1
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Mojica EA, Fu Y, Kültz D. Salinity-responsive histone PTMs identified in the gills and gonads of Mozambique tilapia (Oreochromis mossambicus). BMC Genomics 2024; 25:586. [PMID: 38862901 PMCID: PMC11167857 DOI: 10.1186/s12864-024-10471-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Histone post-translational modifications (PTMs) are epigenetic marks that can be induced by environmental stress and elicit heritable patterns of gene expression. To investigate this process in an ecological context, we characterized the influence of salinity stress on histone PTMs within the gills, kidney, and testes of Mozambique tilapia (Oreochromis mossambicus). A total of 221 histone PTMs were quantified in each tissue sample and compared between freshwater-adapted fish exposed to salinity treatments that varied in intensity and duration. RESULTS Four salinity-responsive histone PTMs were identified in this study. When freshwater-adapted fish were exposed to seawater for two hours, the relative abundance of H1K16ub significantly increased in the gills. Long-term salinity stress elicited changes in both the gills and testes. When freshwater-adapted fish were exposed to a pulse of severe salinity stress, where salinity gradually increased from freshwater to a maximum of 82.5 g/kg, the relative abundance of H1S1ac significantly decreased in the gills. Under the same conditions, the relative abundance of both H3K14ac and H3K18ub decreased significantly in the testes of Mozambique tilapia. CONCLUSIONS This study demonstrates that salinity stress can alter histone PTMs in the gills and gonads of Mozambique tilapia, which, respectively, signify a potential for histone PTMs to be involved in salinity acclimation and adaptation in euryhaline fishes. These results thereby add to a growing body of evidence that epigenetic mechanisms may be involved in such processes.
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Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Sciences & Genome Center, University of California - Davis, One Shields Ave., Meyer Hall, Davis, CA, 95616, USA
| | - Yuhan Fu
- Department of Animal Sciences & Genome Center, University of California - Davis, One Shields Ave., Meyer Hall, Davis, CA, 95616, USA
| | - Dietmar Kültz
- Department of Animal Sciences & Genome Center, University of California - Davis, One Shields Ave., Meyer Hall, Davis, CA, 95616, USA.
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2
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Bursch KL, Goetz CJ, Jiao G, Nuñez R, Olp MD, Dhiman A, Khurana M, Zimmermann MT, Urrutia RA, Dykhuizen EC, Smith BC. Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression. J Biol Chem 2024; 300:107146. [PMID: 38460939 PMCID: PMC11002309 DOI: 10.1016/j.jbc.2024.107146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
The polybromo, brahma-related gene 1-associated factors (PBAF) chromatin remodeling complex subunit polybromo-1 (PBRM1) contains six bromodomains that recognize and bind acetylated lysine residues on histone tails and other nuclear proteins. PBRM1 bromodomains thus provide a link between epigenetic posttranslational modifications and PBAF modulation of chromatin accessibility and transcription. As a putative tumor suppressor in several cancers, PBRM1 protein expression is often abrogated by truncations and deletions. However, ∼33% of PBRM1 mutations in cancer are missense and cluster within its bromodomains. Such mutations may generate full-length PBRM1 variant proteins with undetermined structural and functional characteristics. Here, we employed computational, biophysical, and cellular assays to interrogate the effects of PBRM1 bromodomain missense variants on bromodomain stability and function. Since mutations in the fourth bromodomain of PBRM1 (PBRM1-BD4) comprise nearly 20% of all cancer-associated PBRM1 missense mutations, we focused our analysis on PBRM1-BD4 missense protein variants. Selecting 16 potentially deleterious PBRM1-BD4 missense protein variants for further study based on high residue mutational frequency and/or conservation, we show that cancer-associated PBRM1-BD4 missense variants exhibit varied bromodomain stability and ability to bind acetylated histones. Our results demonstrate the effectiveness of identifying the unique impacts of individual PBRM1-BD4 missense variants on protein structure and function, based on affected residue location within the bromodomain. This knowledge provides a foundation for drawing correlations between specific cancer-associated PBRM1 missense variants and distinct alterations in PBRM1 function, informing future cancer personalized medicine approaches.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Mallika Khurana
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul A Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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3
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Cochran AG, Flynn M. GNE-235: A Lead Compound Selective for the Second Bromodomain of PBRM1. J Med Chem 2023; 66:13116-13134. [PMID: 37702400 DOI: 10.1021/acs.jmedchem.3c01149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Bromodomains are acetyl-lysine binding modules that are found in different classes of chromatin-interacting proteins. Among these are large chromatin remodeling complexes such as BAF and PBAF (variants of human SWI/SNF). Previous work has identified chemical probes targeting a subset of the bromodomains present in the BAF and PBAF complexes. Selective inhibitors of the individual bromodomains have proven challenging to discover, as the domains are highly similar. Here, elaboration of an aminopyridazine scaffold used previously to develop probes for the bromodomains of SMARCA2, SMARCA4, and the fifth bromodomain of PBRM1 yielded compounds with both potency and unusual selectivity for the second bromodomain of PBRM1. One of these, GNE-235, and its enantiomer control GNE-234 are suggested for initial cellular investigations of the function of the second bromodomain of PBRM1.
