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Patil A, Strom AR, Paulo JA, Collings CK, Ruff KM, Shinn MK, Sankar A, Cervantes KS, Wauer T, St Laurent JD, Xu G, Becker LA, Gygi SP, Pappu RV, Brangwynne CP, Kadoch C. A disordered region controls cBAF activity via condensation and partner recruitment. Cell 2023; 186:4936-4955.e26. [PMID: 37788668 PMCID: PMC10792396 DOI: 10.1016/j.cell.2023.08.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 10/06/2022] [Revised: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023]
Abstract
Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate that condensate formation and heterotypic interactions are distinct and separable features of an IDR within the ARID1A/B subunits of the mSWI/SNF chromatin remodeler, cBAF, and establish distinct "sequence grammars" underlying each contribution. Condensation is driven by uniformly distributed tyrosine residues, and partner interactions are mediated by non-random blocks rich in alanine, glycine, and glutamine residues. These features concentrate a specific cBAF protein-protein interaction network and are essential for chromatin localization and activity. Importantly, human disease-associated perturbations in ARID1B IDR sequence grammars disrupt cBAF function in cells. Together, these data identify IDR contributions to chromatin remodeling and explain how phase separation provides a mechanism through which both genomic localization and functional partner recruitment are achieved.
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Affiliation(s)
- Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Min Kyung Shinn
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Akshay Sankar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kasey S Cervantes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Wauer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Jessica D St Laurent
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Department of Obstetrics and Gynecology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Grace Xu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindsay A Becker
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 21044, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 21044, USA.
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2
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Strine MS, Cai WL, Wei J, Alfajaro MM, Filler RB, Biering SB, Sarnik S, Chow RD, Patil A, Cervantes KS, Collings CK, DeWeirdt PC, Hanna RE, Schofield K, Hulme C, Konermann S, Doench JG, Hsu PD, Kadoch C, Yan Q, Wilen CB. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLoS Biol 2023; 21:e3002097. [PMID: 37310920 PMCID: PMC10263356 DOI: 10.1371/journal.pbio.3002097] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 10/26/2022] [Accepted: 03/29/2023] [Indexed: 06/15/2023] Open
Abstract
Identifying host genes essential for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has the potential to reveal novel drug targets and further our understanding of Coronavirus Disease 2019 (COVID-19). We previously performed a genome-wide CRISPR/Cas9 screen to identify proviral host factors for highly pathogenic human coronaviruses. Few host factors were required by diverse coronaviruses across multiple cell types, but DYRK1A was one such exception. Although its role in coronavirus infection was previously undescribed, DYRK1A encodes Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A and is known to regulate cell proliferation and neuronal development. Here, we demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhancer, facilitating transcription and gene expression. Finally, we validate that the proviral activity of DYRK1A is conserved across species using cells of nonhuman primate and human origin. In summary, we report that DYRK1A is a novel regulator of ACE2 and DPP4 expression that may dictate susceptibility to multiple highly pathogenic human coronaviruses.
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Affiliation(s)
- Madison S. Strine
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Wesley L. Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Sylvia Sarnik
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ryan D. Chow
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kasey S. Cervantes
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Clayton K. Collings
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Peter C. DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ruth E. Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin Schofield
- Department of Chemistry and Biochemistry, College of Science, The University of Arizona, Tucson, Arizona, United States of America
| | - Christopher Hulme
- Department of Chemistry and Biochemistry, College of Science, The University of Arizona, Tucson, Arizona, United States of America
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona, United States of America
| | - Silvana Konermann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Patrick D. Hsu
- Arc Institute, Palo Alto, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
| | - Cigall Kadoch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
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3
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Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, Rodriguez Hernaez J, Lee S, Cervantes KS, Hinkley MM, Ntatsoulis K, Cesarano A, Hockemeyer K, Haining WN, Witkowski MT, Qi J, Tsirigos A, Perna F, Aifantis I, Kadoch C. Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion. Mol Cell 2023; 83:1216-1236.e12. [PMID: 36944333 PMCID: PMC10121856 DOI: 10.1016/j.molcel.2023.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 11/04/2022] [Revised: 01/11/2023] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Highly coordinated changes in gene expression underlie T cell activation and exhaustion. However, the mechanisms by which such programs are regulated and how these may be targeted for therapeutic benefit remain poorly understood. Here, we comprehensively profile the genomic occupancy of mSWI/SNF chromatin remodeling complexes throughout acute and chronic T cell stimulation, finding that stepwise changes in localization over transcription factor binding sites direct site-specific chromatin accessibility and gene activation leading to distinct phenotypes. Notably, perturbation of mSWI/SNF complexes using genetic and clinically relevant chemical strategies enhances the persistence of T cells with attenuated exhaustion hallmarks and increased memory features in vitro and in vivo. Finally, pharmacologic mSWI/SNF inhibition improves CAR-T expansion and results in improved anti-tumor control in vivo. These findings reveal the central role of mSWI/SNF complexes in the coordination of T cell activation and exhaustion and nominate small-molecule-based strategies for the improvement of current immunotherapy protocols.
