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Stoler-Barak L, Schmiedel D, Sarusi-Portuguez A, Rogel A, Blecher-Gonen R, Haimon Z, Stopka T, Shulman Z. SMARCA5-mediated chromatin remodeling is required for germinal center formation. J Exp Med 2024; 221:e20240433. [PMID: 39297882 PMCID: PMC11413417 DOI: 10.1084/jem.20240433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/19/2024] [Accepted: 08/15/2024] [Indexed: 09/26/2024] Open
Abstract
The establishment of long-lasting immunity against pathogens is facilitated by the germinal center (GC) reaction, during which B cells increase their antibody affinity and differentiate into antibody-secreting cells (ASC) and memory cells. These events involve modifications in chromatin packaging that orchestrate the profound restructuring of gene expression networks that determine cell fate. While several chromatin remodelers were implicated in lymphocyte functions, less is known about SMARCA5. Here, using ribosomal pull-down for analyzing translated genes in GC B cells, coupled with functional experiments in mice, we identified SMARCA5 as a key chromatin remodeler in B cells. While the naive B cell compartment remained unaffected following conditional depletion of Smarca5, effective proliferation during B cell activation, immunoglobulin class switching, and as a result GC formation and ASC differentiation were impaired. Single-cell multiomic sequencing analyses revealed that SMARCA5 is crucial for facilitating the transcriptional modifications and genomic accessibility of genes that support B cell activation and differentiation. These findings offer novel insights into the functions of SMARCA5, which can be targeted in various human pathologies.
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Affiliation(s)
- Liat Stoler-Barak
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dominik Schmiedel
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Avital Sarusi-Portuguez
- Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ronnie Blecher-Gonen
- The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Zhana Haimon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tomas Stopka
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
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2
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Sun X, Nagahama Y, Singh SK, Kozakai Y, Nabeshima H, Fukushima K, Tanaka H, Motooka D, Fukui E, Vivier E, Diez D, Akira S. Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2-dependent transcription of Ifng. Immunity 2024; 57:1360-1377.e13. [PMID: 38821052 DOI: 10.1016/j.immuni.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/31/2023] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Limited infiltration and activity of natural killer (NK) and T cells within the tumor microenvironment (TME) correlate with poor immunotherapy responses. Here, we examined the role of the endonuclease Regnase-1 on NK cell anti-tumor activity. NK cell-specific deletion of Regnase-1 (Reg1ΔNK) augmented cytolytic activity and interferon-gamma (IFN-γ) production in vitro and increased intra-tumoral accumulation of Reg1ΔNK-NK cells in vivo, reducing tumor growth dependent on IFN-γ. Transcriptional changes in Reg1ΔNK-NK cells included elevated IFN-γ expression, cytolytic effectors, and the chemokine receptor CXCR6. IFN-γ induced expression of the CXCR6 ligand CXCL16 on myeloid cells, promoting further recruitment of Reg1ΔNK-NK cells. Mechanistically, Regnase-1 deletion increased its targets, the transcriptional regulators OCT2 and IκBζ, following interleukin (IL)-12 and IL-18 stimulation, and the resulting OCT2-IκBζ-NF-κB complex induced Ifng transcription. Silencing Regnase-1 in human NK cells increased the expression of IFNG and POU2F2. Our findings highlight NK cell dysfunction in the TME and propose that targeting Regnase-1 could augment active NK cell persistence for cancer immunotherapy.
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Affiliation(s)
- Xin Sun
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Quantitative Immunology Unit, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yasuharu Nagahama
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Host Defense Laboratory, Immunology Unit, Department of Medical Innovations, Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Co. Ltd., 5-1-35 Saito-aokita, Minoh, Osaka 562-0029, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shailendra Kumar Singh
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuuki Kozakai
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Nabeshima
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Host Defense Laboratory, Immunology Unit, Department of Medical Innovations, Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Co. Ltd., 5-1-35 Saito-aokita, Minoh, Osaka 562-0029, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kiyoharu Fukushima
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroki Tanaka
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- NGS Core Facility of the Genome Information Research Center, RIMD, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eriko Fukui
- Department of General Thoracic Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eric Vivier
- Aix-Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille-Luminy, Marseille, France; Innate Pharma Research Laboratories, Marseille, France; APHM, Hôpital de la Timone, Marseille-Immunopole, Marseille, France
| | - Diego Diez
- Quantitative Immunology Unit, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Center for Advanced Modalities and Drug Delivery System (CAMaD), Osaka University, 2-8 Yamada-oka, Suita, Osaka 565-0871, Japan.