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Affiliation(s)
- Andrea G Cochran
- Department of Biological Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Megan Flynn
- Department of Biological Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
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4
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De Silva SM, Dhiman A, Sood S, Mercedes KF, Simmons W, Henen M, Vögeli B, Dykhuizen E, Musselman C. PBRM1 bromodomains associate with RNA to facilitate chromatin association. Nucleic Acids Res 2023; 51:3631-3649. [PMID: 36808431 PMCID: PMC10164552 DOI: 10.1093/nar/gkad072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here, we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.
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Affiliation(s)
- Saumya M De Silva
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Kilsia F Mercedes
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - William J Simmons
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Catherine A Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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5
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Yao X, Hong JH, Nargund AM, Ng MSW, Heng HL, Li Z, Guan P, Sugiura M, Chu PL, Wang LC, Ye X, Qu J, Kwek XY, Lim JCT, Ooi WF, Koh J, Wang Z, Pan YF, Ong YS, Tan KY, Goh JY, Ng SR, Pignata L, Huang D, Lezhava A, Tay ST, Lee M, Yeo XH, Tam WL, Rha SY, Li S, Guccione E, Futreal A, Tan J, Yeong JPS, Hong W, Yauch R, Chang KTE, Sobota RM, Tan P, Teh BT. PBRM1-deficient PBAF complexes target aberrant genomic loci to activate the NF-κB pathway in clear cell renal cell carcinoma. Nat Cell Biol 2023; 25:765-777. [PMID: 37095322 DOI: 10.1038/s41556-023-01122-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 03/06/2023] [Indexed: 04/26/2023]
Abstract
PBRM1 encodes an accessory subunit of the PBAF SWI/SNF chromatin remodeller, and the inactivation of PBRM1 is a frequent event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodelling is not well examined. Here we show that, in VHL-deficient renal tumours, PBRM1 deficiency results in ectopic PBAF complexes that localize to de novo genomic loci, activating the pro-tumourigenic NF-κB pathway. PBRM1-deficient PBAF complexes retain the association between SMARCA4 and ARID2, but have loosely tethered BRD7. The PBAF complexes redistribute from promoter proximal regions to distal enhancers containing NF-κB motifs, heightening NF-κB activity in PBRM1-deficient models and clinical samples. The ATPase function of SMARCA4 maintains chromatin occupancy of pre-existing and newly acquired RELA specific to PBRM1 loss, activating downstream target gene expression. Proteasome inhibitor bortezomib abrogates RELA occupancy, suppresses NF-κB activation and delays growth of PBRM1-deficient tumours. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumourigenic NF-κB target genes by residual PBRM1-deficient PBAF complexes.
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Affiliation(s)
- Xiaosai Yao
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA.
| | - Jing Han Hong
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | | | - Michelle Shu Wen Ng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Hong Lee Heng
- National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Zhimei Li
- National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Peiyong Guan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Masahiro Sugiura
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Republic of Singapore
| | - Pek Lim Chu
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Xiaofen Ye
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - James Qu
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Xiu Yi Kwek
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Republic of Singapore
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wen Fong Ooi
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joanna Koh
- National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Zhenxun Wang
- Duke-NUS Medical School, Singapore, Republic of Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - You-Fu Pan
- National Cancer Centre Singapore, Singapore, Republic of Singapore
- Department of Medical Genetics, Zunyi Medical University, Zunyi, China
| | - Yan Shan Ong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Kiat-Yi Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Jian Yuan Goh
- Duke-NUS Medical School, Singapore, Republic of Singapore
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Republic of Singapore
| | - Sheng Rong Ng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Luca Pignata
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Dachuan Huang
- National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Alexander Lezhava
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Su Ting Tay
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Minghui Lee
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Xun Hui Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Sun Young Rha
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University Health System, Seoul, Republic of Korea
| | - Shang Li
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Ernesto Guccione
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Futreal
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Tan
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Robert Yauch
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Kenneth Tou-En Chang
- Duke-NUS Medical School, Singapore, Republic of Singapore
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Republic of Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Patrick Tan
- Duke-NUS Medical School, Singapore, Republic of Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore
| | - Bin Tean Teh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Duke-NUS Medical School, Singapore, Republic of Singapore.
