1
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Priam P, Krasteva V, Rousseau P, Polsinelli A, Côté L, Desanlis I, Farah A, Lavallée VP, Kmita M, Lessard JA. Smarcd1 subunit of SWI/SNF chromatin-remodeling complexes collaborates with E2a to promote murine lymphoid specification. Dev Cell 2024:S1534-5807(24)00490-8. [PMID: 39232562 DOI: 10.1016/j.devcel.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 05/02/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
Lymphocyte development from murine hematopoietic stem cells (HSCs) entails a loss of self-renewal capacity and a progressive restriction of developmental potential. Previous research from our laboratory suggests that specialized assemblies of ATP-dependent SWI/SNF chromatin-remodeling complexes play lineage-specific roles during murine hematopoiesis. Here, we demonstrate that the Smarcd1 subunit is essential for specification of lymphoid cell fate from multipotent progenitors. Acute deletion of Smarcd1 in murine adult hematopoiesis leads to lymphopenia, characterized by a near-complete absence of early lymphoid progenitors and mature B and T cells, while the myeloid and erythroid lineages remain unaffected. Mechanistically, we demonstrate that Smarcd1 is essential for the coordinated activation of a lymphoid gene signature in murine multipotent progenitors. This is achieved by interacting with the E2a transcription factor at proximal promoters and by regulating the activity of distal enhancers. Globally, these findings identify Smarcd1 as an essential chromatin remodeler that governs lymphoid cell fate.
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Affiliation(s)
- Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Veneta Krasteva
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Philippe Rousseau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Alexandre Polsinelli
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Laurence Côté
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ines Desanlis
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Azer Farah
- Centre de Recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | | | - Marie Kmita
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada.
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2
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Wu J, Fan C, Kabir AU, Krchma K, Kim M, Kwon Y, Xing X, Wang T, Choi K. Baf155 controls hematopoietic differentiation and regeneration through chromatin priming. Cell Rep 2024; 43:114558. [PMID: 39088321 DOI: 10.1016/j.celrep.2024.114558] [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: 10/12/2023] [Revised: 05/06/2024] [Accepted: 07/14/2024] [Indexed: 08/03/2024] Open
Abstract
Chromatin priming promotes cell-type-specific gene expression, lineage differentiation, and development. The mechanism of chromatin priming has not been fully understood. Here, we report that mouse hematopoietic stem and progenitor cells (HSPCs) lacking the Baf155 subunit of the BAF (BRG1/BRM-associated factor) chromatin remodeling complex produce a significantly reduced number of mature blood cells, leading to a failure of hematopoietic regeneration upon transplantation and 5-fluorouracil (5-FU) injury. Baf155-deficient HSPCs generate particularly fewer neutrophils, B cells, and CD8+ T cells at homeostasis, supporting a more immune-suppressive tumor microenvironment and enhanced tumor growth. Single-nucleus multiomics analysis reveals that Baf155-deficient HSPCs fail to establish accessible chromatin in selected regions that are enriched for putative enhancers and binding motifs of hematopoietic lineage transcription factors. Our study provides a fundamental mechanistic understanding of the role of Baf155 in hematopoietic lineage chromatin priming and the functional consequences of Baf155 deficiency in regeneration and tumor immunity.
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Affiliation(s)
- Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ashraf Ul Kabir
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Minseo Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoojung Kwon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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3
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Liu X, Liu K, Wang Y, Meng X, Wang Q, Tao S, Xu Q, Shen X, Gao X, Hong S, Jin H, Wang JQ, Wang D, Lu L, Meng Z, Wang L. SWI/SNF chromatin remodeling factor BAF60b restrains inflammatory diseases by affecting regulatory T cell migration. Cell Rep 2024; 43:114458. [PMID: 38996070 DOI: 10.1016/j.celrep.2024.114458] [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: 12/18/2023] [Revised: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Regulatory T (Treg) cells play a critical regulatory role in the immune system by suppressing excessive immune responses and maintaining immune balance. The effective migration of Treg cells is crucial for controlling the development and progression of inflammatory diseases. However, the mechanisms responsible for directing Treg cells into the inflammatory tissue remain incompletely elucidated. In this study, we identified BAF60b, a subunit of switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complexes, as a positive regulator of Treg cell migration that inhibits the progression of inflammation in experimental autoimmune encephalomyelitis (EAE) and colitis animal models. Mechanistically, transcriptome and genome-wide chromatin-landscaped analyses demonstrated that BAF60b interacts with the transcription factor RUNX1 to promote the expression of CCR9 on Treg cells, which in turn affects their ability to migrate to inflammatory tissues. Our work provides insights into the essential role of BAF60b in regulating Treg cell migration and its impact on inflammatory diseases.
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MESH Headings
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Animals
- Cell Movement
- Mice
- Mice, Inbred C57BL
- Inflammation/pathology
- Inflammation/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/metabolism
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Humans
- Transcription Factors/metabolism
- Core Binding Factor Alpha 2 Subunit/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Colitis/metabolism
- Colitis/pathology
- Colitis/immunology
- Colitis/genetics
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Affiliation(s)
- Xiaoqian Liu
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Kuai Liu
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yuxi Wang
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyu Meng
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qianqian Wang
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Sijue Tao
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Qianying Xu
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Shen
- Co-Facility Center, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xianzhi Gao
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shenghui Hong
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Huihui Jin
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - James Q Wang
- Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China
| | - Di Wang
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Linrong Lu
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhuoxian Meng
- Department of Pathology and Pathophysiology and Department of Cardiology, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou 310009, China
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China; Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China.
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4
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Turkova T, Kokavec J, Zikmund T, Dibus N, Pimkova K, Nemec D, Holeckova M, Ruskova L, Sedlacek R, Cermak L, Stopka T. Differential requirements for Smarca5 expression during hematopoietic stem cell commitment. Commun Biol 2024; 7:244. [PMID: 38424235 PMCID: PMC10904812 DOI: 10.1038/s42003-024-05917-z] [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: 05/29/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
The formation of hematopoietic cells relies on the chromatin remodeling activities of ISWI ATPase SMARCA5 (SNF2H) and its complexes. The Smarca5 null and conditional alleles have been used to study its functions in embryonic and organ development in mice. These mouse model phenotypes vary from embryonic lethality of constitutive knockout to less severe phenotypes observed in tissue-specific Smarca5 deletions, e.g., in the hematopoietic system. Here we show that, in a gene dosage-dependent manner, the hypomorphic allele of SMARCA5 (S5tg) can rescue not only the developmental arrest in hematopoiesis in the hCD2iCre model but also the lethal phenotypes associated with constitutive Smarca5 deletion or Vav1iCre-driven conditional knockout in hematopoietic progenitor cells. Interestingly, the latter model also provided evidence for the role of SMARCA5 expression level in hematopoietic stem cells, as the Vav1iCre S5tg animals accumulate stem and progenitor cells. Furthermore, their hematopoietic stem cells exhibited impaired lymphoid lineage entry and differentiation. This observation contrasts with the myeloid lineage which is developing without significant disturbances. Our findings indicate that animals with low expression of SMARCA5 exhibit normal embryonic development with altered lymphoid entry within the hematopoietic stem cell compartment.
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Grants
- 24-10435S, 24-10353S Grantová Agentura České Republiky (Grant Agency of the Czech Republic)
- NU21-08-00312, NU22-05-00374 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- LX22NPO5102, SVV 260637, UNCE/MED/016, COOPERATIO Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- CZ.02.1.01/0.0/0.0/16_013/0001789, CZ.02.1.01/0.0/0.0/18_046/0015861 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
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Affiliation(s)
- Tereza Turkova
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Juraj Kokavec
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Tomas Zikmund
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Nikol Dibus
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kristyna Pimkova
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Dusan Nemec
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Marketa Holeckova
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Livia Ruskova
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Lukas Cermak
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Tomas Stopka
- Hematology Laboratories, BIOCEV; 1st Faculty of Medicine, Charles University, Vestec, Czech Republic.
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5
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Kharel A, Shen J, Brown R, Chen Y, Nguyen C, Alson D, Bluemn T, Fan J, Gai K, Zhang B, Kudek M, Zhu N, Cui W. Loss of PBAF promotes expansion and effector differentiation of CD8 + T cells during chronic viral infection and cancer. Cell Rep 2023; 42:112649. [PMID: 37330910 PMCID: PMC10592487 DOI: 10.1016/j.celrep.2023.112649] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023] Open
Abstract
During chronic viral infection and cancer, it has been established that a subset of progenitor CD8+ T cells continuously gives rise to terminally exhausted cells and cytotoxic effector cells. Although multiple transcriptional programs governing the bifurcated differentiation trajectories have been previously studied, little is known about the chromatin structure changes regulating CD8+ T cell-fate decision. In this study, we demonstrate that the chromatin remodeling complex PBAF restrains expansion and promotes exhaustion of CD8+ T cells during chronic viral infection and cancer. Mechanistically, transcriptomic and epigenomic analyses reveal the role of PBAF in maintaining chromatin accessibility of multiple genetic pathways and transcriptional programs to restrain proliferation and promote T cell exhaustion. Harnessing this knowledge, we demonstrate that perturbation of PBAF complex constrained exhaustion and promoted expansion of tumor-specific CD8+ T cells resulting in antitumor immunity in a preclinical melanoma model, implicating PBAF as an attractive target for cancer immunotherapeutic.