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3
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Ee LS, Medina-Cano D, Uyehara CM, Schwarz C, Goetzler E, Salataj E, Polyzos A, Madhuranath S, Evans T, Hadjantonakis AK, Apostolou E, Vierbuchen T, Stadtfeld M. Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596630. [PMID: 38854146 PMCID: PMC11160813 DOI: 10.1101/2024.05.30.596630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The molecular mechanisms that drive essential developmental patterning events in the mammalian embryo remain poorly understood. To generate a conceptual framework for gene regulatory processes during germ layer specification, we analyzed transcription factor (TF) expression kinetics around gastrulation and during in vitro differentiation. This approach identified Otx2 as a candidate regulator of definitive endoderm (DE), the precursor of all gut- derived tissues. Analysis of multipurpose degron alleles in gastruloid and directed differentiation models revealed that loss of OTX2 before or after DE specification alters the expression of core components and targets of specific cellular signaling pathways, perturbs adhesion and migration programs as well as de-represses regulators of other lineages, resulting in impaired foregut specification. Key targets of OTX2 are conserved in human DE. Mechanistically, OTX2 is required to establish chromatin accessibility at candidate enhancers, which regulate genes critical to establishing an anterior cell identity in the developing gut. Our results provide a working model for the progressive establishment of spatiotemporal cell identity by developmental TFs across germ layers and species, which may facilitate the generation of gut cell types for regenerative medicine applications.
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Affiliation(s)
- LS Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - D Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - CM Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - C Schwarz
- Emerald Cloud Lab, Austin, TX 78728 USA
| | - E Goetzler
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - E Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - A Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - S Madhuranath
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - T Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - AK Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - E Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - T Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - M Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
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4
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Wright NE, Kennedy DE, Ai J, Veselits ML, Attaway M, Yoon YM, Durkee MS, Veselits J, Maienschein-Cline M, Mandal M, Clark MR. BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591154. [PMID: 38712068 PMCID: PMC11071454 DOI: 10.1101/2024.04.25.591154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Germinal center (GC) B cells segregate into three subsets that compartmentalize the antagonistic molecular programs of selection, proliferation, and somatic hypermutation. In bone marrow, the epigenetic reader BRWD1 orchestrates and insulates the sequential stages of cell proliferation and Igk recombination. We hypothesized BRWD1 might play similar insulative roles in the periphery. In Brwd1 -/- follicular B cells, GC initiation and class switch recombination following immunization were inhibited. In contrast, in Brwd1 -/- GC B cells there was admixing of chromatin accessibility across GC subsets and transcriptional dysregulation including induction of inflammatory pathways. This global molecular GC dysregulation was associated with specific defects in proliferation, affinity maturation, and tolerance. These data suggest that GC subset identity is required for some but not all GC-attributed functions. Furthermore, these data demonstrate a central role for BRWD1 in orchestrating epigenetic transitions at multiple steps along B cell developmental and activation pathways.
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5
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Barisic D, Chin CR, Meydan C, Teater M, Tsialta I, Mlynarczyk C, Chadburn A, Wang X, Sarkozy M, Xia M, Carson SE, Raggiri S, Debek S, Pelzer B, Durmaz C, Deng Q, Lakra P, Rivas M, Steidl C, Scott DW, Weng AP, Mason CE, Green MR, Melnick A. ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis. Cancer Cell 2024; 42:583-604.e11. [PMID: 38458187 PMCID: PMC11407687 DOI: 10.1016/j.ccell.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/20/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. We show that ARID1A orchestrates B cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD40 signaling. The absence of ARID1A tilts GC cell fate toward immature IgM+CD80-PD-L2- memory B cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas (FLs) in mice. Patients with FL with ARID1A-inactivating mutations preferentially display an immature memory B cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive ARID1A-mutant lymphomas through the formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.
