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Chen H, Wang S, Dong R, Yu P, Li T, Hu L, Wang M, Qian Z, Zhou H, Yue X, Wang L, Xiao H. KDM6A Deficiency Induces Myeloid Bias and Promotes CMML-Like Disease Through JAK/STAT3 Activation by Repressing SOCS3. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2413091. [PMID: 40365824 DOI: 10.1002/advs.202413091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 03/11/2025] [Indexed: 05/15/2025]
Abstract
Chronic myelomonocytic leukemia (CMML) is a hematologic malignancy with a poor prognosis and limited targeted therapies. Lysine demethylase 6A (KDM6A), a H3K27 demethylase and key component of the COMPASS complex, is frequently mutated in hematologic malignancies, but its roles in embryonic hematopoiesis and tumor suppression in CMML remain unclear. Using zebrafish models with kdm6a mutants and integrative multi-omics analysis (ATAC-seq, RNA-seq, ChIP), we find that Kdm6a is a critical positive regulator of hematopoietic stem and progenitor cell (HSPC) emergence via Syk-related inflammatory signaling in a H3K27me3-dependent manner. We further find that Kdm6a haploinsufficiency in zebrafish leads to myeloid-biased hematopoiesis and a CMML-like disease, similar to CMML patients with reduced KDM6A expression. This KDM6A haploinsufficiency also significantly alters the chromatin landscape of genes associated with aging and cellular homeostasis in HSPCs. Mechanistically, KAM6A haploinsufficiency represses SOCS3 expression, thereby activating JAK/STAT3 signaling in HSPCs. Importantly, inhibitors targeting JAK or STAT3 phosphorylation alleviate myeloid expansion, providing a rationale for JAK/STAT pathway inhibition in CMML therapy. These findings enhance our understanding of CMML pathogenesis and propose new therapeutic avenues.
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Affiliation(s)
- Huiqiao Chen
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Shufen Wang
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Ruoyu Dong
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Pinghui Yu
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Tianyu Li
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Liangning Hu
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Mowang Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310009, P. R. China
| | - Zijun Qian
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Hongyu Zhou
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Xiaoyan Yue
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
| | - Limengmeng Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310009, P. R. China
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P. R. China
| | - Haowen Xiao
- Department of Hematology and Cell Therapy, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, P. R. China
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P. R. China
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McIntyre TI, Valdez O, Kochhar NP, Davidson B, Samad B, Qiu L, Hu K, Combes AJ, Erlebacher A. KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice. Cell 2025; 188:1265-1279.e18. [PMID: 39842437 PMCID: PMC11890963 DOI: 10.1016/j.cell.2024.12.019] [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: 10/24/2023] [Revised: 09/03/2024] [Accepted: 12/13/2024] [Indexed: 01/24/2025]
Abstract
Current efforts investigating parturition timing mechanisms have focused on the proximal triggers of labor onset generated in late pregnancy. By studying the delayed parturition phenotype of mice with uterine fibroblast deficiencies in the histone H3K27me3 demethylase KDM6B, we provide evidence that parturition timing is regulated by events that take place in early pregnancy. Immediately after copulation, uterine fibroblasts engage in a locus-specific epigenetic program that abruptly adjusts H3K27me3 levels across their genome. In the absence of KDM6B, many of the adjusted loci over-accumulate H3K27me3. This over-accumulation leads to nearby genes being misexpressed in mid-to-late gestation, a delayed effect partly attributable to a second locus-specific but KDM6B-independent process initiated within uterine fibroblasts soon after implantation. This second process employs progressive H3K27me3 loss to temporally structure post-midgestational patterns of gene induction. Further dissection of the ways uterine programming controls parturition timing may have relevance to human pregnancy complications such as preterm labor.
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Affiliation(s)
- Tara I McIntyre
- Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Omar Valdez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nathan P Kochhar
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brittany Davidson
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bushra Samad
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Longhui Qiu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kenneth Hu
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adrian Erlebacher
- Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Science, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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3
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Ma J, Zhang Y, Li J, Dang Y, Hu D. Regulation of histone H3K27 methylation in inflammation and cancer. MOLECULAR BIOMEDICINE 2025; 6:14. [PMID: 40042761 PMCID: PMC11882493 DOI: 10.1186/s43556-025-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 02/17/2025] [Accepted: 02/19/2025] [Indexed: 03/09/2025] Open
Abstract
Inflammation is a multifaceted defense mechanism of the immune system against infection. Chronic inflammation is intricately linked to all stages of tumorigenesis and is therefore associated with an elevated risk of developing serious cancers. Epigenetic mechanisms have the capacity to trigger inflammation as well as facilitate tumor development and transformation within an inflammatory context. They achieve this by dynamically modulating the expression of both pro-inflammatory and anti-inflammatory cytokines, which in turn sustains chronic inflammation. The aberrant epigenetic landscape reconfigures the transcriptional programs of inflammatory and oncogenic genes. This reconfiguration is pivotal in dictating the biological functions of both tumor cells and immune cells. Aberrant histone H3 lysine 27 site (H3K27) methylation has been shown to be involved in biological behaviors such as inflammation development, tumor progression, and immune response. The establishment and maintenance of this repressive epigenetic mark is dependent on the involvement of the responsible histone modifying enzymes enhancer of zeste homologue 2 (EZH2), jumonji domain containing 3 (JMJD3) and ubiquitously transcribed tetratricopeptide repeat gene X (UTX) as well as multiple cofactors. In addition, specific pharmacological agents have been shown to modulate H3K27 methylation levels, thereby modulating inflammation and carcinogenesis. This review comprehensively summarises the current characteristics and clinical significance of epigenetic regulation of H3K27 methylation in the context of inflammatory response and tumor progression.