- National Cancer Centre Singapore, Singapore, Republic of Singapore.
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
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6
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Yamashita N, Morimoto Y, Fushimi A, Ahmad R, Bhattacharya A, Daimon T, Haratake N, Inoue Y, Ishikawa S, Yamamoto M, Hata T, Akiyoshi S, Hu Q, Liu T, Withers H, Liu S, Shapiro GI, Yoshizumi T, Long MD, Kufe D. MUC1-C Dictates PBRM1-Mediated Chronic Induction of Interferon Signaling, DNA Damage Resistance, and Immunosuppression in Triple-Negative Breast Cancer. Mol Cancer Res 2023; 21:274-289. [PMID: 36445328 PMCID: PMC9975675 DOI: 10.1158/1541-7786.mcr-22-0772] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
The polybromo-1 (PBRM1) chromatin-targeting subunit of the SWI/SNF PBAF chromatin remodeling complex drives DNA damage resistance and immune evasion in certain cancer cells through mechanisms that remain unclear. STAT1 and IRF1 are essential effectors of type I and II IFN pathways. Here, we report that MUC1-C is necessary for PBRM1 expression and that it forms a nuclear complex with PBRM1 in triple-negative breast cancer (TNBC) cells. Analysis of global transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) profiles further demonstrated that MUC1-C and PBRM1 drive STAT1 and IRF1 expression by increasing chromatin accessibility of promoter-like signatures (PLS) on their respective genes. We also found that MUC1-C, PBRM1, and IRF1 increase the expression and chromatin accessibility on PLSs of the (i) type II IFN pathway IDO1 and WARS genes and (ii) type I IFN pathway RIG-I, MDA5, and ISG15 genes that collectively contribute to DNA damage resistance and immune evasion. In support of these results, targeting MUC1-C in wild-type BRCA TNBC cells enhanced carboplatin-induced DNA damage and the loss of self-renewal capacity. In addition, MUC1-C was necessary for DNA damage resistance, self-renewal, and tumorigenicity in olaparib-resistant BRCA1-mutant TNBC cells. Analysis of TNBC tumors corroborated that (i) MUC1 and PBRM1 are associated with decreased responsiveness to chemotherapy and (ii) MUC1-C expression is associated with the depletion of tumor-infiltrating lymphocytes (TIL). These findings demonstrate that MUC1-C activates PBRM1, and thereby chromatin remodeling of IFN-stimulated genes that promote chronic inflammation, DNA damage resistance, and immune evasion. IMPLICATIONS MUC1-C is necessary for PBRM1-driven chromatin remodeling in chronic activation of IFN pathway genes that promote DNA damage resistance and immunosuppression.