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Affiliation(s)
- Darko Barisic
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt Teater
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ioanna Tsialta
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Coraline Mlynarczyk
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xuehai Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Margot Sarkozy
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sandra E Carson
- Department of Biochemistry, Cell and Molecular Biology, Weill Cornell Medicine, New York, NY, USA
| | - Santo Raggiri
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sonia Debek
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Benedikt Pelzer
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priya Lakra
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Rivas
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Sylvester Comprehensive Cancer Center, University of Miami, FL, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, British Columbia, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, British Columbia, Vancouver, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael R Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ari Melnick
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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6
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Deng Q, Lakra P, Gou P, Yang H, Meydan C, Teater M, Chin C, Zhang W, Dinh T, Hussein U, Li X, Rojas E, Liu W, Reville PK, Kizhakeyil A, Barisic D, Parsons S, Wilson A, Henderson J, Scull B, Gurumurthy C, Vega F, Chadburn A, Cuglievan B, El-Mallawany NK, Allen C, Mason C, Melnick A, Green MR. SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions. Cancer Cell 2024; 42:605-622.e11. [PMID: 38458188 PMCID: PMC11003852 DOI: 10.1016/j.ccell.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/30/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
SMARCA4 encodes one of two mutually exclusive ATPase subunits in the BRG/BRM associated factor (BAF) complex that is recruited by transcription factors (TFs) to drive chromatin accessibility and transcriptional activation. SMARCA4 is among the most recurrently mutated genes in human cancer, including ∼30% of germinal center (GC)-derived Burkitt lymphomas. In mice, GC-specific Smarca4 haploinsufficiency cooperated with MYC over-expression to drive lymphomagenesis. Furthermore, monoallelic Smarca4 deletion drove GC hyperplasia with centroblast polarization via significantly increased rates of centrocyte recycling to the dark zone. Mechanistically, Smarca4 loss reduced the activity of TFs that are activated in centrocytes to drive GC-exit, including SPI1 (PU.1), IRF family, and NF-κB. Loss of activity for these factors phenocopied aberrant BCL6 activity within murine centrocytes and human Burkitt lymphoma cells. SMARCA4 therefore facilitates chromatin accessibility for TFs that shape centrocyte trajectories, and loss of fine-control of these programs biases toward centroblast cell-fate, GC hyperplasia and lymphoma.
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Affiliation(s)
- Qing Deng
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priya Lakra
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Panhong Gou
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haopeng Yang
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cem Meydan
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matthew Teater
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Chin
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Wenchao Zhang
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tommy Dinh
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Usama Hussein
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xubin Li
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Estela Rojas
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiguang Liu
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick K Reville
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Atish Kizhakeyil
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Darko Barisic
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sydney Parsons
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashley Wilson
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared Henderson
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brooks Scull
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | | | - Francisco Vega
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Branko Cuglievan
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nader Kim El-Mallawany
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - Carl Allen
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - Christopher Mason
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michael R Green
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Jiang Y, Eagles J, Passerini V, Tang Z, Rivas MA, Weigert O, Pugh TJ, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Zappasodi R, Béguelin W, Melnick AM. Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment. Nat Commun 2024; 15:2879. [PMID: 38570506 PMCID: PMC10991284 DOI: 10.1038/s41467-024-47012-1] [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: 06/18/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Despite regulating overlapping gene enhancers and pathways, CREBBP and KMT2D mutations recurrently co-occur in germinal center (GC) B cell-derived lymphomas, suggesting potential oncogenic cooperation. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d induces a more severe mouse lymphoma phenotype (vs either allele alone) and unexpectedly confers an immune evasive microenvironment manifesting as CD8+ T-cell exhaustion and reduced infiltration. This is linked to profound repression of immune synapse genes that mediate crosstalk with T-cells, resulting in aberrant GC B cell fate decisions. From the epigenetic perspective, we observe interaction and mutually dependent binding and function of CREBBP and KMT2D on chromatin. Their combined deficiency preferentially impairs activation of immune synapse-responsive super-enhancers, pointing to a particular dependency for both co-activators at these specialized regulatory elements. Together, our data provide an example where chromatin modifier mutations cooperatively shape and induce an immune-evasive microenvironment to facilitate lymphomagenesis.