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Affiliation(s)
- Jing Ma
- Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, No. 358 Datong Road, Pudong New Area, Shanghai, 200137, China
| | - Yalin Zhang
- Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, No. 358 Datong Road, Pudong New Area, Shanghai, 200137, China
| | - Jingyuan Li
- Institute of Digestive Diseases, Longhua Hospital, China-Canada Center of Research for Digestive Diseases (ccCRDD), Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, (Shanghai University of Traditional Chinese Medicine), Shanghai, 200032, China
| | - Yanqi Dang
- Institute of Digestive Diseases, Longhua Hospital, China-Canada Center of Research for Digestive Diseases (ccCRDD), Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, (Shanghai University of Traditional Chinese Medicine), Shanghai, 200032, China.
| | - Dan Hu
- Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, No. 358 Datong Road, Pudong New Area, Shanghai, 200137, China.
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Muraoka S, Baba T, Akazawa T, Katayama KI, Kusumoto H, Yamashita S, Kohjimoto Y, Iwabuchi S, Hashimoto S, Hara I, Inoue N. Tumor-derived lactic acid promotes acetylation of histone H3K27 and differentiation of IL-10-producing regulatory B cells through direct and indirect signaling pathways. Int J Cancer 2025; 156:840-852. [PMID: 39482832 DOI: 10.1002/ijc.35229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/02/2024] [Accepted: 10/08/2024] [Indexed: 11/03/2024]
Abstract
Tumor cells are known to enhance glycolysis, even under normoxic conditions, via the Warburg effect, producing excess lactic acid in the tumor microenvironment. Lactic acid enhances the IL-23/IL-17 pathway and induces chronic inflammation. The acidic microenvironment formed by lactic acid suppresses immune cell proliferation and activation. In the present study, we clarified that lactic acid had two novel activities for immune cells. First, lactic acid specifically enhanced acetylation at lysine 27 of histone H3 (H3K27ac) in splenic B cells and monocytes/macrophages, and this epigenetically up-regulates the expression of genes. Acetylation and methylation of other residues of histone H3 were rarely induced. Second, lactic acid induced a particularly-marked enhancement of Il10 gene expression in B cells, leading to an increase in IL-10-producing regulatory B (Breg) cells. Furthermore, two pathways should be involved in both the enhancement of H3K27ac and the induction of Breg cells by lactic acid: a direct pathway that enhances the CD40 signal in B cells, and an indirect pathway that affects B cells by activating the exchange protein directly activated by cAMP (EPAC) 1/2 in non-B cells. In tumor-bearing mice, the levels of H3K27ac of tumor-infiltrating B cells were significantly higher than splenic B cells and were suppressed by intraperitoneal injection of the EPAC1/2 inhibitor. In conclusion, tumor-derived lactic acid increases H3K27ac and IL-10-producing Breg cells, causing the suppression of anti-tumor immunity.
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Affiliation(s)
- Satoshi Muraoka
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | - Takashi Baba
- Department of Molecular Genetics, Wakayama Medical University, Wakayama, Japan
| | - Takashi Akazawa
- Department of Cancer Drug Discovery and Development, Research Center, Osaka International Cancer Institute, Chuo-ku, Osaka, Japan
| | - Kei-Ichi Katayama
- Department of Molecular Genetics, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Kusumoto
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | | | - Yasuo Kohjimoto
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | - Sadahiro Iwabuchi
- Department of Molecular Pathophysiology, Wakayama Medical University, Wakayama, Japan
| | - Shinichi Hashimoto
- Department of Molecular Pathophysiology, Wakayama Medical University, Wakayama, Japan
| | - Isao Hara
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | - Norimitsu Inoue
- Department of Molecular Genetics, Wakayama Medical University, Wakayama, Japan
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5
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Bahl A, Pandey S, Rakshit R, Kant S, Tripathi D. Infection-induced trained immunity: a twist in paradigm of innate host defense and generation of immunological memory. Infect Immun 2025; 93:e0047224. [PMID: 39655962 PMCID: PMC11784091 DOI: 10.1128/iai.00472-24] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2025] Open
Abstract
In contrast to adaptive immunity, which relies on memory T and B cells for long-term pathogen-specific responses, trained immunity involves the enhancement of innate immune responses through cellular reprogramming. Experimental evidence from animal models and human studies supports the concept of trained immunity and its potential therapeutic applications in the development of personalized medicine. However, there remains a huge gap in understanding the mechanisms, identifying specific microbial triggers responsible for the induction of trained immunity. This underscores the importance of investigating the potential role of trained immunity in redefining host defense and highlights future research directions. This minireview will provide a comprehensive summary of the new paradigm of trained immunity or innate memory pathways. It will shed light on infection-induced pathways through non-specific stimulation within macrophages and natural killer cells, which will be further elaborated in multiple disease perspectives caused by infectious agents such as bacteria, fungi, and viruses. The article further elaborates on the biochemical and cellular basis of trained immunity and its impact on disease status during recurrent exposures. The review concludes with a perspective segment discussing potential therapeutic benefits, limitations, and future challenges in this area of study. The review also sheds light upon potential risks involved in the induction of trained immunity.