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Affiliation(s)
- Arjun Kharel
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jian Shen
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ryan Brown
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yao Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Christine Nguyen
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donia Alson
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | - Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jie Fan
- Department of Medicine/Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kexin Gai
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bin Zhang
- Department of Medicine/Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Microbiology-Immunology, Northwestern University, Chicago, IL, USA
| | - Matthew Kudek
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.
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6
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Reddy D, Bhattacharya S, Workman JL. (mis)-Targeting of SWI/SNF complex(es) in cancer. Cancer Metastasis Rev 2023; 42:455-470. [PMID: 37093326 PMCID: PMC10349013 DOI: 10.1007/s10555-023-10102-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
The ATP-dependent chromatin remodeling complex SWI/SNF (also called BAF) is critical for the regulation of gene expression. During the evolution from yeast to mammals, the BAF complex has evolved an enormous complexity that contains a high number of subunits encoded by various genes. Emerging studies highlight the frequent involvement of altered mammalian SWI/SNF chromatin-remodeling complexes in human cancers. Here, we discuss the recent advances in determining the structure of SWI/SNF complexes, highlight the mechanisms by which mutations affecting these complexes promote cancer, and describe the promising emerging opportunities for targeted therapies.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
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7
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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8
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Li W, Yuan J. Targeting RIPK1 kinase for modulating inflammation in human diseases. Front Immunol 2023; 14:1159743. [PMID: 36969188 PMCID: PMC10030951 DOI: 10.3389/fimmu.2023.1159743] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Receptor-Interacting Serine/Threonine-Protein Kinase 1 (RIPK1) is a master regulator of TNFR1 signaling in controlling cell death and survival. While the scaffold of RIPK1 participates in the canonical NF-κB pathway, the activation of RIPK1 kinase promotes not only necroptosis and apoptosis, but also inflammation by mediating the transcriptional induction of inflammatory cytokines. The nuclear translocation of activated RIPK1 has been shown to interact BAF-complex to promote chromatin remodeling and transcription. This review will highlight the proinflammatory role of RIPK1 kinase with focus on human neurodegenerative diseases. We will discuss the possibility of targeting RIPK1 kinase for the treatment of inflammatory pathology in human diseases.
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Affiliation(s)
- Wanjin Li
- *Correspondence: Wanjin Li, ; Junying Yuan,
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9
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Identification of Differentially Expressed Genes and Prediction of Expression Regulation Networks in Dysfunctional Endothelium. Genes (Basel) 2022; 13:genes13091563. [PMID: 36140731 PMCID: PMC9498925 DOI: 10.3390/genes13091563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
The detection of early coronary atherosclerosis (ECA) is still a challenge and the mechanism of endothelial dysfunction remains unclear. In the present study, we aimed to identify differentially expressed genes (DEGs) and the regulatory network of miRNAs as well as TFs in dysfunctional endothelium to elucidate the possible pathogenesis of ECA and find new potential markers. The GSE132651 data set of the GEO database was used for the bioinformatic analysis. Principal component analysis (PCA), the identification of DEGs, correlation analysis between significant DEGs, the prediction of regulatory networks of miRNA and transcription factors (TFs), the validation of the selected significant DEGs, and the receiver operating characteristic (ROC) curve analysis as well as area under the curve (AUC) values were performed. We identified ten genes with significantly upregulated signatures and thirteen genes with significantly downregulated signals. Following this, we found twenty-two miRNAs regulating two or more DEGs based on the miRNA–target gene regulatory network. TFs with targets ≥ 10 were E2F1, RBPJ, SSX3, MMS19, POU3F3, HOXB5, and KLF4. Finally, three significant DEGs (TOX, RasGRP3, TSPAN13) were selected to perform validation experiments. Our study identified TOX, RasGRP3, and TSPAN13 in dysfunctional endothelium and provided potential biomarkers as well as new insights into the possible molecular mechanisms of ECA.
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10
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Guo A, Huang H, Zhu Z, Chen MJ, Shi H, Yuan S, Sharma P, Connelly JP, Liedmann S, Dhungana Y, Li Z, Haydar D, Yang M, Beere H, Yustein JT, DeRenzo C, Pruett-Miller SM, Crawford JC, Krenciute G, Roberts CWM, Chi H, Green DR. cBAF complex components and MYC cooperate early in CD8 + T cell fate. Nature 2022; 607:135-141. [PMID: 35732731 PMCID: PMC9623036 DOI: 10.1038/s41586-022-04849-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 05/10/2022] [Indexed: 01/03/2023]
Abstract
The identification of mechanisms to promote memory T (Tmem) cells has important implications for vaccination and anti-cancer immunotherapy1-4. Using a CRISPR-based screen for negative regulators of Tmem cell generation in vivo5, here we identify multiple components of the mammalian canonical BRG1/BRM-associated factor (cBAF)6,7. Several components of the cBAF complex are essential for the differentiation of activated CD8+ T cells into T effector (Teff) cells, and their loss promotes Tmem cell formation in vivo. During the first division of activated CD8+ T cells, cBAF and MYC8 frequently co-assort asymmetrically to the two daughter cells. Daughter cells with high MYC and high cBAF display a cell fate trajectory towards Teff cells, whereas those with low MYC and low cBAF preferentially differentiate towards Tmem cells. The cBAF complex and MYC physically interact to establish the chromatin landscape in activated CD8+ T cells. Treatment of naive CD8+ T cells with a putative cBAF inhibitor during the first 48 h of activation, before the generation of chimeric antigen receptor T (CAR-T) cells, markedly improves efficacy in a mouse solid tumour model. Our results establish cBAF as a negative determinant of Tmem cell fate and suggest that manipulation of cBAF early in T cell differentiation can improve cancer immunotherapy.
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Affiliation(s)
- Ao Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongling Huang
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhexin Zhu
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark J Chen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sujing Yuan
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Piyush Sharma
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Swantje Liedmann
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yogesh Dhungana
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhenrui Li
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mao Yang
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Helen Beere
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason T Yustein
- Baylor Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Han J, Wan M, Ma Z, He P. The TOX subfamily: all-round players in the immune system. Clin Exp Immunol 2022; 208:268-280. [PMID: 35485425 PMCID: PMC9226143 DOI: 10.1093/cei/uxac037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
The thymocyte selection-related HMG box protein (TOX) subfamily comprises evolutionarily conserved DNA-binding proteins, and is expressed in certain immune cell subsets and plays key roles in the development of CD4+ T cells, innate lymphoid cells (ILCs), T follicular helper (Tfh) cells, and in CD8+ T-cell exhaustion. Although its roles in CD4+ T and natural killer (NK) cells have been extensively studied, recent findings have demonstrated previously unknown roles for TOX in the development of ILCs, Tfh cells, as well as CD8+ T-cell exhaustion; however, the molecular mechanism underlying TOX regulation of these immune cells remains to be elucidated. In this review, we discuss recent studies on the influence of TOX on the development of various immune cells and CD8+ T-cell exhaustion and the roles of specific TOX family members in the immune system. Moreover, this review suggests candidate regulatory targets for cell therapy and immunotherapies.
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Affiliation(s)
- Jiawen Han
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Minjie Wan
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China.,Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ping He
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin, China
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12
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Yang X, Wang X, Lei L, Su Y, Zou Y, Liu H, Jiao A, Zhang C, Liu J, Li W, Ding R, Zhou X, Shi L, Zhang D, Sun C, Zhang B. Arid1a promotes thymocyte development through β-selection-dependent and β-selection-independent mechanisms. Immunology 2021; 165:402-413. [PMID: 34921692 DOI: 10.1111/imm.13440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 01/16/2023] Open
Abstract
Early T-cell development from CD4- CD8- double-negative (DN) stage to CD4+ CD8+ double-positive (DP) stage in the thymus is regulated through multiple steps involving a batch of sequentially expressed factors. Our preliminary data and a recent report showed that AT-rich interaction domain 1A (Arid1a) is required for the transition from DN to DP stages, but the mechanism is not fully understood. In this study, we consolidated that conditional deletion of Arid1a in T-cell lineage intrinsically caused developmental blocks from DN3 to DN4 stages, as well as from DN4 to DP stages using both in vivo adoptive T-cell transfer model and in vitro culture system. The expression of intracellular TCRβ is significantly decreased in Arid1a-deficient DN4 cells compared with WT cells. OT1 transgenic TCR can rescue the defect in the transition from DN3 to DN4 stages, but not from DN to DP stages. Furthermore, we observed a comparable or stronger proliferation capacity accompanied by a significant increase in cell death in Arid1a-/- DP cells compared with that in WT controls. RNA-Seq analysis shows a significant enrichment of apoptotic pathway within differentially expressed genes between Arid1a-/- and WT DP cells, including the upregulation of Bim, Casp3 and Trp53 and the downregulation of Rorc, Bcl-XL and Mcl1. Therefore, our study reveals a novel mechanism that Arid1a controls early T-cell development by maintaining intracellular TCRβ expression-mediated β-selection and activating parallel cell survival pathways.