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Affiliation(s)
- Jie Li
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Hsia-Yuan Ying
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew R Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer, Department of Pathology and Laboratorial Medicine, University of British Columbia, Vancouver, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - Chi-Shuen Chu
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Yiyue Jiang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Verena Passerini
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Zhanyun Tang
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Martin A Rivas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Oliver Weigert
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Robert G Roeder
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Roberta Zappasodi
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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8
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Zhu X, Hong S, Bu J, Liu Y, Liu C, Li R, Zhang T, Zhang Z, Li L, Zhou X, Hua Z, Zhu B, Hou B. Antiviral memory B cells exhibit enhanced innate immune response facilitated by epigenetic memory. SCIENCE ADVANCES 2024; 10:eadk0858. [PMID: 38552009 PMCID: PMC10980274 DOI: 10.1126/sciadv.adk0858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/26/2024] [Indexed: 04/01/2024]
Abstract
The long-lasting humoral immunity induced by viral infections or vaccinations depends on memory B cells with greatly increased affinity to viral antigens, which are evolved from germinal center (GC) responses. However, it is unclear whether antiviral memory B cells represent a distinct subset among the highly heterogeneous memory B cell population. Here, we examined memory B cells induced by a virus-mimicking antigen at both transcriptome and epigenetic levels and found unexpectedly that antiviral memory B cells exhibit an enhanced innate immune response, which appeared to be facilitated by the epigenetic memory that is established through the memory B cell development. In addition, T-bet is associated with the altered chromatin architecture and is required for the formation of the antiviral memory B cells. Thus, antiviral memory B cells are distinct from other GC-derived memory B cells in both physiological functions and epigenetic landmarks.
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Affiliation(s)
- Xiping Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng Hong
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiachen Bu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingping Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runhan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiantian Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liping Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaolin Hua
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baidong Hou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Yanagi M, Ikegami I, Kamekura R, Sato T, Sato T, Kamiya S, Murayama K, Jitsukawa S, Ito F, Yorozu A, Kihara M, Abe T, Takaki H, Kawata K, Shigehara K, Miyajima S, Nishikiori H, Sato A, Tohse N, Takano KI, Chiba H, Ichimiya S. Bob1 maintains T follicular helper cells for long-term humoral immunity. Commun Biol 2024; 7:185. [PMID: 38360857 PMCID: PMC10869348 DOI: 10.1038/s42003-024-05827-0] [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: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Humoral immunity is vital for host protection, yet aberrant antibody responses can trigger harmful inflammation and immune-related disorders. T follicular helper (Tfh) cells, central to humoral immunity, have garnered significant attention for unraveling immune mechanisms. This study shows the role of B-cell Oct-binding protein 1 (Bob1), a transcriptional coactivator, in Tfh cell regulation. Our investigation, utilizing conditional Bob1-deficient mice, suggests that Bob1 plays a critical role in modulating inducible T-cell costimulator expression and cellular respiration in Tfh cells. This regulation maintains the long-term functionality of Tfh cells, enabling their reactivation from central memory T cells to produce antibodies during recall responses. In a bronchial asthma model induced by house dust mite (HDM) inhalation, Bob1 is observed to enhance HDM-specific antibodies, including IgE, highlighting its pivotal function in Tfh cell regulation. Further exploration of Bob1-dependent mechanisms in Tfh cells holds promise for governing protective immunity and addressing immune-related disorders.
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Affiliation(s)
- Masahiro Yanagi
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ippei Ikegami
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ryuta Kamekura
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Tatsuya Sato
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Taiki Sato
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Shiori Kamiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Kosuke Murayama
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Sumito Jitsukawa
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Fumie Ito
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Akira Yorozu
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Hiromi Takaki
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Koji Kawata
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Katsunori Shigehara
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Satsuki Miyajima
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Hirotaka Nishikiori
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Akinori Sato
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Rehabilitation, Faculty of Healthcare and Science, Hokkaido Bunkyo University, Eniwa, 061-1449, Japan
| | - Noritsugu Tohse
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ken-Ichi Takano
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Hirofumi Chiba
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Shingo Ichimiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan.
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10
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Nazarov IB, Zilov DS, Gordeev MN, Potapenko EV, Yeremenko N, Tomilin AN. Transcriptional Coactivator BOB1 (OBF1, OCA-B) Modulates the Specificity of DNA Recognition by the POU-Domain Factors OCT1 and OCT2 in a Monomeric Configuration. Biomolecules 2024; 14:123. [PMID: 38254723 PMCID: PMC10812921 DOI: 10.3390/biom14010123] [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: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
BOB1, a mammalian lymphocyte-specific transcriptional coactivator of the transcription factors OCT1 and OCT2 (OCT1/2), plays important roles in normal immune responses, autoimmunity, and hematologic malignancies. The issue of a DNA sequence preference change imposed by BOB1 was raised more than two decades ago but remains unresolved. In this paper, using the EMSA-SELEX-Seq approach, we have reassessed the intrinsic ability of BOB1 to modulate the specificity of DNA recognition by OCT1 and OCT2. Our results have reaffirmed previous conclusions regarding BOB1 selectivity towards the dimer configuration of OCT1/2. However, they suggest that the monomeric configuration of these factors, assembled on the classical octamer ATGCAAAT and related motifs, are the primary targets of BOB1. Our data further specify the DNA sequence preference imposed by BOB1 and predict the probability of ternary complex formation. These results provide an additional insight into the action of BOB1-an essential immune regulator and a promising molecular target for the treatment of autoimmune diseases and hematologic malignancies.
