cell Biology and BioImaging Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Donna O Debets
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Tesa Severson
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Timothy Reddy
- Department of Biostatistics & Bioinformatics, and Centre for Genomic & Computational Biology, Duke University Medical Centre, Durham, NC, USA
| | - Karin E de Visser
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - William Faller
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening Centre, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten Altelaar
- Mass spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rene Medema
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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38
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Palit SAL, van Dorp J, Vis D, Lieftink C, Linder S, Beijersbergen R, Bergman AM, Zwart W, van der Heijden MS. A kinome-centered CRISPR-Cas9 screen identifies activated BRAF to modulate enzalutamide resistance with potential therapeutic implications in BRAF-mutated prostate cancer. Sci Rep 2021; 11:13683. [PMID: 34211036 PMCID: PMC8249522 DOI: 10.1038/s41598-021-93107-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022] Open
Abstract
Resistance to drugs targeting the androgen receptor (AR) signaling axis remains an important challenge in the treatment of prostate cancer patients. Activation of alternative growth pathways is one mechanism used by cancer cells to proliferate despite treatment, conferring drug resistance. Through a kinome-centered CRISPR-Cas9 screen in CWR-R1 prostate cancer cells, we identified activated BRAF signaling as a determinant for enzalutamide resistance. Combined pharmaceutical targeting of AR and MAPK signaling resulted in strong synergistic inhibition of cell proliferation. The association between BRAF activation and enzalutamide resistance was confirmed in two metastatic prostate cancer patients harboring activating mutations in the BRAF gene, as both patients were unresponsive to enzalutamide. Our findings suggest that co-targeting of the MAPK and AR pathways may be effective in patients with an activated MAPK pathway, particularly in patients harboring oncogenic BRAF mutations. These results warrant further investigation of the response to AR inhibitors in BRAF-mutated prostate tumors in clinical settings.
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Affiliation(s)
- Sander A L Palit
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Jeroen van Dorp
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Vis
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Cor Lieftink
- NKI Robotics and Screening Center and ScreeninC, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simon Linder
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- NKI Robotics and Screening Center and ScreeninC, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michiel S van der Heijden
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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39
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Pauletto E, Eickhoff N, Padrão NA, Blattner C, Zwart W. TRIMming Down Hormone-Driven Cancers: The Biological Impact of TRIM Proteins on Tumor Development, Progression and Prognostication. Cells 2021; 10:1517. [PMID: 34208621 PMCID: PMC8234875 DOI: 10.3390/cells10061517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
The tripartite motif (TRIM) protein family is attracting increasing interest in oncology. As a protein family based on structure rather than function, a plethora of biological activities are described for TRIM proteins, which are implicated in multiple diseases including cancer. With hormone-driven cancers being among the leading causes of cancer-related death, TRIM proteins have been described to portrait tumor suppressive or oncogenic activities in these tumor types. This review describes the biological impact of TRIM proteins in relation to hormone receptor biology, as well as hormone-independent mechanisms that contribute to tumor cell biology in prostate, breast, ovarian and endometrial cancer. Furthermore, we point out common functions of TRIM proteins throughout the group of hormone-driven cancers. An improved understanding of the biological impact of TRIM proteins in cancer may pave the way for improved prognostication and novel therapeutics, ultimately improving cancer care for patients with hormone-driven cancers.
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Affiliation(s)
- Eleonora Pauletto
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of Technology, PO-Box 3640, 76021 Karlsruhe, Germany;
| | - Nils Eickhoff
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands; (N.E.); (N.A.P.)
| | - Nuno A. Padrão
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands; (N.E.); (N.A.P.)
| | - Christine Blattner
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of Technology, PO-Box 3640, 76021 Karlsruhe, Germany;
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands; (N.E.); (N.A.P.)