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Affiliation(s)
- Xiaofeng Yang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
| | - Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lei Lei
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yujing Zou
- Duke University Medical Center, Durham, North Carolina, USA
| | - Haiyan Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jun Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenhua Li
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Renyi Ding
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaobo Zhou
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lin Shi
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Dan Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chenming Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
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13
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Wang Z, Liu C, Bai Y, Zhao X, Cui L, Peng Z, Zhang X, Wang X, Zhao Z, Li J, Shen L. Redefine Hyperprogressive Disease During Treatment With Immune-Checkpoint Inhibitors in Patients With Gastrointestinal Cancer. Front Oncol 2021; 11:761110. [PMID: 34858840 PMCID: PMC8630635 DOI: 10.3389/fonc.2021.761110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022] Open
Abstract
Objective Emerging evidence showed that immune checkpoint inhibitors (ICIs) lead to hyperprogressive disease (HPD) in a small proportion of patients. There is no well-recognized standard for the evaluation of HPD. Comprehensive exploration of HPD definition system in gastrointestinal cancer treated with ICI is lacking to date. Methods A total of 126 patients with advanced or metastatic gastrointestinal cancer treated with ICI monotherapy were analyzed. Seven definitions of HPD were defined with tumor growth kinetics (TGK) or tumor growth rate (TGR) by including new lesions or not, and with different cutoffs. Incidence and performance of different criteria were compared. Clinicopathologic characteristics and baseline genomic variations associated with HPD were also explored. Results Tumor growth kinetics ratio of more than two fold that incorporated new lesions into calculation of HPD outperformed other definitions by successfully stratifying 14 patients (11.1%) with both accelerated disease progression (median PFS, 1.62 versus 1.93 months; hazard ratio, 1.85; 95% CI, 0.98 to 3.48; P = 0.059) and worse overall survival (median OS, 3.97 versus 10.23 months; hazard ratio, 2.30; 95% CI, 1.11 to 4.78; P = 0.021). Baseline genomic alterations in circulating tumor DNA, including SMARCA2, MSH6, APC signaling pathway, and Wnt signaling pathway, might be associated with the risk of HPD. Conclusion Incorporating new lesions emerging during the treatment was shown to be reliable for the assessment of TGK. TGK serves as a more convenient way to reflect tumor growth acceleration compared with TGR. Genomic alterations were suggested to be associated with the occurrence of HPD.
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Affiliation(s)
- Zhenghang Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Chang Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuezong Bai
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | | | - Longgang Cui
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Zhi Peng
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaotian Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Xicheng Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhengyi Zhao
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Jian Li
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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14
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Hofmeister B, von Stülpnagel C, Betzler C, Mari F, Renieri A, Baldassarri M, Haberlandt E, Jansen K, Schilling S, Weber P, Ahlbory K, Tang S, Berweck S, Kluger G. Epilepsy in Nicolaides-Baraitser Syndrome: Review of Literature and Report of 25 Patients Focusing on Treatment Aspects. Neuropediatrics 2021; 52:109-122. [PMID: 33578439 DOI: 10.1055/s-0041-1722878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Nicolaides-Baraitser syndrome (NCBRS), caused by a mutation in the SMARCA2 gene, which goes along with intellectual disability, congenital malformations, especially of face and limbs, and often difficult-to-treat epilepsy, is surveyed focusing on epilepsy and its treatment. Patients were recruited via "Network Therapy of Rare Epilepsies (NETRE)" and an international NCBRS parent support group. Inclusion criterion is NCBRS-defining SMARCA2 mutation. Clinical findings including epilepsy classification, anticonvulsive treatment, electroencephalogram (EEG) findings, and neurodevelopmental outcome were collected with an electronic questionnaire. Inclusion of 25 NCBRS patients with epilepsy in 23 of 25. Overall, 85% of the participants (17/20) reported generalized seizures, the semiology varied widely. EEG showed generalized epileptogenic abnormalities in 53% (9/17), cranial magnetic resonance imaging (cMRI) was mainly inconspicuous. The five most frequently used anticonvulsive drugs were valproic acid (VPA [12/20]), levetiracetam (LEV [12/20]), phenobarbital (PB [8/20]), topiramate (TPM [5/20]), and carbamazepine (CBZ [5/20]). LEV (9/12), PB (6/8), TPM (4/5), and VPA (9/12) reduced the seizures' frequency in more than 50%. Temporary freedom of seizures (>6 months) was reached with LEV (4/12), PB (3/8), TPM (1/5, only combined with PB and nitrazepam [NZP]), and VPA (4/12). Seizures aggravation was observed under lamotrigine (LTG [2/4]), LEV (1/12), PB (1/8), and VPA (1/12). Ketogenic diet (KD) and vagal nerve stimulation (VNS) reduced seizures' frequency in one of two each. This first worldwide retrospective analysis of anticonvulsive therapy in NCBRS helps to treat epilepsy in NCBRS that mostly shows only initial response to anticonvulsive therapy, especially with LEV and VPA, but very rarely shows complete freedom of seizures in this, rather genetic than structural epilepsy.
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Affiliation(s)
- Benedikt Hofmeister
- Department of Gastroenterology, Hepatology and Gastrointestinal Oncology, Technical University of Munich, Bogenhausen Academic Teaching Hospital, Munich, Germany
| | - Celina von Stülpnagel
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Private Medical University of Salzburg, Salzburg, Austria.,Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Comprehensive Epilepsy Program for Children, University Hospital Munich, Munich, Germany
| | - Cornelia Betzler
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Private Medical University of Salzburg, Salzburg, Austria.,Clinic for Neuropediatrics and Neurological Rehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik Vogtareuth, Vogtareuth, Germany
| | - Francesca Mari
- Department of Medical Genetics, University of Siena, Sienna, Italy
| | | | | | - Edda Haberlandt
- Department of Pediatrics, Krankenhaus der Stadt Dornbirn, Dornbirn, Austria
| | - Katrien Jansen
- Department of Development and Regeneration, University Hospitals of Leuven, Leuven, Belgium
| | - Stefan Schilling
- Department of Neuropediatrics, Krankenhaus Barmherzige Brüder Regensburg, Regensburg, Germany
| | - Peter Weber
- Department of Neuro- and Developmental Pediatrics, University Children's Hospital Basel, Basel, Switzerland
| | - Katja Ahlbory
- Department of Neuropediatrics, Children's Hospital Amsterdamer Straße, Kliniken Köln, Cologne, Germany
| | - Shan Tang
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, United Kingdom
| | - Steffen Berweck
- Clinic for Neuropediatrics and Neurological Rehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik Vogtareuth, Vogtareuth, Germany.,Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Gerhard Kluger
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Private Medical University of Salzburg, Salzburg, Austria.,Clinic for Neuropediatrics and Neurological Rehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik Vogtareuth, Vogtareuth, Germany
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15
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Bluemn T, Schmitz J, Chen Y, Zheng Y, Zhang Y, Zheng S, Burns R, DeJong J, Christiansen L, Izaguirre-Carbonell J, Wang D, Zhu N. Arid2 regulates hematopoietic stem cell differentiation in normal hematopoiesis. Exp Hematol 2021; 94:37-46. [PMID: 33346030 PMCID: PMC10041880 DOI: 10.1016/j.exphem.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 01/25/2023]
Abstract
The switch/sugar nonfermenting (SWI/SNF) family of chromatin remodeling complexes have been implicated in normal hematopoiesis. The ARID2 protein is a component of the polybromo-associated BAF (PBAF), one of the two main SWI/SNF complexes. In the current study, we used a conditional Arid2 knockout mouse model to determine its role in normal hematopoiesis. We found that the loss of Arid2 has no discernable effects on steady-state hematopoiesis, with the exception of a modest effect on erythropoiesis. On bone marrow transplantation, however, the loss of Arid2 affects HSC differentiation in a cell-autonomous manner, resulting in significant decreases in the ability to reconstitute the lymphoid lineage. Gene expression analysis of Arid2 knockout cells revealed enrichment of myeloid-biased multipotent progenitor (MPP) cell signatures, while the lymphoid-biased MPPs are enriched in the wild type, consistent with the observed phenotype. Moreover, Arid2 knockout cells revealed enrichment of inflammatory pathways with upregulation of TLR receptors, as well as downstream signaling cascade genes. Furthermore, under lymphocyte-biased growth conditions in vitro, Arid2 null bone marrow cells have significantly impaired proliferation, which decreased further on lipopolysaccharide stimulation. Overall, these data suggest that the loss of Arid2 impairs HSC differentiation ability, and this effect may be mediated through upregulation of inflammatory pathways.