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Affiliation(s)
- Igor B. Nazarov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Danil S. Zilov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Mikhail N. Gordeev
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Evgenii V. Potapenko
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
- University of Haifa, Haifa 3498838, Israel
| | - Nataliya Yeremenko
- Center for Research in Transplantation and Translational Immunology UMR1064, 30 Bd Jean Monnet, Nantes University, CEDEX 01, 44093 Nantes, France;
| | - Alexey N. Tomilin
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
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11
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Welsh SJ, Barwick BG, Meermeier EW, Riggs DL, Shi CX, Zhu YX, Sharik ME, Du MT, Abrego Rocha LD, Garbitt VM, Stein CK, Petit JL, Meurice N, Tafoya Alvarado Y, Fonseca R, Todd KT, Brown S, Hammond ZJ, Cuc NH, Wittenberg C, Herzog C, Roschke AV, Demchenko YN, Chen WDD, Li P, Liao W, Leonard WJ, Lonial S, Bahlis NJ, Neri P, Boise LH, Chesi M, Bergsagel PL. Transcriptional Heterogeneity Overcomes Super-Enhancer Disrupting Drug Combinations in Multiple Myeloma. Blood Cancer Discov 2024; 5:34-55. [PMID: 37767768 PMCID: PMC10772542 DOI: 10.1158/2643-3230.bcd-23-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple myeloma (MM) is a malignancy that is often driven by MYC and that is sustained by IRF4, which are upregulated by super-enhancers. IKZF1 and IKZF3 bind to super-enhancers and can be degraded using immunomodulatory imide drugs (IMiD). Successful IMiD responses downregulate MYC and IRF4; however, this fails in IMiD-resistant cells. MYC and IRF4 downregulation can also be achieved in IMiD-resistant tumors using inhibitors of BET and EP300 transcriptional coactivator proteins; however, in vivo these drugs have a narrow therapeutic window. By combining IMiDs with EP300 inhibition, we demonstrate greater downregulation of MYC and IRF4, synergistic killing of myeloma in vitro and in vivo, and an increased therapeutic window. Interestingly, this potent combination failed where MYC and IRF4 expression was maintained by high levels of the AP-1 factor BATF. Our results identify an effective drug combination and a previously unrecognized mechanism of IMiD resistance. SIGNIFICANCE These results highlight the dependence of MM on IKZF1-bound super-enhancers, which can be effectively targeted by a potent therapeutic combination pairing IMiD-mediated degradation of IKZF1 and IKZF3 with EP300 inhibition. They also identify AP-1 factors as an unrecognized mechanism of IMiD resistance in MM. See related article by Neri, Barwick, et al., p. 56. See related commentary by Yun and Cleveland, p. 5. This article is featured in Selected Articles from This Issue, p. 4.