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40
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van der Zande K, van der Noort V, Busard M, Hamberg P, Ras - van Spijk S, De Feijter J, Dezentjé VO, Tascilar M, Houtsma D, Beeker A, van den Berg HP, ten Oever D, Oving IM, Zwart W, Bergman AM. First results from a randomized phase II study of cabazitaxel (CBZ) versus an androgen receptor targeted agent (ARTA) in patients with poor-prognosis castration-resistant prostate cancer (mCRPC). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.5059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5059 Background: In the OSTRICh trial, poor-prognosis mCRPC patients were randomized between CBZ and ARTA, following progression on docetaxel (DOC) treatment. Methods: The OSTRICh trial is an open label, multicenter, phase IIb study. Patients with poor-prognosis mCRPC (visceral metastases AND/OR < 12 months responsive to androgen deprivation AND/OR progressing during or within 6 months after DOC completion), were randomized 1:1 between CBZ (25 mg/m2 IV Q3W and prednisone 2 d 5 mg PO) and ARTA (daily abiraterone 1000 mg and prednisone 2 d 5 mg PO OR enzalutamide 160 mg PO). Life prolonging therapy between DOC and randomization was not allowed. Primary endpoint was to establish the Clinical Benefit Rate (no radiotherapy, no ECOG PS increase ≥2, no change of therapy AND no radiological progression) at 12 weeks (CBR) in the study arms, while formal comparison of the CBR was a secondary endpoint. A Fisher Exact test was used to assess differences in rates and a log rank test to assess differences in progression free and overall survival. All time to event endpoints were estimated with the Kaplan-Meier method and censored at last follow-up. Results: A total of 106 patients were randomized, 53 in each arm. Baseline median age was 70 (IQR 67-75) years and PSA 79.4 (IQR 29.0 - 160) ng/ml. ECOG PS score was 0/1 in 99 (93%) and 2 in 7 (7%) patients. Al patients fulfilled the criteria for poor-prognosis disease. Thirty-six (34%) patients received DOC in the metastatic hormone sensitive stage, while 41 (39%) previously received ARTA. Twenty-six of 43 evaluable patients in the CBZ arm had clinical benefit at 12 weeks (CBR: 60%, 95% CI: 44%-75%) and 20 of 39 (CBR: 51%, 95% CI: 35%-68%) in the ARTA arm (p = 0.50). At 12 weeks, 30 of 34 (88%, 95% CI: 73% - 97%) patients in the CBZ arm and 24 of 36 (67%, 95% CI: 49% - 81%) patients in the ARTA arm had no radiological progression (p = 0.046). After a median follow-up of 16.4 months (95% CI: 13.6–27.8), a serum PSA decrease ≥50% from baseline was established in 12 (23%, 95% CI: 12% - 36%) and 26 (49%, 95% CI: 35% - 63%)(p = 0.008) patients treated with CBZ and ARTA, respectively. Median radiological progression free survival (rPFS) was 6.0 months (95%CI: 4.11-14.5) in the CBZ arm and 5.8 months (95% CI: 5.22-10.2) months in the ARTA arm (p = 0.5), while median overall survival (OS) was 15.3 months (95%CI 9.49-22.4) and 13.8 months (95%CI 11.7-16.4) in CBZ and ARTA treated patients, respectively (p = 0.8). Grade ≥3 adverse events (AEs) occurred in 15 (29%) and 8 (15%) of patients treated with CBZ and ARTA, respectively. Conclusions: No significant difference in CBR was established between CBZ and ARTA treated patients. However, at 12 weeks significantly more CBZ treated patients had no radiological progression, while ≥50% PSA response rates were higher in ARTA treated patients. Clinical trial information: NCT03295565.
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Affiliation(s)
| | | | - Milou Busard
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Paul Hamberg
- Franciscus Gasthuis & Vlietland, Rotterdam, Netherlands
| | | | - Jeantine De Feijter
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Vincent O. Dezentjé
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Wilbert Zwart
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Andre M. Bergman
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
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41
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Huang CCF, Lingadahalli S, Morova T, Ozturan D, Hu E, Yu IPL, Linder S, Hoogstraat M, Stelloo S, Sar F, van der Poel H, Altintas UB, Saffarzadeh M, Le Bihan S, McConeghy B, Gokbayrak B, Feng FY, Gleave ME, Bergman AM, Collins C, Hach F, Zwart W, Emberly E, Lack NA. Functional mapping of androgen receptor enhancer activity. Genome Biol 2021; 22:149. [PMID: 33975627 PMCID: PMC8112059 DOI: 10.1186/s13059-021-02339-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/02/2021] [Indexed: 01/22/2023] Open
Abstract
Background Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10–100× more binding sites than differentially expressed genes. It is unclear how or if these excess binding sites impact gene transcription. Results To characterize the regulatory logic of AR-mediated transcription, we generated a locus-specific map of enhancer activity by functionally testing all common clinical AR binding sites with Self-Transcribing Active Regulatory Regions sequencing (STARRseq). Only 7% of AR binding sites displayed androgen-dependent enhancer activity. Instead, the vast majority of AR binding sites were either inactive or constitutively active enhancers. These annotations strongly correlated with enhancer-associated features of both in vitro cell lines and clinical prostate cancer samples. Evaluating the effect of each enhancer class on transcription, we found that AR-regulated enhancers frequently interact with promoters and form central chromosomal loops that are required for transcription. Somatic mutations of these critical AR-regulated enhancers often impact enhancer activity. Conclusions Using a functional map of AR enhancer activity, we demonstrated that AR-regulated enhancers act as a regulatory hub that increases interactions with other AR binding sites and gene promoters.