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Affiliation(s)
- Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI
| | | | - Yuhong Chen
- Blood Research Institute, Versiti, Milwaukee, WI
| | | | | | - Shikan Zheng
- Blood Research Institute, Versiti, Milwaukee, WI
| | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI
| | | | - Luke Christiansen
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI
| | | | - Demin Wang
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI.
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16
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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17
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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18
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Abstract
The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.
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19
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Estrada-Rivera M, Hernández-Oñate MÁ, Dautt-Castro M, Gallardo-Negrete JDJ, Rebolledo-Prudencio OG, Uresti-Rivera EE, Arenas-Huertero C, Herrera-Estrella A, Casas-Flores S. IPA-1 a Putative Chromatin Remodeler/Helicase-Related Protein of Trichoderma virens Plays Important Roles in Antibiosis Against Rhizoctonia solani and Induction of Arabidopsis Systemic Disease Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:808-824. [PMID: 32101077 DOI: 10.1094/mpmi-04-19-0092-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, either indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma spp. emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to cocultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell wall-degrading enzymes putatively relevant for root colonization. Repression of such genes reached their basal levels at later times in the interaction, when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell wall-degrading enzymes with the auxiliary activities class. RNA-Seq analyses showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (increased protection of Arabidopsis-1). Sequence analyses of IPA-1 showed its closest relatives to be members of the Rad5/Rad16 and SNF2 subfamilies; however, it grouped into a different clade. Although deletion of IPA-1 in T. virens did not affect its growth, the antibiotic activity of Δipa-1 culture filtrates against Rhizoctonia solani diminished but it remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared with the wild type.
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Affiliation(s)
- Magnolia Estrada-Rivera
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - Miguel Ángel Hernández-Oñate
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, Carretera Gustavo Enrique Astiazarán Rosas No. 46, La Victoria, C.P. 83304. Hermosillo, Sonora, Mexico
| | - Mitzuko Dautt-Castro
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - José de Jesús Gallardo-Negrete
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | | | - Edith Elena Uresti-Rivera
- Facultad de Ciencias Químicas, Departamento de Inmunología y Biología Celular y Molecular, Universidad Autónoma de San Luis Potosí, Av. Salvador Nava s/n, Zona Universitaria, 78290, San Luis Potosí, Mexico
| | - Catalina Arenas-Huertero
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec No. 1570. Priv. del Pedregal 78295, San Luis Potosí, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, C.P. 36824, Irapuato, Gto., México
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
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20
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Gatchalian J, Liao J, Maxwell MB, Hargreaves DC. Control of Stimulus-Dependent Responses in Macrophages by SWI/SNF Chromatin Remodeling Complexes. Trends Immunol 2020; 41:126-140. [PMID: 31928914 PMCID: PMC6995420 DOI: 10.1016/j.it.2019.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic regulation plays an important role in controlling the activation, timing, and resolution of innate immune responses in macrophages. Previously, SWI/SNF chromatin remodeling was found to define the kinetics and selectivity of gene activation in response to microbial ligands; however, these studies do not reflect a comprehensive understanding of SWI/SNF complex regulation. In 2018, a new variant of the SWI/SNF complex was identified with unknown function in inflammatory gene regulation. Here, we summarize the biochemical and genomic properties of SWI/SNF complex variants and the potential for increased regulatory control of innate immune transcriptional programs in light of such biochemical diversity. Finally, we review the development of SWI/SNF complex chemical inhibitors and degraders that could be used to modulate immune responses.
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Affiliation(s)
- Jovylyn Gatchalian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingwen Liao
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Matthew B Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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21
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Kalmbach A, Schröder C, Klein-Hitpass L, Nordström K, Ulz P, Heitzer E, Speicher MR, Rahmann S, Wieczorek D, Horsthemke B, Bramswig NC. Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenet Genome Res 2019; 159:1-11. [PMID: 31658463 DOI: 10.1159/000503266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 01/15/2023] Open
Abstract
The switch/sucrose non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in ARID1B. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14+ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous ARID1B mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14+ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14+ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B.
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22
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Ho PJ, Lloyd SM, Bao X. Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Development 2019; 146:146/19/dev178780. [PMID: 31570369 DOI: 10.1242/dev.178780] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The BAF (SWI/SNF) chromatin remodeling complex plays a crucial role in modulating spatiotemporal gene expression during mammalian development. Although its remodeling activity was characterized in vitro decades ago, the complex actions of BAF in vivo have only recently begun to be unraveled. In living cells, BAF only binds to and remodels a subset of genomic locations. This selectivity of BAF genomic targeting is crucial for cell-type specification and for mediating precise responses to environmental signals. Here, we provide an overview of the distinct molecular mechanisms modulating BAF chromatin binding, including its combinatory assemblies, DNA/histone modification-binding modules and post-translational modifications, as well as its interactions with proteins, RNA and lipids. This Review aims to serve as a primer for future studies to decode the actions of BAF in developmental processes.
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Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA .,Department of Dermatology, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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23
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Abstract
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively. Together with increasing knowledge of epigenetic regulators, these findings have advanced our understanding of the transcription factor network regulating the CD4/CD8 dichotomy. It has also become apparent that CD4+ T cells retain developmental plasticity, allowing them to acquire cytotoxic activity in the periphery. Despite such advances, further studies are necessary to identify the molecular links between TCR signaling and the nuclear machinery regulating expression of ThPOK and Runx3.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan;
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24
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Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA. ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells. Clin Epigenetics 2019; 11:92. [PMID: 31217031 PMCID: PMC6585056 DOI: 10.1186/s13148-019-0690-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.
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Affiliation(s)
- Madhobi Sen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Xin Wang
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Gastroenterology Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jacobe Rapp
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jessica Eggert
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Ana Patricia Kutschat
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Fereshteh S Younesi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Elisabeth Hessmann
- Department of Gastroenterology & Gastrointestinal Oncology, University Medical Center Gӧttingen, 37075, Göttingen, Germany
| | - Argyris Papantonis
- Department of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Philipp Strӧbel
- Department of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Gastroenterology Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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25
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Güneş C, Paszkowski-Rogacz M, Rahmig S, Khattak S, Camgöz A, Wermke M, Dahl A, Bornhäuser M, Waskow C, Buchholz F. Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator. Stem Cell Reports 2019; 12:1084-1098. [PMID: 31031192 PMCID: PMC6523874 DOI: 10.1016/j.stemcr.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/20/2022] Open
Abstract
Large-scale RNAi screens are a powerful approach to identify functions of genes in a cell-type-specific manner. For model organisms, genetically identical (isogenic) cells from different cell types are readily available, making comparative studies meaningful. However, large-scale screens in isogenic human primary cells remain challenging. Here, we show that RNAi screens are possible in genetically identical human stem cells, using induced pluripotent stem cells as intermediates. The screens revealed SMARCA4 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4) as a stemness regulator, while balancing differentiation distinctively for each cell type. SMARCA4 knockdown in hematopoietic stem and progenitor cells caused impaired self-renewal in vitro and in vivo with skewed myeloid differentiation; whereas, in neural stem cells, it impaired self-renewal while biasing differentiation toward neural lineage, through combinatorial SWI/SNF subunit assembly. Our findings pose a powerful approach for deciphering human stem cell biology and attribute distinct roles to SMARCA4 in stem cell maintenance. Comparative RNAi screens on isogenic hHSPCs and hNSCs, using iPSCs as bridging cell type SMARCA4 is a differential regulator of self-renewal and differentiation SMARCA4 loss impairs HSPC engraftment in vivo and myeloid differentiation in vitro SMARCA4 loss in NSCs causes exit from self-renewal and biased neural differentiation
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Affiliation(s)
- Ceren Güneş
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Susann Rahmig
- Regeneration in Hematopoiesis, Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Shahryar Khattak
- Stem Cell Engineering Facility, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Aylin Camgöz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Martin Wermke
- Department of Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany; Medical Faculty and University Hospital Carl Gustav Carus, Early Clinical Trial Unit, 01307 Dresden, Germany
| | - Andreas Dahl
- Dresden Genome Center (DGC), TU Dresden, 01307 Dresden, Germany
| | - Martin Bornhäuser
- Department of Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis, Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany; Department of Medicine III, Faculty of Medicine, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg and German Research Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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26
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Bosselut R. Control of Intra-Thymic αβ T Cell Selection and Maturation by H3K27 Methylation and Demethylation. Front Immunol 2019; 10:688. [PMID: 31001282 PMCID: PMC6456692 DOI: 10.3389/fimmu.2019.00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022] Open
Abstract
In addition to transcription factor binding, the dynamics of DNA modifications (methylation) and chromatin structure are essential contributors to the control of transcription in eukaryotes. Research in the past few years has emphasized the importance of histone H3 methylation at lysine 27 for lineage specific gene repression, demonstrated that deposition of this mark at specific genes is subject to differentiation-induced changes during development, and identified enzymatic activities, methyl transferases and demethylases, that control these changes. The present review discusses the importance of these mechanisms during intrathymic αβ T cell selection and late differentiation.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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27
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smarce1 mutants have a defective endocardium and an increased expression of cardiac transcription factors in zebrafish. Sci Rep 2018; 8:15369. [PMID: 30337622 PMCID: PMC6194089 DOI: 10.1038/s41598-018-33746-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/05/2018] [Indexed: 12/11/2022] Open
Abstract
SWI/SNF or BAF chromatin-remodeling complexes are polymorphic assemblies of homologous subunit families that remodel nucleosomes and facilitate tissue-specific gene regulation during development. BAF57/SMARCE1 is a BAF complex subunit encoded in animals by a single gene and is a component of all mammalian BAF complexes. In vivo, the loss of SMARCE1 would lead to the formation of deficient combinations of the complex which might present limited remodeling activities. To address the specific contribution of SMARCE1 to the function of the BAF complex, we generated CRISPR/Cas9 mutations of smarce1 in zebrafish. Smarce1 mutants showed visible defects at 72 hpf, including smaller eyes, abnormal body curvature and heart abnormalities. Gene expression analysis revealed that the mutant embryos displayed defects in endocardial development since early stages, which led to the formation of a misshapen heart tube. The severe morphological and functional cardiac problems observed at 4 dpf were correlated with the substantially increased expression of different cardiac transcription factors. Additionally, we showed that Smarce1 binds to cis-regulatory regions of the gata5 gene and is necessary for the recruitment of the BAF complex to these regions.