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Affiliation(s)
- Aayush Bahl
- Microbial Pathogenesis and Microbiome Lab, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Saurabh Pandey
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, Delhi, India
| | - Roopshali Rakshit
- Microbial Pathogenesis and Microbiome Lab, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Sashi Kant
- Bacterial Pathogenesis, Boehringer Ingelheim Animal Health USA Inc, Ames, Iowa, USA
| | - Deeksha Tripathi
- Microbial Pathogenesis and Microbiome Lab, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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He XB, Guo F, Zhang W, Fan J, Le W, Chen Q, Ma Y, Zheng Y, Lee SH, Wang HJ, Wu Y, Zhou Q, Yang R. JMJD3 deficiency disturbs dopamine biosynthesis in midbrain and aggravates chronic inflammatory pain. Acta Neuropathol Commun 2024; 12:201. [PMID: 39716224 DOI: 10.1186/s40478-024-01912-x] [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: 09/25/2024] [Accepted: 12/09/2024] [Indexed: 12/25/2024] Open
Abstract
Midbrain dopamine (mDA) neurons participate in a wide range of brain functions through an intricate regulation of DA biosynthesis. The epigenetic factors and mechanisms in this process are not well understood. Here we report that histone demethylase JMJD3 is a critical regulator for DA biosynthesis in adult mouse mDA neurons. Mice carrying Jmjd3 conditional knockout or undergoing pharmaceutical inhibition of JMJD3 showed consistent reduction of DA content in midbrain and striatum. Histological examination of both mice confirmed that TH and NURR1, two key molecules in DA biosynthesis pathway, were decreased in mDA neurons. Mechanistic experiments in vivo and in vitro further demonstrated that the transcriptions of Th and Nurr1 in mDA neurons were suppressed by JMJD3 deficiency, because of increased repressive H3K27me3 and attenuated bindings of JMJD3 and NURR1 on the promoters of both genes. On behavioral level, a significant prolonged inflammation-induced mechanical hyperalgesia was found in conditional knockout mice regardless of sex and age, whereas motor function appeared to be intact. Our findings establish a novel link between DA level in mDA neurons with intrinsic JMJD3 activity, and suggest prolonged chronic inflammatory pain as a major loss-of-function consequence.
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Affiliation(s)
- Xi-Biao He
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China.
| | - Fang Guo
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
| | - Wei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiacheng Fan
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
| | - Weidong Le
- Center for Translational Medicine, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Qi Chen
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
| | - Yongjun Ma
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
- The Interdisciplinary Research Center of Biology and Chemistry, Chinese Academy of sciences, Shanghai, 200120, China
| | - Yong Zheng
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
| | - Sang-Hun Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hui-Jing Wang
- Laboratory of Neuropsychopharmacology, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Yi Wu
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qinming Zhou
- Department of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rui Yang
- Laboratory of Stem Cell Biology and Epigenetics, School of Basic Medical Sciences, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
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Feng M, Chai C, Hao X, Lai X, Luo Y, Zhang H, Tang W, Gao N, Pan G, Liu X, Wang Y, Xiong W, Wu Q, Wang J. Inherited KDM6A A649T facilitates tumor-immune escape and exacerbates colorectal signet-ring cell carcinoma outcomes. Oncogene 2024; 43:1757-1768. [PMID: 38622203 DOI: 10.1038/s41388-024-03029-w] [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: 07/09/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024]
Abstract
Childhood onset of colorectal signet-ring cell carcinoma (CR-SRCC) is extremely rare and featured as highly malignant with poor prognosis. Here we reported a CR-SRCC case of 11-year-old boy with a novel inherited X-linked KDM6AA694T mutation. The H3K27me3 demethylase KDM6A was frequently mutated in varieties of tumors and acts as a tumor suppressor. In vivo H3K27me3 demethylation assay demonstrated that KDM6AA694T had dampened H3K27me3 demethylase activity. Overexpression of KDM6AA694T in SRCC cell line KATO3 promoted cell proliferation, invasion and migration, which were further confirmed in vivo by constructing orthotopic tumor growth and lung metastasis model. Besides, expression of KDM6AA694T in immune cells suppresses inflammatory macrophage response and effector T cell response. In conclusion, we characterized a novel inherited KDM6AA694T mutant from a childhood-onset SRCC case and demonstrated that the mutant with impaired H3K27me3 demethylase activity could potentiate tumor malignancy and suppress antitumor immunity.