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Affiliation(s)
- Chia-Chi Flora Huang
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Shreyas Lingadahalli
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Tunc Morova
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Dogancan Ozturan
- School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Eugene Hu
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Ivan Pak Lok Yu
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marlous Hoogstraat
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Funda Sar
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Henk van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Umut Berkay Altintas
- School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Mohammadali Saffarzadeh
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Stephane Le Bihan
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Brian McConeghy
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Bengul Gokbayrak
- School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Faraz Hach
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven, The Netherlands
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada. .,School of Medicine, Koç University, Istanbul, Turkey. .,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey.
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42
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Mayayo-Peralta I, Zwart W, Prekovic S. Duality of glucocorticoid action in cancer: tumor-suppressor or oncogene? Endocr Relat Cancer 2021; 28:R157-R171. [PMID: 33852423 DOI: 10.1530/erc-20-0489] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/14/2021] [Indexed: 11/08/2022]
Abstract
Glucocorticoid receptor (GR) is a key homeostatic regulator involved in governing immune response, neuro-integration, metabolism and lung function. In conjunction with its pivotal role in human biology, GR action is critically linked to the pathology of various disease types, including cancer. While pharmacological activation of GR has been used for the treatment of various liquid cancers, its role in solid cancers is less clearly defined and seems to be cancer-type dependent. This review focuses on the molecular aspects of GR biology, spanning the structural and functional basis of response to glucocorticoids, as well as how this transcription factor operates in cancer, including the implications in disease development, progression and drug resistance.
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Affiliation(s)
- Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
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43
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Kulik M, Bothe M, Kibar G, Fuchs A, Schöne S, Prekovic S, Mayayo-Peralta I, Chung HR, Zwart W, Helsen C, Claessens F, Meijsing SH. Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites. Nucleic Acids Res 2021; 49:3856-3875. [PMID: 33751115 PMCID: PMC8053126 DOI: 10.1093/nar/gkab185] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/16/2021] [Accepted: 03/12/2021] [Indexed: 12/22/2022] Open
Abstract
The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.
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Affiliation(s)
- Marina Kulik
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Melissa Bothe
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Gözde Kibar
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Alisa Fuchs
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
- Institute for Medical Bioinformatics and Biostatistics, Philipps University of Marburg, 35037, Marburg, Germany
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Christine Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
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44
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Almekinders MMM, Schaapveld M, Thijssen B, Visser LL, Bismeijer T, Sanders J, Isnaldi E, Hofland I, Mertz M, Wessels LFA, Broeks A, Hooijberg E, Zwart W, Lips EH, Desmedt C, Wesseling J. Breast adipocyte size associates with ipsilateral invasive breast cancer risk after ductal carcinoma in situ. NPJ Breast Cancer 2021; 7:31. [PMID: 33753731 PMCID: PMC7985299 DOI: 10.1038/s41523-021-00232-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/03/2021] [Indexed: 12/25/2022] Open
Abstract
Although ductal carcinoma in situ (DCIS) is a non-obligate precursor to ipsilateral invasive breast cancer (iIBC), most DCIS lesions remain indolent. Hence, overdiagnosis and overtreatment of DCIS is a major concern. There is an urgent need for prognostic markers that can distinguish harmless from potentially hazardous DCIS. We hypothesised that features of the breast adipose tissue may be associated with risk of subsequent iIBC. We performed a case-control study nested in a population-based DCIS cohort, consisting of 2658 women diagnosed with primary DCIS between 1989 and 2005, uniformly treated with breast conserving surgery (BCS) alone. We assessed breast adipose features with digital pathology (HALO®, Indica Labs) and related these to iIBC risk in 108 women that developed subsequent iIBC (cases) and 168 women who did not (controls) by conditional logistic regression, accounting for clinicopathological and immunohistochemistry variables. Large breast adipocyte size was significantly associated with iIBC risk (odds ratio (OR) 2.75, 95% confidence interval (95% CI) = 1.25-6.05). High cyclooxygenase (COX)-2 protein expression in the DCIS cells was also associated with subsequent iIBC (OR 3.70 (95% CI = 1.59-8.64). DCIS with both high COX-2 expression and large breast adipocytes was associated with a 12-fold higher risk (OR 12.0, 95% CI = 3.10-46.3, P < 0.001) for subsequent iIBC compared with women with smaller adipocyte size and low COX-2 expression. Large breast adipocytes combined with high COX-2 expression in DCIS is associated with a high risk of subsequent iIBC. Besides COX-2, adipocyte size has the potential to improve clinical management in patients diagnosed with primary DCIS.