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28
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Moon JS, Lee HJ, Ho CC, Shin JS, Ghosh S, Kim JH, Lee SK. Immuno-suppressive function of nucleus-transducible BAF57-ΔPH in T cell activation via degradation of endogenous BAF57. Int J Hematol 2018; 108:375-383. [PMID: 29978433 DOI: 10.1007/s12185-018-2491-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 11/28/2022]
Abstract
The BAF57 subunit, an indispensable member of the BAF complex, is functionally implicated in apoptosis, cell cycle, and T cell development through chromosomal remodeling. However, the precise roles of BAF57 in the T cell receptor (TcR)-mediated signaling pathway have not been elucidated. In this study, a nucleus-transducible form of BAF57, absent the proline-rich and HMG domains (ntBAF57-ΔPH), was generated to interfere with the interaction between BAF57 and its binding protein, BAF155. ntBAF57-ΔPH was effectively delivered into mouse CD4+ T cells in a dose- and time-dependent manner, without cellular toxicity. Inhibition of T cell activation by ntBAF57-ΔPH was mediated by its disruption of the interaction between BAF155 and BAF57, leading to the degradation of endogenous BAF57 and BAF155. This phenomenon led to alterations in gene expression similar to those associated with Ciclosporin A treatment. In vivo administration of ntBAF57-ΔPH enhanced survival rate of sepsis-induced mice and reduced the LPS-induced secretion of pro-inflammatory cytokines and the expression of endogenous BAF57. These results reveal a novel function of BAF57 as an essential regulator of T cell activation. ntBAF57-ΔPH represents a novel immune-suppressive drug candidate with potential uses in the treatment of autoimmunity and graft rejection.
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Affiliation(s)
- Jae-Seung Moon
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Hong-Jai Lee
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Chun-Chang Ho
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Jin-Su Shin
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Jung-Ho Kim
- Good T cells, Inc, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Sang-Kyou Lee
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea. .,Good T cells, Inc, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea.
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29
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Zhao X, Wang Y, Guo J, Wang J. Correlation analyses of CpG island methylation of cluster of differentiation 4 protein with gene expression and T lymphocyte subpopulation traits. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018. [PMID: 29514434 PMCID: PMC6043439 DOI: 10.5713/ajas.17.0805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Objective Cluster of differentiation 4 protein (CD4) gene is an important immune related gene which plays a significant role in T cell development and host resistance during viral infection. Methods In order to unravel the relationship of CpG island methylation level of CD4 gene with its gene expression and T lymphocyte subpopulation traits, we used one typical Chinese indigenous breed (Dapulian, DP) and one commercial breed (Landrace), then predicted the CpG island of CD4 gene, determined the methylation status of CpG sites by bisulfite sequencing polymerase chain reaction (BSP), and carried out the correlation analyses of methylation frequencies of CpG sites with mRNA expression and T lymphocyte subpopulation traits. Results There was one CpG island predicted in the upstream −2 kb region and exon one of porcine CD4 gene, which located 333 bp upstream from the start site of gene and contained nine CpG sites. The correlation analysis results indicated that the methylation frequency of CpG_2 significantly correlated with CD4 mRNA expression in the DP and Landrace combined population, though it did not reach significance level in DP and Landrace separately. Additionally, 15 potential binding transcription factors (TFs) were predicted within the CpG island, and one of them (Jumonji) contained CpG_2 site, suggesting that it may influence the CD4 gene expression through the potential binding TFs. We also found methylation frequency of CpG_2 negatively correlated with T lymphocyte subpopulation traits CD4+CD8−CD3−, CD4−CD8+CD3− and CD4+/CD8+, and positively correlated with CD4−CD8+CD3+ and CD4+CD8+CD3+ (for all correlation, p<0.01) in DP and Landrace combined population. Thus, the CpG_2 was a critical methylation site for porcine CD4 gene expression and T lymphocyte subpopulation traits. Conclusion We speculated that increased methylation frequency of CpG_2 may lead to the decreased expression of CD4, which may have some kind of influence on T lymphocyte subpopulation traits and the immunity of DP population.
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Affiliation(s)
- Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jianfeng Guo
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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30
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Arnaud O, Le Loarer F, Tirode F. BAFfling pathologies: Alterations of BAF complexes in cancer. Cancer Lett 2018; 419:266-279. [PMID: 29374542 DOI: 10.1016/j.canlet.2018.01.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 01/08/2023]
Abstract
To activate or repress specific genes, chromatin is constantly modified by chromatin-remodeling complexes. Among these complexes, the SWItch/Sucrose Non-Fermenting (SWI/SNF) complex, also referred to as BRG1-Associated Factor (BAF) complex, moves the nucleosome along chromatin using energy provided by ATP hydrolysis. In mammalian organisms, the SWI/SNF complex is composed of 10-15 subunits, depending on cell type, and a defect in one of these subunits can have dramatic consequences. In this review we will focus on the alterations identified in the SWI/SNF (BAF) complex subunits that lead to cancerous pathologies. While SMARCB1 was the first mutated subunit to be reported in a majority of malignant rhabdoid tumors, the advent of next-generation sequencing allowed the discovery of mutations in various SWI/SNF subunits within a broad spectrum of cancers. In most cases, the mutation leads to a loss of expression or to a truncated subunit unable to perform its function. Even though it is now commonly acknowledged that approximately 20% of all cancers present a mutation in a SWI/SNF subunit, some cancers are associated to a specific alteration of a SWI/SNF subunit, which acts either as tumor suppressor genes or as oncogenes, and therefore constitute diagnostic or prognostic biomarkers. Consistently, therapeutic strategies targeting SWI/SNF subunits or the genes affected downstream have been revealed to treat cancers.
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Affiliation(s)
- Ophelie Arnaud
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, F-69008, Lyon, France
| | | | - Franck Tirode
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, F-69008, Lyon, France; Department of Translational Research and Innovation, Centre Léon Bérard, F-69008, Lyon, France.