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Affiliation(s)
- Nami Yamashita
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Yoshihiro Morimoto
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Atsushi Fushimi
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Rehan Ahmad
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Atrayee Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Tatsuaki Daimon
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Naoki Haratake
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Yuka Inoue
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Ishikawa
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Masaaki Yamamoto
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Tsuyoshi Hata
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Sayuri Akiyoshi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Qiang Hu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Henry Withers
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mark D. Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
- Corresponding Authors: Donald Kufe, Dana-Farber Cancer Institute, 450 Brookline Avenue, D830, Boston, MA 02215. E-mail: ; and Mark D. Long,
| | - Donald Kufe
- Department of Medical Oncology, Dana-Farber Cancer Institute Harvard Medical School, Boston, Massachusetts
- Corresponding Authors: Donald Kufe, Dana-Farber Cancer Institute, 450 Brookline Avenue, D830, Boston, MA 02215. E-mail: ; and Mark D. Long,
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7
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Kufe D. Dependence on MUC1-C in Progression of Neuroendocrine Prostate Cancer. Int J Mol Sci 2023; 24:3719. [PMID: 36835130 PMCID: PMC9967814 DOI: 10.3390/ijms24043719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Castration resistant prostate cancer (CRPC) is responsive to androgen receptor (AR) axis targeted agents; however, patients invariably relapse with resistant disease that often progresses to neuroendocrine prostate cancer (NEPC). Treatment-related NEPC (t-NEPC) is highly aggressive with limited therapeutic options and poor survival outcomes. The molecular basis for NEPC progression remains incompletely understood. The MUC1 gene evolved in mammals to protect barrier tissues from loss of homeostasis. MUC1 encodes the transmembrane MUC1-C subunit, which is activated by inflammation and contributes to wound repair. However, chronic activation of MUC1-C contributes to lineage plasticity and carcinogenesis. Studies in human NEPC cell models have demonstrated that MUC1-C suppresses the AR axis and induces the Yamanaka OSKM pluripotency factors. MUC1-C interacts directly with MYC and activates the expression of the BRN2 neural transcription factor (TF) and other effectors, such as ASCL1, of the NE phenotype. MUC1-C also induces the NOTCH1 stemness TF in promoting the NEPC cancer stem cell (CSC) state. These MUC1-C-driven pathways are coupled with activation of the SWI/SNF embryonic stem BAF (esBAF) and polybromo-BAF (PBAF) chromatin remodeling complexes and global changes in chromatin architecture. The effects of MUC1-C on chromatin accessibility integrate the CSC state with the control of redox balance and induction of self-renewal capacity. Importantly, targeting MUC1-C inhibits NEPC self-renewal, tumorigenicity and therapeutic resistance. This dependence on MUC1-C extends to other NE carcinomas, such as SCLC and MCC, and identify MUC1-C as a target for the treatment of these aggressive malignancies with the anti-MUC1 agents now under clinical and preclinical development.
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Affiliation(s)
- Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
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8
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Walton J, Lawson K, Prinos P, Finelli A, Arrowsmith C, Ailles L. PBRM1, SETD2 and BAP1 - the trinity of 3p in clear cell renal cell carcinoma. Nat Rev Urol 2023; 20:96-115. [PMID: 36253570 DOI: 10.1038/s41585-022-00659-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 02/08/2023]
Abstract
Biallelic inactivation of the tumour suppressor gene Von Hippel-Lindau (VHL) occurs in the vast majority of clear cell renal cell carcinoma (ccRCC) instances, disrupting cellular oxygen-sensing mechanisms to yield a state of persistent pseudo-hypoxia, defined as a continued hypoxic response despite the presence of adequate oxygen levels. However, loss of VHL alone is often insufficient to drive oncogenesis. Results from genomic studies have shown that co-deletions of VHL with one (or more) of three genes encoding proteins involved in chromatin modification and remodelling, polybromo-1 gene (PBRM1), BRCA1-associated protein 1 (BAP1) and SET domain-containing 2 (SETD2), are common and important co-drivers of tumorigenesis. These genes are all located near VHL on chromosome 3p and are often altered following cytogenetic rearrangements that lead to 3p loss and precede the establishment of ccRCC. These three proteins have multiple roles in the regulation of crucial cancer-related pathways, including protection of genomic stability, antagonism of polycomb group (PcG) complexes to maintain a permissive transcriptional landscape in physiological conditions, and regulation of genes that mediate responses to immune checkpoint inhibitor therapy. An improved understanding of these mechanisms will bring new insights regarding cellular drivers of ccRCC growth and therapy response and, ultimately, will support the development of novel translational therapeutics.
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Affiliation(s)
- Joseph Walton
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Keith Lawson
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cheryl Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurie Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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9
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Unfolded protein response at the cross roads of tumourigenesis, oxygen sensing and drug resistance in clear cell renal cell carcinoma. Biochim Biophys Acta Rev Cancer 2022; 1877:188814. [DOI: 10.1016/j.bbcan.2022.188814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022]
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10
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Shishodia S, Nuñez R, Strohmier BP, Bursch KL, Goetz CJ, Olp MD, Jensen DR, Fenske TG, Ordonez-Rubiano SC, Blau ME, Roach MK, Peterson FC, Volkman BF, Dykhuizen EC, Smith BC. Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening. J Med Chem 2022; 65:13714-13735. [PMID: 36227159 PMCID: PMC9630929 DOI: 10.1021/acs.jmedchem.2c00864] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PBRM1 is a subunit of the PBAF chromatin remodeling complex that uniquely contains six bromodomains. PBRM1 can operate as a tumor suppressor or tumor promoter. PBRM1 is a tumor promoter in prostate cancer, contributing to migratory and immunosuppressive phenotypes. Selective chemical probes targeting PBRM1 bromodomains are desired to elucidate the association between aberrant PBRM1 chromatin binding and cancer pathogenesis and the contributions of PBRM1 to immunotherapy. Previous PBRM1 inhibitors unselectively bind SMARCA2 and SMARCA4 bromodomains with nanomolar potency. We used our protein-detected NMR screening pipeline to screen 1968 fragments against the second PBRM1 bromodomain, identifying 17 hits with Kd values from 45 μM to >2 mM. Structure-activity relationship studies on the tightest-binding hit resulted in nanomolar inhibitors with selectivity for PBRM1 over SMARCA2 and SMARCA4. These chemical probes inhibit the association of full-length PBRM1 to acetylated histone peptides and selectively inhibit growth of a PBRM1-dependent prostate cancer cell line.