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Affiliation(s)
- Seth J. Welsh
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Erin W. Meermeier
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Daniel L. Riggs
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Chang-Xin Shi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Yuan Xiao Zhu
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Meaghen E. Sharik
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Megan T. Du
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Leslie D. Abrego Rocha
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Victoria M. Garbitt
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Caleb K. Stein
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Joachim L. Petit
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nathalie Meurice
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Yuliza Tafoya Alvarado
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Rodrigo Fonseca
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Kennedi T. Todd
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Sochilt Brown
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Zachery J. Hammond
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nicklus H. Cuc
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Courtney Wittenberg
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Camille Herzog
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Anna V. Roschke
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | | | - Wei-dong D. Chen
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Wei Liao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Warren J. Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Nizar J. Bahlis
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada
| | - Paola Neri
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - P. Leif Bergsagel
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
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12
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Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Rivas MA, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Béguelin W, Melnick AM. Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B cell fate decisions and yields T cell-depleted lymphomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528351. [PMID: 36824887 PMCID: PMC9949106 DOI: 10.1101/2023.02.13.528351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Mutations affecting enhancer chromatin regulators CREBBP and KMT2D are highly co-occurrent in germinal center (GC)-derived lymphomas and other tumors, even though regulating similar pathways. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) indeed accelerated lymphomagenesis. C+K haploinsufficiency induced GC hyperplasia by altering cell fate decisions, skewing B cells away from memory and plasma cell differentiation. C+K deficiency particularly impaired enhancer activation for immune synapse genes involved in exiting the GC reaction. This effect was especially severe at super-enhancers for immunoregulatory and differentiation genes. Mechanistically, CREBBP and KMT2D formed a complex, were highly co-localized on chromatin, and were required for each-other's stable recruitment to enhancers. Notably, C+K lymphomas in mice and humans manifested significantly reduced CD8 + T-cell abundance. Hence, deficiency of C+K cooperatively induced an immune evasive phenotype due at least in part to failure to activate key immune synapse super-enhancers, associated with altered immune cell fate decisions. SIGNIFICANCE Although CREBBP and KMT2D have similar enhancer regulatory functions, they are paradoxically co-mutated in lymphomas. We show that their combined loss causes specific disruption of super-enhancers driving immune synapse genes. Importantly, this leads to reduction of CD8 cells in lymphomas, linking super-enhancer function to immune surveillance, with implications for immunotherapy resistance.
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13
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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14
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Wu S, Yin Y, Wang X. The epigenetic regulation of the germinal center response. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194828. [PMID: 35643396 DOI: 10.1016/j.bbagrm.2022.194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
In response to T-cell-dependent antigens, antigen-experienced B cells migrate to the center of the B-cell follicle to seed the germinal center (GC) response after cognate interactions with CD4+ T cells. These GC B cells eventually mature into memory and long-lived antibody-secreting plasma cells, thus generating long-lived humoral immunity. Within GC, B cells undergo somatic hypermutation of their B cell receptors (BCR) and positive selection for the emergence of high-affinity antigen-specific B-cell clones. However, this process may be dangerous, as the accumulation of aberrant mutations could result in malignant transformation of GC B cells or give rise to autoreactive B cell clones that can cause autoimmunity. Because of this, better understanding of GC development provides diagnostic and therapeutic clues to the underlying pathologic process. A productive GC response is orchestrated by multiple mechanisms. An emerging important regulator of GC reaction is epigenetic modulation, which has key transcriptional regulatory properties. In this review, we summarize the current knowledge on the biology of epigenetic mechanisms in the regulation of GC reaction and outline its importance in identification of immunotherapy decision making.
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Affiliation(s)
- Shusheng Wu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuye Yin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China.
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15
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Papin A, Cesarman E, Melnick A. 3D chromosomal architecture in germinal center B cells and its alterations in lymphomagenesis. Curr Opin Genet Dev 2022; 74:101915. [PMID: 35550952 DOI: 10.1016/j.gde.2022.101915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
Abstract
In eukaryotic cells, the genome is three dimensionally (3D) organized with DNA interaction dynamics and topology changes that regulate gene expression and drive cell fate. Upon antigen stimulation, naive B cells are activated and form germinal centers (GC) for the generation of memory B cells and plasma cells. Thereby, terminal B-cell differentiation and associated humoral immune response require massive but rigorous 3D DNA reorganization. Here, we review the dynamics of genome reorganization during GC formation and the impact of its alterations on lymphomagenesis from the nucleosome structure to the higher order chromosome organization. We particularly discuss the identified architects of 3D DNA in GC B cells and the role of their mutations in B-cell lymphomas.
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Affiliation(s)
- Antonin Papin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations. Curr Opin Genet Dev 2022; 75:101919. [PMID: 35609422 DOI: 10.1016/j.gde.2022.101919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022]
Abstract
Aberrant gene expression is a cancer hallmark and it is known that almost every tumor acquires somatic mutations in transcription factors, chromatin regulators, or the DNA regulatory elements that are critical for transcriptional control and cell phenotype. While the role of transcription factors and chromatin regulators has been widely studied, relatively few noncoding driver mutations have been identified and functionally characterized to date. Here, we review the current understanding of somatic variants in noncoding regions of the cancer genome and their impact on chromatin architecture and transcriptional networks. We also discuss approaches and ongoing challenges for noncoding driver discovery, and highlight insights gained from recent studies exploring the nature and impact of noncoding drivers on tumor formation.
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