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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Dogra P, Ghoneim HE, Abdelsamed HA, Youngblood B. Generating long-lived CD8(+) T-cell memory: Insights from epigenetic programs. Eur J Immunol 2017; 46:1548-62. [PMID: 27230488 DOI: 10.1002/eji.201545550] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/28/2016] [Accepted: 05/24/2016] [Indexed: 12/13/2022]
Abstract
T-cell-based immunological memory has the potential to provide the host with life-long protection against pathogen reexposure and thus offers tremendous promise for the design of vaccines targeting chronic infections or cancer. In order to exploit this potential in the design of new vaccines, it is necessary to understand how and when memory T cells acquire their poised effector potential, and moreover, how they maintain these properties during homeostatic proliferation. To gain insight into the persistent nature of memory T-cell functions, investigators have turned their attention to epigenetic mechanisms. Recent efforts have revealed that many of the properties acquired among memory T cells are coupled to stable changes in DNA methylation and histone modifications. Furthermore, it has recently been reported that the delineating features among memory T cells subsets are also linked to distinct epigenetic events, such as permissive and repressive histone modifications and DNA methylation programs, providing exciting new hypotheses regarding their cellular ancestry. Here, we review recent studies focused on epigenetic programs acquired during effector and memory T-cell differentiation and discuss how these data may shed new light on the developmental path for generating long-lived CD8(+) T-cell memory.
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Affiliation(s)
- Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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Priam P, Krasteva V, Rousseau P, D'Angelo G, Gaboury L, Sauvageau G, Lessard JA. SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. Nat Genet 2017; 49:753-764. [PMID: 28369034 DOI: 10.1038/ng.3812] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/14/2017] [Indexed: 12/15/2022]
Abstract
Recent studies suggest that individual subunits of chromatin-remodeling complexes produce biologically specific meaning in different cell types through combinatorial assembly. Here we show that granulocyte development requires SMARCD2, a subunit of ATP-dependent SWI/SNF (BAF) chromatin-remodeling complexes. Smarcd2-deficient mice fail to generate functionally mature neutrophils and eosinophils, a phenotype reminiscent of neutrophil-specific granule deficiency (SGD) in humans, for which loss-of-function mutations in CEBPE (encoding CEBPɛ) have been reported. SMARCD2-containing SWI/SNF complexes are necessary for CEBPɛ transcription factor recruitment to the promoter of neutrophilic secondary granule genes and for granulocyte differentiation. The homologous SMARCD1 protein (63% identical at the amino acid level) cannot replace the role of SMARCD2 in granulocyte development. We find that SMARCD2 functional specificity is conferred by its divergent coiled-coil 1 and SWIB domains. Strikingly, both CEBPE and SMARCD2 loss-of-function mutations identified in patients with SGD abolish the interaction with SWI/SNF and thereby secondary granule gene expression, thus providing a molecular basis for this disease.
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Affiliation(s)
- Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Veneta Krasteva
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Philippe Rousseau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada
| | - Giovanni D'Angelo
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Louis Gaboury
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
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The BAF45a/PHF10 subunit of SWI/SNF-like chromatin remodeling complexes is essential for hematopoietic stem cell maintenance. Exp Hematol 2017; 48:58-71.e15. [DOI: 10.1016/j.exphem.2016.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/12/2016] [Accepted: 11/25/2016] [Indexed: 11/22/2022]
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36
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Issuree PDA, Ng CP, Littman DR. Heritable Gene Regulation in the CD4:CD8 T Cell Lineage Choice. Front Immunol 2017; 8:291. [PMID: 28382035 PMCID: PMC5360760 DOI: 10.3389/fimmu.2017.00291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 12/04/2022] Open
Abstract
The adaptive immune system is dependent on functionally distinct lineages of T cell antigen receptor αβ-expressing T cells that differentiate from a common progenitor in the thymus. CD4+CD8+ progenitor thymocytes undergo selection following interaction with MHC class I and class II molecules bearing peptide self-antigens, giving rise to CD8+ cytotoxic and CD4+ helper or regulatory T cell lineages, respectively. The strict correspondence of CD4 and CD8 expression with distinct cellular phenotypes has made their genes useful surrogates for investigating molecular mechanisms of lineage commitment. Studies of Cd4 and Cd8 transcriptional regulation have uncovered cis-regulatory elements that are critical for mediating epigenetic modifications at distinct stages of development to establish heritable transcriptional programs. In this review, we examine the epigenetic mechanisms involved in Cd4 and Cd8 gene regulation during T cell lineage specification and highlight the features that make this an attractive system for uncovering molecular mechanisms of heritability.
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Affiliation(s)
- Priya D A Issuree
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Charles P Ng
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
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37
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Abstract
There has been speculation as to how bi-potent CD4(+) CD8(+) double-positive precursor thymocytes choose their distinct developmental fate, becoming either CD4(+) helper or CD8(+) cytotoxic T cells. Based on the clear correlation of αβT cell receptor (TCR) specificity to major histocompatibility complex (MHC) classes with this lineage choice, various studies have attempted to resolve this question by examining the cellular signaling events initiated by TCR engagements, a strategy referred to as a 'top-down' approach. On the other hand, based on the other correlation of CD4/CD8 co-receptor expression with its selected fate, other studies have addressed this question by gradually unraveling the sequential mechanisms that control the phenotypic outcome of this fate decision, a method known as the 'bottom-up' approach. Bridging these two approaches will contribute to a more comprehensive understanding of how TCR signals are coupled with developmental programs in the nucleus. Advances made during the last two decades seemed to make these two approaches more closely linked. For instance, identification of two transcription factors, ThPOK and Runx3, which play central roles in the development of helper and cytotoxic lineages, respectively, provided significant insights into the transcriptional network that controls a CD4/CD8 lineage choice. This review summarizes achievements made using the 'bottom-up' approach, followed by a perspective on future pathways toward coupling TCR signaling with nuclear programs.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
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38
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Xiao C, Gao L, Hou Y, Xu C, Chang N, Wang F, Hu K, He A, Luo Y, Wang J, Peng J, Tang F, Zhu X, Xiong JW. Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish. Nat Commun 2016; 7:13787. [PMID: 27929112 PMCID: PMC5476829 DOI: 10.1038/ncomms13787] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
The zebrafish possesses a remarkable capacity of adult heart regeneration, but the underlying mechanisms are not well understood. Here we report that chromatin remodelling factor Brg1 is essential for adult heart regeneration. Brg1 mRNA and protein are induced during heart regeneration. Transgenic over-expression of dominant-negative Xenopus Brg1 inhibits the formation of BrdU+/Mef2C+ and Tg(gata4:EGFP) cardiomyocytes, leading to severe cardiac fibrosis and compromised myocardial regeneration. RNA-seq and RNAscope analyses reveal that inhibition of Brg1 increases the expression of cyclin-dependent kinase inhibitors such as cdkn1a and cdkn1c in the myocardium after ventricular resection; and accordingly, myocardial-specific expression of dn-xBrg1 blunts myocardial proliferation and regeneration. Mechanistically, injury-induced Brg1, via its interaction with Dnmt3ab, suppresses the expression of cdkn1c by increasing the methylation level of CpG sites at the cdkn1c promoter. Taken together, our results suggest that Brg1 promotes heart regeneration by repressing cyclin-dependent kinase inhibitors partly through Dnmt3ab-dependent DNA methylation.
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Affiliation(s)
- Chenglu Xiao
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Lu Gao
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Yu Hou
- Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China.,College of Life Sciences, Peking University, Beijing 100871, China
| | - Congfei Xu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Nannan Chang
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Fang Wang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Keping Hu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China.,Peking Union Medical College, Beijing 100730, China
| | - Aibin He
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Ying Luo
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Jun Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fuchou Tang
- Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China.,College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaojun Zhu
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Jing-Wei Xiong
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
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Wu B, Wang Y, Wang C, Wang GG, Wu J, Wan YY. BPTF Is Essential for T Cell Homeostasis and Function. THE JOURNAL OF IMMUNOLOGY 2016; 197:4325-4333. [PMID: 27799308 DOI: 10.4049/jimmunol.1600642] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022]
Abstract
Bromodomain PHD finger transcription factor (BPTF), a ubiquitously expressed ATP-dependent chromatin-remodeling factor, is critical for epigenetically regulating DNA accessibility and gene expression. Although BPTF is important for the development of thymocytes, its function in mature T cells remains largely unknown. By specifically deleting BPTF from late double-negative 3/double-negative 4 stage of developing T cells, we found that BPTF was critical for the homeostasis of T cells via a cell-intrinsic manner. In addition, BPTF was essential for the maintenance and function of regulatory T (Treg) cells. Treg cell-specific BPTF deletion led to reduced Foxp3 expression, increased lymphocyte infiltration in the nonlymphoid organs, and a systemic autoimmune syndrome. These findings therefore reveal a vital role for BPTF in T and Treg cell function and immune homeostasis.