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Affiliation(s)
- Maoxiao Feng
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Chengwei Chai
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- Department of Pediatric General Surgery, Guangdong Women and Children Hospital, Guangzhou, 511442, China.
| | - Xiaodong Hao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University Dezhou Hospital, Dezhou, 253000, China
| | - Xiaojiang Lai
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Yuanyuan Luo
- Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Hong Zhang
- Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Wenzhu Tang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Ningxin Gao
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Guihong Pan
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Xiaojie Liu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Wenjing Xiong
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Qiang Wu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Jun Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China.
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Walters BW, Rainsford SR, Heuer RA, Dias N, Huang X, de Rooij D, Lesch BJ. KDM6A/UTX promotes spermatogenic gene expression across generations and is not required for male fertility†. Biol Reprod 2024; 110:391-407. [PMID: 37861693 PMCID: PMC11484508 DOI: 10.1093/biolre/ioad141] [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] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023] Open
Abstract
Paternal chromatin undergoes extensive structural and epigenetic changes during mammalian spermatogenesis, producing sperm with an epigenome optimized for the transition to embryogenesis. Lysine demethylase 6a (KDM6A, also called UTX) promotes gene activation in part via demethylation of H3K27me3, a developmentally important repressive modification abundant throughout the epigenome of spermatogenic cells and sperm. We previously demonstrated increased cancer risk in genetically wild-type mice derived from a paternal germ line lacking Kdm6a (Kdm6a cKO), indicating a role for KDM6A in regulating heritable epigenetic states. However, the regulatory function of KDM6A during spermatogenesis is not known. Here, we show that Kdm6a is transiently expressed in spermatogenesis, with RNA and protein expression largely limited to late spermatogonia and early meiotic prophase. Kdm6a cKO males do not have defects in fertility or the overall progression of spermatogenesis. However, hundreds of genes are deregulated upon loss of Kdm6a in spermatogenic cells, with a strong bias toward downregulation coinciding with the time when Kdm6a is expressed. Misregulated genes encode factors involved in chromatin organization and regulation of repetitive elements, and a subset of these genes was persistently deregulated in the male germ line across two generations of offspring of Kdm6a cKO males. Genome-wide epigenetic profiling revealed broadening of H3K27me3 peaks in differentiating spermatogonia of Kdm6a cKO mice, suggesting that KDM6A demarcates H3K27me3 domains in the male germ line. Our findings highlight KDM6A as a transcriptional activator in the mammalian male germ line that is dispensable for spermatogenesis but important for safeguarding gene regulatory state intergenerationally.
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Affiliation(s)
| | | | - Rachel A Heuer
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Nicolas Dias
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Xiaofang Huang
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Dirk de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bluma J Lesch
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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Ge G, Zhang P, Sui P, Chen S, Yang H, Guo Y, Rubalcava IP, Noor A, Delma CR, Agosto-Peña J, Geng H, Medina EA, Liang Y, Nimer SD, Mesa R, Abdel-Wahab O, Xu M, Yang FC. Targeting lysine demethylase 6B ameliorates ASXL1 truncation-mediated myeloid malignancies in preclinical models. J Clin Invest 2024; 134:e163964. [PMID: 37917239 PMCID: PMC10760961 DOI: 10.1172/jci163964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 10/31/2023] [Indexed: 11/04/2023] Open
Abstract
ASXL1 mutation frequently occurs in all forms of myeloid malignancies and is associated with aggressive disease and poor prognosis. ASXL1 recruits Polycomb repressive complex 2 (PRC2) to specific gene loci to repress transcription through trimethylation of histone H3 on lysine 27 (H3K27me3). ASXL1 alterations reduce H3K27me3 levels, which results in leukemogenic gene expression and the development of myeloid malignancies. Standard therapies for myeloid malignancies have limited efficacy when mutated ASXL1 is present. We discovered upregulation of lysine demethylase 6B (KDM6B), a demethylase for H3K27me3, in ASXL1-mutant leukemic cells, which further reduces H3K27me3 levels and facilitates myeloid transformation. Here, we demonstrated that heterozygous deletion of Kdm6b restored H3K27me3 levels and normalized dysregulated gene expression in Asxl1Y588XTg hematopoietic stem/progenitor cells (HSPCs). Furthermore, heterozygous deletion of Kdm6b decreased the HSPC pool, restored their self-renewal capacity, prevented biased myeloid differentiation, and abrogated progression to myeloid malignancies in Asxl1Y588XTg mice. Importantly, administration of GSK-J4, a KDM6B inhibitor, not only restored H3K27me3 levels but also reduced the disease burden in NSG mice xenografted with human ASXL1-mutant leukemic cells in vivo. This preclinical finding provides compelling evidence that targeting KDM6B may be a therapeutic strategy for myeloid malignancies with ASXL1 mutations.