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Affiliation(s)
- Shifali Shishodia
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Raymundo Nuñez
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Karina L Bursch
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Christopher J Goetz
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Michael D Olp
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Davin R Jensen
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Tyler G Fenske
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Maya E Blau
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Mallory K Roach
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Francis C Peterson
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F Volkman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brian C Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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11
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Kufe DW. Chronic activation of MUC1-C in wound repair promotes progression to cancer stem cells. JOURNAL OF CANCER METASTASIS AND TREATMENT 2022; 8. [PMID: 35539431 PMCID: PMC9083497 DOI: 10.20517/2394-4722.2022.03] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mucin 1 (MUC1) gene emerged in mammals to afford protection of barrier epithelial tissues from the external environment. MUC1 encodes a transmembrane C-terminal (MUC1-C) subunit that is activated by loss of homeostasis and induces inflammatory, proliferative, and remodeling pathways associated with wound repair. As a consequence, chronic activation of MUC1-C promotes lineage plasticity, epigenetic reprogramming, and carcinogenesis. In driving cancer progression, MUC1-C is imported into the nucleus, where it induces NF-κB inflammatory signaling and the epithelial-mesenchymal transition (EMT). MUC1-C represses gene expression by activating (i) DNA methyltransferase 1 (DNMT1) and DNMT3b, (ii) Polycomb Repressive Complex 1 (PRC1) and PRC2, and (iii) the nucleosome remodeling and deacetylase (NuRD) complex. PRC1/2-mediated gene repression is counteracted by the SWI/SNF chromatin remodeling complexes. MUC1-C activates the SWI/SNF BAF and PBAF complexes in cancer stem cell (CSC) models with the induction of genome-wide differentially accessible regions and expressed genes. MUC1-C regulates chromatin accessibility of enhancer-like signatures in association with the induction of the Yamanaka pluripotency factors and recruitment of JUN and BAF, which promote increases in histone activation marks and opening of chromatin. These and other findings described in this review have uncovered a pivotal role for MUC1-C in integrating lineage plasticity and epigenetic reprogramming, which are transient in wound repair and sustained in promoting CSC progression.
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Affiliation(s)
- Donald W Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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12
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Kenworthy CA, Haque N, Liou SH, Chandris P, Wong V, Dziuba P, Lavis LD, Liu WL, Singer RH, Coleman RA. Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. Biophys J 2022; 121:1738-1752. [PMID: 35364106 PMCID: PMC9117891 DOI: 10.1016/j.bpj.2022.03.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/20/2021] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Abstract
Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA polymerase II during transcriptional bursting. It is poorly understood how chromatin remodelers such as PBAF dynamically target different chromatin states inside a live cell. Our live-cell single-molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF's bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome-binding kinetic profiles that mimic chromatin stability. Removal of PBAF's bromodomains stabilizes H3.3 binding within chromatin, indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data suggests that PBAF's dynamic bromodomain-mediated engagement of a nucleosome may reflect the chromatin-remodeling potential of differentially bound chromatin states.
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Affiliation(s)
- Charles A Kenworthy
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Nayem Haque
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Shu-Hao Liou
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Panagiotis Chandris
- Section on High Resolution Optical Imaging, National Institute on Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Vincent Wong
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Patrycja Dziuba
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Wei-Li Liu
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Robert H Singer
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Robert A Coleman
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York.