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Affiliation(s)
- Bing Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Yunqi Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Chaojun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jie Wu
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Yisong Y Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; .,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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Takikita S, Muro R, Takai T, Otsubo T, Kawamura YI, Dohi T, Oda H, Kitajima M, Oshima K, Hattori M, Endo TA, Toyoda T, Weis J, Shinkai Y, Suzuki H. A Histone Methyltransferase ESET Is Critical for T Cell Development. THE JOURNAL OF IMMUNOLOGY 2016; 197:2269-79. [PMID: 27511731 DOI: 10.4049/jimmunol.1502486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/08/2016] [Indexed: 12/15/2022]
Abstract
ESET/SETDB1, one of the major histone methyltransferases, catalyzes histone 3 lysine 9 (H3K9) trimethylation. ESET is critical for suppressing expression of retroviral elements in embryonic stem cells; however, its role in the immune system is not known. We found that thymocyte-specific deletion of ESET caused impaired T cell development, with CD8 lineage cells being most severely affected. Increased apoptosis of CD8 single-positive cells was observed, and TCR-induced ERK activation was severely inhibited in ESET(-/-) thymocytes. Genome-wide comprehensive analysis of mRNA expression and H3K9 trimethylation revealed that ESET regulates expression of numerous genes in thymocytes. Among them, FcγRIIB, whose signaling can inhibit ERK activation, was strongly and ectopically expressed in ESET(-/-) thymocytes. Indeed, genetic depletion of FcγRIIB in ESET(-/-) thymocytes rescued impaired ERK activation and partially restored defective positive selection in ESET(-/-) mice. Therefore, impaired T cell development in ESET(-/-) mice is partly due to the aberrant expression of FcγRIIB. Collectively, to our knowledge, we identify ESET as the first trimethylated H3K9 histone methyltransferase playing a crucial role in T cell development.
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Affiliation(s)
- Shoichi Takikita
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Ryunosuke Muro
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Toshiyuki Takai
- Department of Experimental Immunology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Takeshi Otsubo
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Yuki I Kawamura
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Taeko Dohi
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Hiroyo Oda
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Masayuki Kitajima
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Kenshiro Oshima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Chiba 272-8561, Japan
| | - Masahira Hattori
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Chiba 272-8561, Japan; Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Takaho A Endo
- Integrated Database Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tetsuro Toyoda
- Integrated Database Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - John Weis
- Division of Cell Biology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132; Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132; and
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Harumi Suzuki
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan;
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41
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Dubey R, Lebensohn AM, Bahrami-Nejad Z, Marceau C, Champion M, Gevaert O, Sikic BI, Carette JE, Rohatgi R. Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1. Cancer Res 2016; 76:5810-5821. [PMID: 27503929 DOI: 10.1158/0008-5472.can-16-0716] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 02/07/2023]
Abstract
Anthracyclines are among the most effective yet most toxic drugs used in the oncology clinic. The nucleosome-remodeling SWI/SNF complex, a potent tumor suppressor, is thought to promote sensitivity to anthracyclines by recruiting topoisomerase IIa (TOP2A) to DNA and increasing double-strand breaks. In this study, we discovered a novel mechanism through which SWI/SNF influences resistance to the widely used anthracycline doxorubicin based on the use of a forward genetic screen in haploid human cells, followed by a rigorous single and double-mutant epistasis analysis using CRISPR/Cas9-mediated engineering. Doxorubicin resistance conferred by loss of the SMARCB1 subunit of the SWI/SNF complex was caused by transcriptional upregulation of a single gene, encoding the multidrug resistance pump ABCB1. Remarkably, both ABCB1 upregulation and doxorubicin resistance caused by SMARCB1 loss were dependent on the function of SMARCA4, a catalytic subunit of the SWI/SNF complex. We propose that residual SWI/SNF complexes lacking SMARCB1 are vital determinants of drug sensitivity, not just to TOP2A-targeted agents, but to the much broader range of cancer drugs effluxed by ABCB1. Cancer Res; 76(19); 5810-21. ©2016 AACR.
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Affiliation(s)
- Ramin Dubey
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California. Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Andres M Lebensohn
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California. Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Zahra Bahrami-Nejad
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California
| | - Caleb Marceau
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Magali Champion
- Stanford Center for Biomedical Informatics Research, Dept. of Medicine, Stanford, California
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Dept. of Medicine, Stanford, California
| | - Branimir I Sikic
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California.
| | - Rajat Rohatgi
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California. Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California.
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Lomelí H, Castillo-Robles J. The developmental and pathogenic roles of BAF57, a special subunit of the BAF chromatin-remodeling complex. FEBS Lett 2016; 590:1555-69. [PMID: 27149204 DOI: 10.1002/1873-3468.12201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/22/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
Mammalian SWI/SNF or BAF chromatin-remodeling complexes are polymorphic assemblies of homologous subunit families that remodel nucleosomes. BAF57 is a subunit of the BAF complexes; it is encoded only in higher eukaryotes and is present in all mammalian assemblies. Its main structural feature is a high-mobility group domain, the DNA-binding properties of which suggest that BAF57 may play topological roles as the BAF complex enters or exits the nucleosome. BAF57 displays specific interactions with a number of proteins outside the BAF complex. Through these interactions, it can accomplish specific functions. In the embryo, BAF57 is responsible for the silencing of the CD4 gene during T-cell differentiation, and during the repression of neuronal genes in non-neuronal cells, BAF57 interacts with the transcriptional corepressor, Co-REST, and facilitates repression. Extensive work has demonstrated a specific role of BAF57 in regulating the interactions between BAF and nuclear hormone receptors. Despite its involvement in oncogenic pathways, new generation sequencing studies do not support a prominent role for BAF57 in the initiation of cancer. On the other hand, evidence has emerged to support a role for BAF57 as a metastasis factor, a prognosis marker and a therapeutic target. In humans, BAF57 is associated with disease, as mutations in this gene predispose to important congenital disorders, including menigioma disease or the Coffin-Siris syndrome. In this article, we present an exhaustive analysis of the BAF57 molecular and biochemical properties, cellular functions, loss-of-function phenotypes in living organisms and pathological manifestations in cases of human mutations.
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Affiliation(s)
- Hilda Lomelí
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jorge Castillo-Robles
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Panamarova M, Cox A, Wicher KB, Butler R, Bulgakova N, Jeon S, Rosen B, Seong RH, Skarnes W, Crabtree G, Zernicka-Goetz M. The BAF chromatin remodelling complex is an epigenetic regulator of lineage specification in the early mouse embryo. Development 2016; 143:1271-83. [PMID: 26952987 PMCID: PMC4852518 DOI: 10.1242/dev.131961] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/22/2016] [Indexed: 12/16/2022]
Abstract
Dynamic control of gene expression is essential for the development of a totipotent zygote into an embryo with defined cell lineages. The accessibility of genes responsible for cell specification to transcriptional machinery is dependent on chromatin remodelling complexes such as the SWI\SNF (BAF) complex. However, the role of the BAF complex in early mouse development has remained unclear. Here, we demonstrate that BAF155, a major BAF complex subunit, regulates the assembly of the BAF complex in vivo and regulates lineage specification of the mouse blastocyst. We find that associations of BAF155 with other BAF complex subunits become enriched in extra-embryonic lineages just prior to implantation. This enrichment is attributed to decreased mobility of BAF155 in extra-embryonic compared with embryonic lineages. Downregulation of BAF155 leads to increased expression of the pluripotency marker Nanog and its ectopic expression in extra-embryonic lineages, whereas upregulation of BAF155 leads to the upregulation of differentiation markers. Finally, we show that the arginine methyltransferase CARM1 methylates BAF155, which differentially influences assembly of the BAF complex between the lineages and the expression of pluripotency markers. Together, our results indicate a novel role of BAF-dependent chromatin remodelling in mouse development via regulation of lineage specification. Summary: Associations of BAF155 with other BAF complex subunits are enriched in extra-embryonic lineages prior to implantation, while changes in BAF155 levels modulate the expression of early developmental markers.
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Affiliation(s)
- Maryna Panamarova
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Andy Cox
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Krzysztof B Wicher
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Richard Butler
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Natalia Bulgakova
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Bateson Centre and Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Shin Jeon
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-747, South Korea
| | - Barry Rosen
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Rho H Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-747, South Korea
| | | | - Gerald Crabtree
- Department of Developmental Biology, Stanford University Medical School, Stanford, CA 94305, USA
| | - Magdalena Zernicka-Goetz
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
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Quantitative Analysis of Global Proteome and Lysine Acetylome Reveal the Differential Impacts of VPA and SAHA on HL60 Cells. Sci Rep 2016; 6:19926. [PMID: 26822725 PMCID: PMC4731804 DOI: 10.1038/srep19926] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/21/2015] [Indexed: 01/08/2023] Open
Abstract
Valproic acid (VPA) and suberoylanilide hydroxamic acid (SAHA) are both HDAC inhibitors (HDACi). Previous studies indicated that both inhibitors show therapeutic effects on acute myeloid leukaemia (AML), while the differential impacts of the two different HDACi on AML treatment still remains elusive. In this study, using 3-plex SILAC based quantitative proteomics technique, anti-acetyllysine antibody based affinity enrichment, high resolution LC-MS/MS and intensive bioinformatic analysis, the quantitative proteome and acetylome in SAHA and VPA treated AML HL60 cells were extensively studied. In total, 5,775 proteins and 1,124 lysine acetylation sites were successfully obtained in response to VAP and SAHA treatment. It is found that VPA and SAHA treatment differently induced proteome and acetylome profiling in AML HL60 cells. This study revealed the differential impacts of VPA and SAHA on proteome/acetylome in AML cells, deepening our understanding of HDAC inhibitor mediated AML therapeutics.