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Affiliation(s)
- Guo Ge
- Department of Cell Systems and Anatomy
| | - Peng Zhang
- Department of Cell Systems and Anatomy
- Mays Cancer Center
| | - Pinpin Sui
- Department of Cell Systems and Anatomy
- Mays Cancer Center
| | - Shi Chen
- Department of Molecular Medicine, and
| | - Hui Yang
- Department of Cell Systems and Anatomy
| | - Ying Guo
- Department of Cell Systems and Anatomy
| | | | - Asra Noor
- Department of Cell Systems and Anatomy
| | - Caroline R. Delma
- Department of Cell Systems and Anatomy
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | - Hui Geng
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Edward A. Medina
- Mays Cancer Center
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Ying Liang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, USA
| | - Stephen D. Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mingjiang Xu
- Mays Cancer Center
- Department of Molecular Medicine, and
| | - Feng-Chun Yang
- Department of Cell Systems and Anatomy
- Mays Cancer Center
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10
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Fazazi MR, Ruda GF, Brennan PE, Rangachari M. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system. Brain Res Bull 2023; 202:110748. [PMID: 37657612 DOI: 10.1016/j.brainresbull.2023.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
T cell-driven autoimmune responses are subject to striking sex-dependent effects. While the contributions of sex hormones are well-understood, those of sex chromosomes are meeting with increased appreciation. Here, we outline what is known about the contribution of sex chromosome-linked factors to experimental autoimmune encephalomyelitis (EAE), a mouse model that recapitulates many of the T cell-driven mechanisms of multiple sclerosis (MS) pathology. Particular attention is paid to the KDM family of histone demethylases, several of which - KDM5C, KDM5D and KDM6A - are sex chromosome encoded. Finally, we provide evidence that functional inhibition of KDM5 molecules can suppress interferon (IFN)γ production from murine male effector T cells, and that an increased ratio of inflammatory Kdm6a to immunomodulatory Kdm5c transcript is observed in T helper 17 (Th17) cells from women with the autoimmune disorder ankylosing spondylitis (AS). Histone lysine demethlyases thus represent intriguing targets for the treatment of T cell-driven autoimmune disorders.
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Affiliation(s)
- Mohamed Reda Fazazi
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Gian Filippo Ruda
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Manu Rangachari
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada.
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11
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Hong LYQ, Yeung ESH, Tran DT, Yerra VG, Kaur H, Kabir MDG, Advani SL, Liu Y, Batchu SN, Advani A. Altered expression, but small contribution, of the histone demethylase KDM6A in obstructive uropathy in mice. Dis Model Mech 2023; 16:dmm049991. [PMID: 37655466 PMCID: PMC10482012 DOI: 10.1242/dmm.049991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/04/2023] [Indexed: 09/02/2023] Open
Abstract
Epigenetic processes have emerged as important modulators of kidney health and disease. Here, we studied the role of KDM6A (a histone demethylase that escapes X-chromosome inactivation) in kidney tubule epithelial cells. We initially observed an increase in tubule cell Kdm6a mRNA in male mice with unilateral ureteral obstruction (UUO). However, tubule cell knockout of KDM6A had relatively minor consequences, characterized by a small reduction in apoptosis, increase in inflammation and downregulation of the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In proximal tubule lineage HK-2 cells, KDM6A knockdown decreased PPARγ coactivator-1α (PGC-1α) protein levels and mRNA levels of the encoding gene, PPARGC1A. Tubule cell Kdm6a mRNA levels were approximately 2-fold higher in female mice than in male mice, both under sham and UUO conditions. However, kidney fibrosis after UUO was similar in both sexes. The findings demonstrate Kdm6a to be a dynamically regulated gene in the kidney tubule, varying in expression levels by sex and in response to injury. Despite the context-dependent variation in Kdm6a expression, knockout of tubule cell KDM6A has subtle (albeit non-negligible) effects in the adult kidney, at least in males.
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Affiliation(s)
- Lisa Y. Q. Hong
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Emily S. H. Yeung
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Duc Tin Tran
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Veera Ganesh Yerra
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Harmandeep Kaur
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - M. D. Golam Kabir
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Suzanne L. Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Youan Liu
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Sri Nagarjun Batchu
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
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12
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Qu L, Yin T, Zhao Y, Lv W, Liu Z, Chen C, Liu K, Shan S, Zhou R, Li X, Dong H. Histone demethylases in the regulation of immunity and inflammation. Cell Death Discov 2023; 9:188. [PMID: 37353521 DOI: 10.1038/s41420-023-01489-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogens or danger signals trigger the immune response. Moderate immune response activation removes pathogens and avoids excessive inflammation and tissue damage. Histone demethylases (KDMs) regulate gene expression and play essential roles in numerous physiological processes by removing methyl groups from lysine residues on target proteins. Abnormal expression of KDMs is closely associated with the pathogenesis of various inflammatory diseases such as liver fibrosis, lung injury, and autoimmune diseases. Despite becoming exciting targets for diagnosing and treating these diseases, the role of these enzymes in the regulation of immune and inflammatory response is still unclear. Here, we review the underlying mechanisms through which KDMs regulate immune-related pathways and inflammatory responses. In addition, we also discuss the future applications of KDMs inhibitors in immune and inflammatory diseases.