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Affiliation(s)
- Mathilde M M Almekinders
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Michael Schaapveld
- Division of Psychosocial Research, Epidemiology and Biostatistics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lindy L Visser
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joyce Sanders
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Edoardo Isnaldi
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Internal Medicine and Medical Specialties, Università degli Studi di Genova, IT-16132, Genova, Italy
| | - Ingrid Hofland
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjolijn Mertz
- Bio-Imaging Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Erik Hooijberg
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Oncode Institute, Utrecht, The Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jelle Wesseling
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
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45
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Severson TM, Zhu Y, De Marzo AM, Jones T, Simons JW, Nelson WG, Yegnasubramanian S, Freedman ML, Wessels L, Bergman AM, Haffner MC, Zwart W. Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases. Mol Oncol 2021; 15:1942-1955. [PMID: 33576154 PMCID: PMC8253095 DOI: 10.1002/1878-0261.12923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/22/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
The epigenomic regulation of transcriptional programs in metastatic prostate cancer is poorly understood. We studied the epigenomic landscape of prostate cancer drivers using transcriptional profiling and ChIP‐seq in four clonal metastatic tumors derived from a single prostate cancer patient. Our epigenomic analyses focused on androgen receptor (AR), which is a key oncogenic driver in prostate cancer, the AR pioneer factor FOXA1, chromatin insulator CCCTC‐Binding Factor, as well as for modified histones H3K27ac and H3K27me3. The vast majority of AR binding sites were shared among healthy prostate, primary prostate cancer, and metastatic tumor samples, signifying core AR‐driven transcriptional regulation within the prostate cell lineage. Genes associated with core AR‐binding events were significantly enriched for essential genes in prostate cancer cell proliferation. Remarkably, the metastasis‐specific active AR binding sites showed no differential transcriptional output, indicating a robust transcriptional program across metastatic samples. Combined, our data reveal a core transcriptional program in clonal metastatic prostate cancer, despite epigenomic differences in the AR cistrome.