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45
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Bosselut R. Pleiotropic Functions of H3K27Me3 Demethylases in Immune Cell Differentiation. Trends Immunol 2016; 37:102-113. [PMID: 26796037 DOI: 10.1016/j.it.2015.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 12/12/2015] [Accepted: 12/13/2015] [Indexed: 02/06/2023]
Abstract
The trimethylation of histone H3 lysine 27 (H3K27Me3) contributes to gene repression, notably through recruitment of Polycomb complexes, and has long been considered essential to maintain cell identity. Whereas H3K27Me3 was thought to be stable and not catalytically reversible, the discovery of the Utx and Jmjd3 demethylases changed this notion, raising new questions on the role of these enzymes in gene expression and cell differentiation. Recent studies have demonstrated critical roles for Utx and Jmjd3 in the development and function of immune cells, and revealed both demethylase and demethylase-independent activities of these enzymes. I review these finding here, and discuss the current understanding of the mechanisms that underlie the broad, yet highly cell- and gene-specific, impact of these enzymes in vivo.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Kondo M, Tanaka Y, Kuwabara T, Naito T, Kohwi-Shigematsu T, Watanabe A. SATB1 Plays a Critical Role in Establishment of Immune Tolerance. THE JOURNAL OF IMMUNOLOGY 2015; 196:563-72. [DOI: 10.4049/jimmunol.1501429] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/13/2015] [Indexed: 01/21/2023]
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47
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Sakaguchi S, Hainberger D, Tizian C, Tanaka H, Okuda T, Taniuchi I, Ellmeier W. MAZR and Runx Factors Synergistically Repress ThPOK during CD8+ T Cell Lineage Development. THE JOURNAL OF IMMUNOLOGY 2015; 195:2879-87. [PMID: 26254341 DOI: 10.4049/jimmunol.1500387] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/13/2015] [Indexed: 11/19/2022]
Abstract
Th-inducing Pox virus and zinc finger/Krüppel-like factor (ThPOK) is a key commitment factor for CD4(+) lineage T cells and is essential for the maintenance of CD4 lineage integrity; thus, the expression of ThPOK has to be tightly controlled. In this article, we demonstrate that Myc-associated zinc finger-related factor (MAZR) and Runt-related transcription factor 1 (Runx1) together repressed ThPOK in preselection double-positive thymocytes, whereas MAZR acted in synergy with Runx3 in the repression of ThPOK in CD8(+) T cells. Furthermore, MAZR-Runx1 and MAZR-Runx3 double-mutant mice showed enhanced derepression of Cd4 in double-negative thymocytes and in CD8(+) T cells in comparison with Runx1 or Runx3 single-deficient mice, respectively, indicating that MAZR modulates Cd4 silencing. Thus, our data demonstrate developmental stage-specific synergistic activities between MAZR and Runx/core-binding factor β (CBFβ) complexes. Finally, retroviral Cre-mediated conditional deletion of MAZR in peripheral CD8(+) T cells led to the derepression of ThPOK, thus showing that MAZR is also part of the molecular machinery that maintains a repressed state of ThPOK in CD8(+) T cells.
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Affiliation(s)
- Shinya Sakaguchi
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Daniela Hainberger
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Caroline Tizian
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Hirokazu Tanaka
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; and
| | - Tsukasa Okuda
- Department of Biochemistry and Molecular Biology, Kyoto Prefectural University of Medicine Kyoto, Kyoto 602-8566, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; and
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria;
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48
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Yamaguchi T, Kurita T, Nishio K, Tsukada J, Hachisuga T, Morimoto Y, Iwai Y, Izumi H. Expression of BAF57 in ovarian cancer cells and drug sensitivity. Cancer Sci 2015; 106:359-66. [PMID: 25611552 PMCID: PMC4409878 DOI: 10.1111/cas.12612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 01/01/2023] Open
Abstract
The SMARCE1 (SWI / SNF-related, matrix-associated, and actin-dependent regulator of chromatin, subfamily e, member 1) encodes BAF57 protein. Previously, we reported that BAF57 is a predictive marker of endometrial carcinoma. In this study, we investigated BAF57 expression in ovarian cancer cell lines and their sensitivities to cisplatin, doxorubicin, paclitaxel, and 5-fluorouracil. BAF57 expression was strongly correlated with sensitivities to cisplatin, doxorubicin, and 5-fluorouracil in 10 ovarian cancer cell lines. Paclitaxel sensitivity was also correlated with BAF57 expression, but without significance. In A2780 ovarian cancer cells, knockdown of BAF57 using specific siRNA increased cell cycle arrest at G1 phase and the sensitivities to these anticancer agents. cDNA microarray analysis of A2780 cells transfected with BAF57 siRNA showed that 134 genes were positively regulated by BAF57, including ATP-binding cassette, sub-family G (WHITE), member 2 (ABCG2) encoding breast cancer resistance protein (BCRP). We confirmed that knockdown of BAF57 decreased BCRP expression in ovarian cancer cells by Western blot analysis, and that ABCG2 gene expression might be regulated transcriptionally. These results suggested that BAF57 is involved in ovarian cancer cell growth and sensitivity to anticancer agents, and that BAF57 may be a target for ovarian cancer therapy.
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Affiliation(s)
- Takahiro Yamaguchi
- Hematology, University of Occupational and Environmental Health, Kitakyushu, Japan
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The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:347571. [PMID: 25789315 PMCID: PMC4348595 DOI: 10.1155/2015/347571] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
Here, we review the role of sucrose nonfermenting (SNF2) family enzymes in blood cell development. The SNF2 family comprises helicase-like ATPases, originally discovered in yeast, that can remodel chromatin by changing chromatin structure and composition. The human genome encodes 30 different SNF2 enzymes. SNF2 family enzymes are often part of multisubunit chromatin remodeling complexes (CRCs), which consist of noncatalytic/auxiliary subunit along with the ATPase subunit. However, blood cells express a limited set of SNF2 ATPases that are necessary to maintain the pool of hematopoietic stem cells (HSCs) and drive normal blood cell development and differentiation. The composition of CRCs can be altered by the association of specific auxiliary subunits. Several auxiliary CRC subunits have specific functions in hematopoiesis. Aberrant expressions of SNF2 ATPases and/or auxiliary CRC subunit(s) are often observed in hematological malignancies. Using large-scale data from the International Cancer Genome Consortium (ICGC) we observed frequent mutations in genes encoding SNF2 helicase-like enzymes and auxiliary CRC subunits in leukemia. Hence, orderly function of SNF2 family enzymes is crucial for the execution of normal blood cell developmental program, and defects in chromatin remodeling caused by mutations or aberrant expression of these proteins may contribute to leukemogenesis.
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50
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Histone acetylation mediated by Brd1 is crucial for Cd8 gene activation during early thymocyte development. Nat Commun 2014; 5:5872. [PMID: 25519988 DOI: 10.1038/ncomms6872] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 11/14/2014] [Indexed: 11/08/2022] Open
Abstract
During T-cell development, Cd8 expression is controlled via dynamic regulation of its cis-regulatory enhancer elements. Insufficiency of enhancer activity causes variegated Cd8 expression in CD4(+)CD8(+) double-positive (DP) thymocytes. Brd1 is a subunit of the Hbo1 histone acetyltransferase (HAT) complex responsible for acetylation of histone H3 at lysine 14 (H3K14). Here we show that deletion of Brd1 in haematopoietic progenitors causes variegated expression of Cd8, resulting in the appearance of CD4(+)CD8(-)TCRβ(-/low) thymocytes indistinguishable from DP thymocytes in their properties. Biochemical analysis confirms that Brd1 forms a HAT complex with Hbo1 in thymocytes. ChIP analysis demonstrates that Brd1 localizes at the known enhancers in the Cd8 genes and is responsible for acetylation at H3K14. These findings indicate that the Brd1-mediated HAT activity is crucial for efficient activation of Cd8 expression via acetylation at H3K14, which serves as an epigenetic mark that promotes the recruitment of transcription machinery to the Cd8 enhancers.
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