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Affiliation(s)
- Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Tong Yin
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yijin Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenting Lv
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Ziqi Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Shigang Shan
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaoqing Li
- Biological Targeted Therapy Key Laboratory in Hubei, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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13
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Ramesh V, Liu F, Minto MS, Chan U, West AE. Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics. eLife 2023; 12:e86273. [PMID: 37092728 PMCID: PMC10181825 DOI: 10.7554/elife.86273] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 04/25/2023] Open
Abstract
The functional maturation of neurons is a prolonged process that extends past the mitotic exit and is mediated by the chromatin-dependent orchestration of gene transcription programs. We find that expression of this maturation gene program in mouse cerebellar granule neurons (CGNs) requires dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), demonstrating a function for this chromatin modification beyond its role in cell fate specification. The developmental loss of H3K27me3 at promoters of genes activated as CGNs mature is facilitated by the lysine demethylase and ASD-risk gene, Kdm6b. Interestingly, inhibition of the H3K27 methyltransferase EZH2 in newborn CGNs not only blocks the repression of progenitor genes but also impairs the induction of mature CGN genes, showing the importance of bidirectional H3K27me3 regulation across the genome. These data demonstrate that H3K27me3 turnover in developing postmitotic neurons regulates the temporal coordination of gene expression programs that underlie functional neuronal maturation.
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Affiliation(s)
- Vijyendra Ramesh
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
| | - Fang Liu
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Melyssa S Minto
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Urann Chan
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Anne E West
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
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14
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Noda H, Suzuki J, Matsuoka Y, Matsumoto A, Kuwahara M, Kamei Y, Takada Y, Yamashita M. The histone demethylase Utx controls CD8 + T-cell-dependent antitumor immunity via epigenetic regulation of the effector function. Cancer Sci 2023. [PMID: 37068788 DOI: 10.1111/cas.15814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/18/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023] Open
Abstract
CD8+ T cells play a central role in antitumor immune responses. Epigenetic gene regulation is essential to acquire the effector function of CD8+ T cells. However, the role of Utx, a demethylase of histone H3K27, in antitumor immunity remains unclear. In this study, we examined the roles of Utx in effector CD8+ T-cell differentiation and the antitumor immune response. In a murine tumor-bearing model, an increased tumor size and decreased survival rate were observed in T-cell-specific Utx KO (Utx KO) mice compared with wild-type (WT) mice. The number of CD8+ T cells in tumor-infiltrating lymphocytes (TILs) was significantly decreased in Utx KO mice. We found that the acquisition of effector function was delayed and attenuated in Utx KO CD8+ T cells. RNA sequencing revealed that the expression of effector signature genes was decreased in Utx KO effector CD8+ T cells, while the expression of naïve or memory signature genes was increased. Furthermore, the expression of Cxcr3, which is required for the migration of effector CD8+ T cells to tumor sites, was substantially decreased in Utx KO CD8+ T cells. These findings suggest that Utx promotes CD8+ T-cell-dependent antitumor immune responses partially through epigenetic regulation of the effector function.
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Affiliation(s)
- Haruna Noda
- Breast Center, Ehime University Hospital, Toon, Japan
- Department of Hepato-Biliary-Pancreatic Surgery and Breast Surgery, Graduate School of Medicine, Ehime University, Toon, Japan
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Junpei Suzuki
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Yuko Matsuoka
- Department of Translational Research Center, Ehime University Hospital, Toon, Japan
| | - Akira Matsumoto
- Department of Infections and Host Defenses, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Makoto Kuwahara
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Yoshiaki Kamei
- Breast Center, Ehime University Hospital, Toon, Japan
- Department of Hepato-Biliary-Pancreatic Surgery and Breast Surgery, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Yasutsugu Takada
- Department of Hepato-Biliary-Pancreatic Surgery and Breast Surgery, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon, Japan
- Department of Infections and Host Defenses, Graduate School of Medicine, Ehime University, Toon, Japan
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15
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Chen LJ, Xu XY, Zhong XD, Liu YJ, Zhu MH, Tao F, Li CY, She QS, Yang GJ, Chen J. The role of lysine-specific demethylase 6A (KDM6A) in tumorigenesis and its therapeutic potentials in cancer therapy. Bioorg Chem 2023; 133:106409. [PMID: 36753963 DOI: 10.1016/j.bioorg.2023.106409] [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: 12/24/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Histone demethylation is a key post-translational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Lysine specific demethylase 6A (KDM6A, also known as UTX) is an Fe2+- and α-ketoglutarate- dependent oxidase which belongs to KDM6 Jumonji histone demethylase subfamily, and it can remove mono-, di- and tri-methyl groups from methylated lysine 27 of histone H3 (H3K27me1/2/3). Mounting studies indicate that KDM6A is responsible for driving multiple human diseases, particularly cancers and pharmacological inhibition of KDM6A is an effective strategy to treat varieties of KDM6A-amplified cancers in cellulo and in vivo. Although there are several reviews on the roles of KDM6 subfamily in cancer development and therapy, all of them only simply introduce the roles of KDM6A in cancer without systematically summarizing the specific mechanisms of KDM6A in tumorigenesis, which greatly limits the advances on the understanding of roles KDM6A in varieties of cancers, discovering targeting selective KDM6A inhibitors, and exploring the adaptive profiles of KDM6A antagonists. Herein, we present the structure and functions of KDM6A, simply outline the functions of KDM6A in homeostasis and non-cancer diseases, summarize the role of KDM6A and its distinct target genes/ligand proteins in development of varieties of cancers, systematically classify KDM6A inhibitors, sum up the difficulties encountered in the research of KDM6A and the discovery of related drugs, and provide the corresponding solutions, which will contribute to understanding the roles of KDM6A in carcinogenesis and advancing the progression of KDM6A as a drug target in cancer therapy.