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Affiliation(s)
- Tesa M. Severson
- Division of OncogenomicsOncode InstituteNetherlands Cancer InstituteAmsterdamthe Netherlands
- Division of Molecular OncogenesisOncode InstituteNetherlands Cancer InstituteAmsterdamthe Netherlands
| | - Yanyun Zhu
- Division of OncogenomicsOncode InstituteNetherlands Cancer InstituteAmsterdamthe Netherlands
| | - Angelo M. De Marzo
- Sidney Kimmel Comprehensive Cancer CenterDepartment of PathologyBrady Urological InstituteJohns Hopkins School of MedicineBaltimoreMDUSA
| | - Tracy Jones
- Department of PathologyJohns Hopkins School of MedicineBaltimoreMDUSA
| | | | - William G. Nelson
- Sidney Kimmel Comprehensive Cancer CenterDepartment of PathologyBrady Urological InstituteJohns Hopkins School of MedicineBaltimoreMDUSA
| | | | - Matthew L. Freedman
- Department of Medical OncologyDana‐Farber Cancer InstituteHarvard Medical SchoolBostonMAUSA
- The Eli and Edythe L. Broad InstituteCambridgeMAUSA
| | - Lodewyk Wessels
- Division of Molecular OncogenesisOncode InstituteNetherlands Cancer InstituteAmsterdamthe Netherlands
| | - Andries M. Bergman
- Division of OncogenomicsOncode InstituteNetherlands Cancer InstituteAmsterdamthe Netherlands
- Department of Medical OncologyNetherlands Cancer InstituteAmsterdamthe Netherlands
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical ResearchFred Hutchinson Cancer Research CenterSeattleWAUSA
- Department of PathologyUniversity of WashingtonSeattleWAUSA
- Department of PathologyJohns Hopkins School of MedicineBaltimoreMDUSA
| | - Wilbert Zwart
- Division of OncogenomicsOncode InstituteNetherlands Cancer InstituteAmsterdamthe Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyEindhoventhe Netherlands
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Alsaleem M, Kurozumi S, Bhardwaj K, Monteiro C, Joosten SEP, Green AR, Fujii T, Shirabe K, Ellis IO, Rakha EA, Mongan NP, Heery DM, Zwart W, Oesterreich S, Johnston SJ. Abstract PS6-11: Targetable ERBB2 mutation status is an independent marker of adverse prognosis in estrogen receptor positive, ERBB2 non-amplified primary lobular breast carcinoma: Validation using a novel gene signature of HER2 activation. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps6-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Invasive lobular carcinoma (ILC) accounts for 10-15% of primary breast cancer and is typically ER+ and ERBB2 non-amplified. There is preclinical evidence that somatic ERBB2 mutation may provide an alternative and tractable mechanism for upregulation of HER2 activity in tumors that do not express HER2 by current clinical criteria. Using large public datasets, we previously demonstrated that targetable ERBB2 mutations are enriched in ILC versus invasive ductal carcinoma (IDC) and are an independent prognostic factor in ILC (HR=3.7, 95% CI 1.2-11.0; p=0.021)*. We next hypothesized that a gene expression signature incorporating HER2 activity due to ERBB2 mutation and / or amplification would validate the prognostic signal we found in ILC.
To derive a novel gene expression signature of HER2 activity that accounted for the effect of potentially targetable ERBB2 mutations in ERBB2 non-amplified tumors, we applied a weighted average difference method to gene expression data in cases from the METABRIC 2012 (N=1,980) and TCGA 2015 (N=817) cohorts. To compare our novel gene expression signature with an established signature of HER2 activity, we performed multivariate regression modeling of response to neratinib, a small molecule tyrosine kinase inhibitor of HER1, 2 and 4, using pharmacogenomic data accessed via the CellMinerCDB online portal.
We show that our novel HER2 pathway signature score uniquely enriches for ERBB2 mutated tumors. Using a Cox regression model and stratifying gene expression scores into upper versus lower quartiles, we were able to validate the prognostic signal of ERBB2 mutations in ILC tumors (HR for 10-year OS in ILC=2.3, 95% CI 1.04-5.05; p=0.040). In contrast, no relationship was found between ERBB2 mutation status or novel HER2 pathway enrichment score and patient outcome in cases of IDC.
We conclude that ERBB2 mutations that are enriched in ILC provide a robust biomarker of HER2 pathway activation and can be detected via gene expression signature. Novel clinical trials of HER2-targeted therapy in ERBB2 non-amplified primary ILC are warranted.
*Reference: Kurozumi S et al, Cancer Research 2019, 80(4) suppl: SABCS 2019 Abstract P1-18-06 and medRxiv 2020.01.24.20018622
Citation Format: Mansour Alsaleem, Sasagu Kurozumi, Kartikeya Bhardwaj, Cintia Monteiro, Stacey EP Joosten, Andrew R Green, Takaaki Fujii, Ken Shirabe, Ian O Ellis, Emad A Rakha, Nigel P Mongan, David M Heery, Wilbert Zwart, Steffi Oesterreich, Simon J Johnston. Targetable ERBB2 mutation status is an independent marker of adverse prognosis in estrogen receptor positive, ERBB2 non-amplified primary lobular breast carcinoma: Validation using a novel gene signature of HER2 activation [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS6-11.