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Affiliation(s)
- Elena Battistello
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kimberlee A Hixon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Dawn E Comstock
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xufeng Chen
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Javier Rodriguez Hernaez
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Soobeom Lee
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kasey S Cervantes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Madeline M Hinkley
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konstantinos Ntatsoulis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annamaria Cesarano
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kathryn Hockemeyer
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Matthew T Witkowski
- Department of Pediatrics-HemeOnc and Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Cambridge, MA, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, Office of Science & Research, NYU Grossman School of Medicine, New York, NY, USA
| | - Fabiana Perna
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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4
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Patil A, Strom AR, Collings CK, Paulo JA, Wauer T, Sankar A, St.Laurent JD, Cervantes KS, Gygi SP, Brangwynne CP, Kadoch C. Abstract 3485: Intrinsically disordered regions of the ARID1A/B tumor suppressors encode an interaction network within biomolecular condensates that directs mSWI/SNF chromatin remodeler complex activity. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3485] [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: 04/07/2023]
Abstract
Abstract
The mammalian SWI/SNF (mSWI/SNF or BAF) ATP-dependent chromatin remodeling complexes collectively represent one of the most frequently mutated cellular entities in cancer, second only to TP53. Mutations across the 29 human genes that encode mSWI/SNF complex subunits occur in over 20% of human cancers, with mutations affecting ARID1A and ARID1B, the largest BAF subunits, being the most frequent. However, the functional contributions of these subunits, particularly their commonly mutated N-terminal intrinsically disordered regions (IDRs) and a highly conserved ARID DNA-binding domain, to BAF function remain poorly understood. Here, we demonstrate that the IDRs of ARID1A/B, coupled with the ARID domain, drive biomolecular condensate formation and BAF chromatin localization in cells. We define ARID1A/B IDRs as two-part systems, facilitating homotypic BAF complex interactions (i.e., valence generated by localized condensation) and heterotypic complex interactions, that together establish a highly specific, sequence-encoded protein interaction network within condensates. Both types of interactions are required for appropriate genome-wide targeting of BAF complexes, DNA accessibility generation, and appropriate gene expression. Replacement of the ARID1A N-terminal IDR with IDRs derived from two unrelated proteins FUS and DDX4, rescues generic condensation of BAF but not chromatin occupancy, DNA accessibility, and heterotypic interactions, highlighting the sequence-specificity embedded in the IDR of ARID1A. Taken together, these data establish a role for the largest and most frequently perturbed IDRs within a major chromatin remodeler and explain how biomolecular condensate formation enables both genomic localization and functional partner recruitment. Furthermore, these findings lay the groundwork for mapping IDR sequence specificity or “grammar”, that dictates the co-condensation network formation, and suggests that targeted disruption of these mechanisms may represent new targeted therapeutic opportunities across multiple cancers.
Citation Format: Ajinkya Patil, Amy R. Strom, Clayton K. Collings, Joao A. Paulo, Tobias Wauer, Akshay Sankar, Jessica D. St.Laurent, Kasey S. Cervantes, Steven P. Gygi, Clifford P. Brangwynne, Cigall Kadoch. Intrinsically disordered regions of the ARID1A/B tumor suppressors encode an interaction network within biomolecular condensates that directs mSWI/SNF chromatin remodeler complex activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3485.
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Affiliation(s)
- Ajinkya Patil
- 1Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA
| | | | | | | | - Tobias Wauer
- 1Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA
| | - Akshay Sankar
- 1Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA
| | | | | | | | | | - Cigall Kadoch
- 1Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA
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