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Affiliation(s)
- Li-Juan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Xin-Yang Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Xiao-Dan Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Fan Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China
| | - Qiu-Sheng She
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan 467044, Henan, China.
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315211, China.
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16
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Mei Y, Xin Y, Li X, Yin H, Xiong F, Yang M, Wu H. Aberrant expression of JMJD3 in SLE promotes B-cell differentiation. Immunobiology 2023; 228:152347. [PMID: 36791533 DOI: 10.1016/j.imbio.2023.152347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/20/2023] [Accepted: 02/04/2023] [Indexed: 02/13/2023]
Abstract
Systemic lupus erythematosus (SLE) is a typical autoimmune disease distinguished by multiple organ dysfunction, which is related to a variety of causative factors. B-cell overactivation is a key factor in SLE. However, the pathogenesis underlying anomalous B cells has not been well elucidated. B-cell fate is regulated in diverse epigenetic ways apart from traditional ways. As one of the mechanisms of epigenetics, histone modification mainly affects transcription and translation by changing the chemical groups on histones by histone modification enzymes. JMJD3, a histone demethylase, can promote T-cell proliferation in SLE patients, which exacerbates SLE. However, the mechanism of JMJD3 in B cells in SLE has not been studied. Here, we found that the mean fluorescence intensity (MFI) of JMJD3 in classical memory B cells (CMBs) was higher than that in naïve B cells (NBs) from human tonsil tissue; JMJD3 was overexpressed in B cells from the peripheral blood of SLE patients compared with healthy controls (HCs). In vitro, our experiment showed that JMJD3 could regulate B-cell differentiation by promoting naïve B-cell differentiation into CD27+ B cells, and Blimp-1 and Bcl-6 also decreased after inhibitor treatment. These findings provide a new direction for the pathogenesis of SLE and may supply a new idea for subsequent drug development.
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Affiliation(s)
- Yang Mei
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Yue Xin
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Xi Li
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Heng Yin
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Feng Xiong
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ming Yang
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.
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17
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Tayari MM, Fang C, Ntziachristos P. Context-Dependent Functions of KDM6 Lysine Demethylases in Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:139-165. [PMID: 37751139 DOI: 10.1007/978-3-031-38176-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Histone lysine methylation is a major epigenetic modification that participates in several cellular processes including gene regulation and chromatin structure. This mark can go awry in disease contexts such as cancer. Two decades ago, the discovery of histone demethylase enzymes thirteen years ago sheds light on the complexity of the regulation of this mark. Here we address the roles of lysine demethylases JMJD3 and UTX in physiological and disease contexts. The two demethylases play pivotal roles in many developmental and disease contexts via regulation of di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) in repressing gene expression programs. JMJD3 and UTX participate in several biochemical settings including methyltransferase and chromatin remodeling complexes. They have histone demethylase-dependent and -independent activities and a variety of context-specific interacting factors. The structure, amounts, and function of the demethylases can be altered in disease due to genetic alterations or aberrant gene regulation. Therefore, academic and industrial initiatives have targeted these enzymes using a number of small molecule compounds in therapeutic approaches. In this chapter, we will touch upon inhibitor formulations, their properties, and current efforts to test them in preclinical contexts to optimize their therapeutic outcomes. Demethylase inhibitors are currently used in targeted therapeutic approaches that might be particularly effective when used in conjunction with systemic approaches such as chemotherapy.