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Affiliation(s)
| | | | | | | | | | | | - Takaaki Fujii
- 2Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ken Shirabe
- 2Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ian O Ellis
- 1University of Nottingham, Nottingham, United Kingdom
| | - Emad A Rakha
- 1University of Nottingham, Nottingham, United Kingdom
| | | | - David M Heery
- 1University of Nottingham, Nottingham, United Kingdom
| | - Wilbert Zwart
- 3Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Steffi Oesterreich
- 4Womens Cancer Research Center, UPMC Hillman Cancer Center and Magee-Women Research Institute, Pittsburgh, PA
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47
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Hickey TE, Selth LA, Chia KM, Laven-Law G, Milioli HH, Roden D, Jindal S, Hui M, Finlay-Schultz J, Ebrahimie E, Birrell SN, Stelloo S, Iggo R, Alexandrou S, Caldon CE, Abdel-Fatah TM, Ellis IO, Zwart W, Palmieri C, Sartorius CA, Swarbrick A, Lim E, Carroll JS, Tilley WD. The androgen receptor is a tumor suppressor in estrogen receptor-positive breast cancer. Nat Med 2021; 27:310-320. [PMID: 33462444 DOI: 10.1038/s41591-020-01168-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/03/2020] [Indexed: 01/28/2023]
Abstract
The role of the androgen receptor (AR) in estrogen receptor (ER)-α-positive breast cancer is controversial, constraining implementation of AR-directed therapies. Using a diverse, clinically relevant panel of cell-line and patient-derived models, we demonstrate that AR activation, not suppression, exerts potent antitumor activity in multiple disease contexts, including resistance to standard-of-care ER and CDK4/6 inhibitors. Notably, AR agonists combined with standard-of-care agents enhanced therapeutic responses. Mechanistically, agonist activation of AR altered the genomic distribution of ER and essential co-activators (p300, SRC-3), resulting in repression of ER-regulated cell cycle genes and upregulation of AR target genes, including known tumor suppressors. A gene signature of AR activity positively predicted disease survival in multiple clinical ER-positive breast cancer cohorts. These findings provide unambiguous evidence that AR has a tumor suppressor role in ER-positive breast cancer and support AR agonism as the optimal AR-directed treatment strategy, revealing a rational therapeutic opportunity.
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Affiliation(s)
- Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
- Freemason's Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Kee Ming Chia
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Heloisa H Milioli
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Roden
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Shalini Jindal
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Mun Hui
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Esmaeil Ebrahimie
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen N Birrell
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Suzan Stelloo
- Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Richard Iggo
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Institut Bergonié, University of Bordeaux, Bordeaux, France
| | - Sarah Alexandrou
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | | | | | - Wilbert Zwart
- Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Carlo Palmieri
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool & Clatterbridge Centre NHS Foundation Trust, Liverpool, UK
| | | | - Alex Swarbrick
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
- Freemason's Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia.
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48
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Haffner MC, Zwart W, Roudier MP, True LD, Nelson WG, Epstein JI, De Marzo AM, Nelson PS, Yegnasubramanian S. Genomic and phenotypic heterogeneity in prostate cancer. Nat Rev Urol 2021; 18:79-92. [PMID: 33328650 PMCID: PMC7969494 DOI: 10.1038/s41585-020-00400-w] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 02/07/2023]
Abstract
From a clinical, morphological and molecular perspective, prostate cancer is a heterogeneous disease. Primary prostate cancers are often multifocal, having topographically and morphologically distinct tumour foci. Sequencing studies have revealed that individual tumour foci can arise as clonally distinct lesions with no shared driver gene alterations. This finding demonstrates that multiple genomically and phenotypically distinct primary prostate cancers can be present in an individual patient. Lethal metastatic prostate cancer seems to arise from a single clone in the primary tumour but can exhibit subclonal heterogeneity at the genomic, epigenetic and phenotypic levels. Collectively, this complex heterogeneous constellation of molecular alterations poses obstacles for the diagnosis and treatment of prostate cancer. However, advances in our understanding of intra-tumoural heterogeneity and the development of novel technologies will allow us to navigate these challenges, refine approaches for translational research and ultimately improve patient care.