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13
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Molecular features of primary hepatic undifferentiated carcinoma. Mod Pathol 2022; 35:680-687. [PMID: 34949765 DOI: 10.1038/s41379-021-00970-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022]
Abstract
The clinicopathological and molecular characteristics of primary hepatic undifferentiated carcinoma are poorly defined. It is speculated that primary hepatic undifferentiated carcinoma develops in the setting of preceding primary hepatic carcinoma. We investigated 14 primary hepatic undifferentiated carcinomas through targeted next-generation sequencing and immunohistochemistry. A panel of genes commonly mutated in primary liver carcinomas were examined. We found a similar clinical context as primary hepatic carcinoma, including a high prevalence of chronic viral hepatitis (86%), cirrhosis (57%), and elevated alpha-fetoprotein (29%). Tumors had sheet-like and poorly cohesive growth patterns. Rhabdoid cytomorphology was observed in four samples. Notably, the most common genetic mutations in primary hepatic undifferentiated carcinoma were in the promoter of TERT (n = 8, 57%) and TP53 (n = 8, 57%), which are common in hepatocellular carcinoma. The mutation rate of TP53 was elevated compared with hepatocellular carcinoma. No other typical genetic features of intrahepatic cholangiocarcinoma were identified, such as an IDH1/IDH2 mutation, FGFR2 fusions, or aberrant BAP1 expression. Furthermore, novel switch/sucrose nonfermenting complex inactivation was found, including SMARCA4/SMARCA2 (n = 1) and PBRM1 deficiency (n = 2). The three tumors demonstrated poorly cohesive histology, including rhabdoid features. High PD-L1 expression (57%) was observed in a majority of the tumors. Primary hepatic undifferentiated carcinoma shares clinical and genetic features with hepatocellular carcinoma but harbors progressive molecular characteristics that may initiate tumor dedifferentation. High PD-L1 expression in primary hepatic undifferentiated carcinoma may be a useful biomarker for potential immunotherapeutic strategies.
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14
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Antonios JP, Yalcin K, Darbinyan A, Koo A, Hong CS, DiLuna M, Erson-Omay Z. Biallelic inactivation of PBRM1 as a molecular driver in a rare pineoblastoma case: illustrative case. JOURNAL OF NEUROSURGERY: CASE LESSONS 2022; 3:CASE2213. [PMID: 36303510 PMCID: PMC9379698 DOI: 10.3171/case2213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pineoblastomas are a rare and aggressive pediatric neuroectodermal tumor subtype. Because of their rarity, pineoblastomas are still poorly understood, and there is little research delineating their molecular development and underlying genetic phenotype. Recent multiomic studies in pineoblastomas and pineal parenchymal tumors identified four clinically and biologically relevant consensus groups driven by signaling/processing pathways; however, molecular level alterations leading to these pathway changes are yet to be discovered, hence the importance of individually profiling every case of this rare tumor type. OBSERVATIONS The authors present the comprehensive somatic genomic profiling of a patient with pineoblastoma presenting with the loss of protein polybromo-1 (PBRM1) as a candidate genomic driver. Loss of PBRM1, a tumor suppressor, has been reported as a driver event in various cancer types, including renal cell carcinoma, bladder carcinoma, and meningiomas with papillary features. LESSONS This is the first report presenting biallelic loss of PBRM1 as a candidate molecular driver in relation to pineoblastoma.
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15
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Xiao Z, Locasale JW. Epigenomic links from metabolism-methionine and chromatin architecture. Curr Opin Chem Biol 2021; 63:11-18. [PMID: 33667809 PMCID: PMC9889272 DOI: 10.1016/j.cbpa.2021.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/12/2021] [Accepted: 01/31/2021] [Indexed: 02/03/2023]
Abstract
Chromatin and associated epigenetic marks provide important platforms for gene regulation in response to metabolic changes associated with environmental exposures, including physiological stress, nutritional deprivation, and starvation. Numerous studies have shown that fluctuations of key metabolites can influence chromatin modifications, but their effects on chromatin structure (e.g. chromatin compaction, nucleosome arrangement, and chromatin loops) and how they appropriately deposit specific chemical modification on chromatin are largely unknown. Here, focusing on methionine metabolism, we discuss recent developments of metabolic effects on chromatin modifications and structure, as well as consequences on gene regulation.