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Affiliation(s)
- Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Pathology, University of Washington, Seattle, WA, USA,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Lawrence D. True
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - William G. Nelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan I. Epstein
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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49
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Siersbæk R, Scabia V, Nagarajan S, Chernukhin I, Papachristou EK, Broome R, Johnston SJ, Joosten SEP, Green AR, Kumar S, Jones J, Omarjee S, Alvarez-Fernandez R, Glont S, Aitken SJ, Kishore K, Cheeseman D, Rakha EA, D'Santos C, Zwart W, Russell A, Brisken C, Carroll JS. IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis. Cancer Cell 2020; 38:412-423.e9. [PMID: 32679107 PMCID: PMC7116707 DOI: 10.1016/j.ccell.2020.06.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/20/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023]
Abstract
The cytokine interleukin-6 (IL6) and its downstream effector STAT3 constitute a key oncogenic pathway, which has been thought to be functionally connected to estrogen receptor α (ER) in breast cancer. We demonstrate that IL6/STAT3 signaling drives metastasis in ER+ breast cancer independent of ER. STAT3 hijacks a subset of ER enhancers to drive a distinct transcriptional program. Although these enhancers are shared by both STAT3 and ER, IL6/STAT3 activity is refractory to standard ER-targeted therapies. Instead, inhibition of STAT3 activity using the JAK inhibitor ruxolitinib decreases breast cancer invasion in vivo. Therefore, IL6/STAT3 and ER oncogenic pathways are functionally decoupled, highlighting the potential of IL6/STAT3-targeted therapies in ER+ breast cancer.
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Affiliation(s)
- Rasmus Siersbæk
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - Valentina Scabia
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sankari Nagarajan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Rebecca Broome
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Simon J Johnston
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK
| | - Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK
| | - Sanjeev Kumar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Julia Jones
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Soleilmane Omarjee
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Silvia Glont
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Sarah J Aitken
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Danya Cheeseman
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK
| | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Cathrin Brisken
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
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50
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Cioni B, Zaalberg A, van Beijnum JR, Melis MHM, van Burgsteden J, Muraro MJ, Hooijberg E, Peters D, Hofland I, Lubeck Y, de Jong J, Sanders J, Vivié J, van der Poel HG, de Boer JP, Griffioen AW, Zwart W, Bergman AM. Androgen receptor signalling in macrophages promotes TREM-1-mediated prostate cancer cell line migration and invasion. Nat Commun 2020; 11:4498. [PMID: 32908142 PMCID: PMC7481219 DOI: 10.1038/s41467-020-18313-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
The androgen receptor (AR) is the master regulator of prostate cancer (PCa) development, and inhibition of AR signalling is the most effective PCa treatment. AR is expressed in PCa cells and also in the PCa-associated stroma, including infiltrating macrophages. Macrophages have a decisive function in PCa initiation and progression, but the role of AR in macrophages remains largely unexplored. Here, we show that AR signalling in the macrophage-like THP-1 cell line supports PCa cell line migration and invasion in culture via increased Triggering Receptor Expressed on Myeloid cells-1 (TREM-1) signalling and expression of its downstream cytokines. Moreover, AR signalling in THP-1 and monocyte-derived macrophages upregulates IL-10 and markers of tissue residency. In conclusion, our data suggest that AR signalling in macrophages may support PCa invasiveness, and blocking this process may constitute one mechanism of anti-androgen therapy. Anti-androgen therapy inhibits prostate cancer (PC) progression, and is thought to act directly on cancer cells. Here the authors show that androgen receptor is expressed on normal and PC-associated macrophages, and its stimulation alters macrophage secretome to promote migration of cultured PC cell lines.
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Affiliation(s)
- Bianca Cioni
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Anniek Zaalberg
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Judy R van Beijnum
- Angiogenesis laboratory, Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Monique H M Melis
- Molecular Genetics, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | | | - Mauro J Muraro
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Erik Hooijberg
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Dennis Peters
- Core Facility Molecular Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Ingrid Hofland
- Core Facility Molecular Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Yoni Lubeck
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Jeroen de Jong
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Joyce Sanders
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Judith Vivié
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Henk G van der Poel
- Urology and Medical Oncology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Jan Paul de Boer
- Urology and Medical Oncology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Arjan W Griffioen
- Angiogenesis laboratory, Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. .,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands. .,, Oncode Institute, The Netherlands.
| | - Andries M Bergman
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. .,Urology and Medical Oncology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
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