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Affiliation(s)
- Zhengtao Xiao
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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16
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Hagiwara M, Fushimi A, Yamashita N, Bhattacharya A, Rajabi H, Long MD, Yasumizu Y, Oya M, Liu S, Kufe D. MUC1-C activates the PBAF chromatin remodeling complex in integrating redox balance with progression of human prostate cancer stem cells. Oncogene 2021; 40:4930-4940. [PMID: 34163028 PMCID: PMC8321896 DOI: 10.1038/s41388-021-01899-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/20/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022]
Abstract
The polybromo-associated PBAF (SWI/SNF) chromatin remodeling complex, which includes PBRM1, ARID2, and BRD7, regulates cell differentiation and genomic integrity. MUC1-C is an oncogenic protein that drives lineage plasticity in prostate cancer (PC) progression. The present work demonstrates that MUC1-C induces PBRM1, ARID2, and BRD7 expression by the previously unrecognized E2F1-mediated activation of their respective promoters. The functional significance of the MUC1-C→PBAF pathway is supported by demonstrating involvement of MUC1-C in associating with nuclear PBAF and driving the NRF2 antioxidant gene transcriptome in PC cells. Mechanistically, MUC1-C forms a complex with NRF2 and PBRM1 on the NRF2 target SLC7A11 gene that encodes the xCT cystine-glutamate antiporter, increases chromatin accessibility and induces SLC7A11/xCT expression. We also show that MUC1-C and PBRM1 are necessary for induction of other NRF2 target genes, including G6PD and PGD that regulate the pentose phosphate pathway. Our results further demonstrate that MUC1-C integrates activation of PBRM1 with the regulation of antioxidant genes, ROS levels, pluripotency factor expression and the cancer stem cell (CSC) state. These findings reveal a role for MUC1-C in regulating PBAF, redox balance and lineage plasticity of PC CSC progression. Our findings also uncover involvement of MUC1-C in integrating the PBAF and BAF pathways in cancer.
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Affiliation(s)
- Masayuki Hagiwara
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nami Yamashita
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Hasan Rajabi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yota Yasumizu
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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17
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Chabanon RM, Morel D, Eychenne T, Colmet-Daage L, Bajrami I, Dorvault N, Garrido M, Meisenberg C, Lamb A, Ngo C, Hopkins SR, Roumeliotis TI, Jouny S, Hénon C, Kawai-Kawachi A, Astier C, Konde A, Del Nery E, Massard C, Pettitt SJ, Margueron R, Choudhary JS, Almouzni G, Soria JC, Deutsch E, Downs JA, Lord CJ, Postel-Vinay S. PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer. Cancer Res 2021; 81:2888-2902. [PMID: 33888468 DOI: 10.1158/0008-5472.can-21-0628] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Inactivation of Polybromo 1 (PBRM1), a specific subunit of the PBAF chromatin remodeling complex, occurs frequently in cancer, including 40% of clear cell renal cell carcinomas (ccRCC). To identify novel therapeutic approaches to targeting PBRM1-defective cancers, we used a series of orthogonal functional genomic screens that identified PARP and ATR inhibitors as being synthetic lethal with PBRM1 deficiency. The PBRM1/PARP inhibitor synthetic lethality was recapitulated using several clinical PARP inhibitors in a series of in vitro model systems and in vivo in a xenograft model of ccRCC. In the absence of exogenous DNA damage, PBRM1-defective cells exhibited elevated levels of replication stress, micronuclei, and R-loops. PARP inhibitor exposure exacerbated these phenotypes. Quantitative mass spectrometry revealed that multiple R-loop processing factors were downregulated in PBRM1-defective tumor cells. Exogenous expression of the R-loop resolution enzyme RNase H1 reversed the sensitivity of PBRM1-deficient cells to PARP inhibitors, suggesting that excessive levels of R-loops could be a cause of this synthetic lethality. PARP and ATR inhibitors also induced cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) innate immune signaling in PBRM1-defective tumor cells. Overall, these findings provide the preclinical basis for using PARP inhibitors in PBRM1-defective cancers. SIGNIFICANCE: This study demonstrates that PARP and ATR inhibitors are synthetic lethal with the loss of PBRM1, a PBAF-specific subunit, thus providing the rationale for assessing these inhibitors in patients with PBRM1-defective cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/11/2888/F1.large.jpg.
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MESH Headings
- Animals
- Apoptosis
- Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Proliferation
- DNA Repair
- DNA-Binding Proteins/deficiency
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Synthetic Lethal Mutations
- Transcription Factors/deficiency
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Roman M Chabanon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Thomas Eychenne
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Léo Colmet-Daage
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicolas Dorvault
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Cornelia Meisenberg
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Carine Ngo
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Suzanna R Hopkins
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Samuel Jouny
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | | | - Clémence Astier
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Asha Konde
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | | | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Raphaël Margueron
- Institut Curie, PSL Research University, INSERM Unit U934, CNRS UMR 3215, Paris, France
| | - Jyoti S Choudhary
- Functional Proteomics Team, The Institute of Cancer Research, London, United Kingdom
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR 3664, Equipe Labellisée Ligue contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris-VI, CNRS, UMR3664, Paris, France
| | - Jean-Charles Soria
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Eric Deutsch
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- INSERM UMR1030 Molecular Radiotherapy and Therapeutic Innovations, Gustave Roussy, Villejuif, France
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France.
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
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18
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Liu T, Xia Q, Zhang H, Wang Z, Yang W, Gu X, Hou T, Chen Y, Pei X, Zhu G, He D, Li L, Xu S. CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients. Aging (Albany NY) 2020; 12:21809-21836. [PMID: 33177244 PMCID: PMC7695370 DOI: 10.18632/aging.103999] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
We investigated the mechanisms affecting tumor progression and survival outcomes in Polybromo-1-mutated (PBRM1MUT) clear cell renal cell carcinoma (ccRCC) patients. PBRM1MUT ccRCC tissues contained higher numbers of mast cells and lower numbers of CD8+ and CD4+ T cells than tissues from PBRM1WT ccRCC patients. Hierarchical clustering, pathway enrichment and GSEA analyses demonstrated that PBRM1 mutations promote tumor progression by activating hypoxia inducible factor (HIF)-related signaling pathways and increasing expression of vascular endothelial growth factor family genes. PBRM1MUT ccRCC tissues also show increased expression of C-C motif chemokine ligand 5 (CCL5). PBRM1-silenced ccRCC cells exhibited greater Matrigel tube formation and cell proliferation than controls. In addition, HMC-1 human mast cells exhibited CCL5-dependent in vitro migration on Transwell plates. High CCL5 expression in PBRM1MUT ccRCC patients correlated with increased expression of genes encoding IFN-γ, IFN-α, IL-6, JAK-STAT3, TNF-α, and NF-ΚB. Moreover, high CCL5 expression was associated with poorer survival outcomes in ccRCC patients. These findings demonstrate that CCL5-dependent mast cell infiltration promotes immunosuppression within the tumor microenvironment, resulting in tumor progression and adverse survival outcomes in PBRM1MUT ccRCC patients.
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Affiliation(s)
- Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Qing Xia
- Department of Oncology, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai Cancer Institute, Shanghai 200127, P.R. China
| | - Haibao Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Zixi Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Wenjie Yang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Xiaoyun Gu
- Shaanxi Health Information Center, Health Commission of Shaanxi Province, Xi'an 710061, Shaanxi, P.R. China
| | - Tao Hou
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Yule Chen
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Xinqi Pei
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Guodong Zhu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Dalin He
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Shan Xu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
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19
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Chen M, Wen T, Horn HT, Chandrahas VK, Thapa N, Choi S, Cryns VL, Anderson RA. The nuclear phosphoinositide response to stress. Cell Cycle 2020; 19:268-289. [PMID: 31902273 PMCID: PMC7028212 DOI: 10.1080/15384101.2019.1711316] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accumulating evidence reveals that nuclear phosphoinositides (PIs) serve as central signaling hubs that control a multitude of nuclear processes by regulating the activity of nuclear proteins. In response to cellular stressors, PIs accumulate in the nucleus and multiple PI isomers are synthesized by the actions of PI-metabolizing enzymes, kinases, phosphatases and phospholipases. By directly interacting with effector proteins, phosphoinositide signals transduce changes in cellular functions. Here we describe nuclear phosphoinositide signaling in multiple sub-nuclear compartments and summarize the literature that demonstrates roles for specific kinases, phosphatases, and phospholipases in the orchestration of nuclear phosphoinositide signaling in response to cellular stress. Additionally, we discuss the specific PI-protein complexes through which these lipids execute their functions by regulating the configuration, stability, and transcription activity of their effector proteins. Overall, our review provides a detailed landscape of the current understanding of the nuclear PI-protein interactome and its role in shaping the coordinated response to cellular stress.
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Affiliation(s)
- Mo Chen
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Tianmu Wen
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hudson T. Horn
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Narendra Thapa
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Suyong Choi
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Vincent L. Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Richard A. Anderson
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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20
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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