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Affiliation(s)
- Mina Masoumeh Tayari
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Center for Medical Genetics, Ghent University, Medical Research Building 2 (MRB2), Entrance 38, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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18
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Han X, Cao X, Cabrera RM, Pimienta Ramirez PA, Zhang C, Ramaekers VT, Finnell RH, Lei Y. KDM6B Variants May Contribute to the Pathophysiology of Human Cerebral Folate Deficiency. BIOLOGY 2022; 12:74. [PMID: 36671766 PMCID: PMC9855468 DOI: 10.3390/biology12010074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/25/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
(1) Background: The genetic etiology of most patients with cerebral folate deficiency (CFD) remains poorly understood. KDM6B variants were reported to cause neurodevelopmental diseases; however, the association between KDM6B and CFD is unknown; (2) Methods: Exome sequencing (ES) was performed on 48 isolated CFD cases. The effect of KDM6B variants on KDM6B protein expression, Histone H3 lysine 27 epigenetic modification and FOLR1 expression were examined in vitro. For each patient, serum FOLR1 autoantibodies were measured; (3) Results: Six KDM6B variants were identified in five CFD patients, which accounts for 10% of our CFD cohort cases. Functional experiments indicated that these KDM6B variants decreased the amount of KDM6B protein, which resulted in elevated H3K27me2, lower H3K27Ac and decreased FOLR1 protein concentrations. In addition, FOLR1 autoantibodies have been identified in serum; (4) Conclusion: Our study raises the possibility that KDM6B may be a novel CFD candidate gene in humans. Variants in KDM6B could downregulate FOLR1 gene expression, and might also predispose carriers to the development of FOLR1 autoantibodies.
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Affiliation(s)
- Xiao Han
- Department of Reproductive Medicine Center, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuanye Cao
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert M. Cabrera
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paula Andrea Pimienta Ramirez
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cuilian Zhang
- Department of Reproductive Medicine Center, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Vincent T. Ramaekers
- Department of Pediatric Neurology, University Hospital Center Liège, 4000 Liège, Belgium
| | - Richard H. Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Kolev HM, Swisa A, Manduchi E, Lan Y, Stine RR, Testa G, Kaestner KH. H3K27me3 Demethylases Maintain the Transcriptional and Epigenomic Landscape of the Intestinal Epithelium. Cell Mol Gastroenterol Hepatol 2022; 15:821-839. [PMID: 36503150 PMCID: PMC9971508 DOI: 10.1016/j.jcmgh.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 02/23/2023]
Abstract
BACKGROUND & AIMS Although trimethylation of histone H3 lysine 27 (H3K27me3) by polycomb repressive complex 2 is required for intestinal function, the role of the antagonistic process-H3K27me3 demethylation-in the intestine remains unknown. The aim of this study was to determine the contribution of H3K27me3 demethylases to intestinal homeostasis. METHODS An inducible mouse model was used to simultaneously ablate the 2 known H3K27me3 demethylases, lysine (K)-specific demethylase 6A (Kdm6a) and lysine (K)-specific demethylase 6B (Kdm6b), from the intestinal epithelium. Mice were analyzed at acute and prolonged time points after Kdm6a/b ablation. Cellular proliferation and differentiation were measured using immunohistochemistry, while RNA sequencing and chromatin immunoprecipitation followed by sequencing for H3K27me3 were used to identify gene expression and chromatin changes after Kdm6a/b loss. Intestinal epithelial renewal was evaluated using a radiation-induced injury model, while Paneth cell homeostasis was measured via immunohistochemistry, immunoblot, and transmission electron microscopy. RESULTS We did not detect any effect of Kdm6a/b ablation on intestinal cell proliferation or differentiation toward the secretory cell lineages. Acute and prolonged Kdm6a/b loss perturbed expression of gene signatures belonging to multiple cell lineages (adjusted P value < .05), and a set of 72 genes was identified as being down-regulated with an associated increase in H3K27me3 levels after Kdm6a/b ablation (false discovery rate, <0.05). After prolonged Kdm6a/b loss, dysregulation of the Paneth cell gene signature was associated with perturbed matrix metallopeptidase 7 localization (P < .0001) and expression. CONCLUSIONS Although KDM6A/B does not regulate intestinal cell differentiation, both enzymes are required to support the full transcriptomic and epigenomic landscape of the intestinal epithelium and the expression of key Paneth cell genes.
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Affiliation(s)
- Hannah M Kolev
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Avital Swisa
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elisabetta Manduchi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yemin Lan
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rachel R Stine
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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20
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Simper MS, Coletta LD, Gaddis S, Lin K, Mikulec CD, Takata T, Tomida MW, Zhang D, Tang DG, Estecio MR, Shen J, Lu Y. Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets. J Biomol Tech 2022; 33:3fc1f5fe.7910785e. [PMID: 36910579 PMCID: PMC10001930 DOI: 10.7171/3fc1f5fe.7910785e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels. Results In this study, we evaluated the performance of 4 ChIP-Seq library preparation protocols (New England Biolabs [NEB] NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo [now PerkinElmer] NEXTflex) on 3 target proteins, chosen to represent the 3 typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3), and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments. Conclusions Our results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries. For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice, as it performed well for each of the 3 targets we tested across a wide array of input DNA levels.
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Affiliation(s)
- M S Simper
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - L Della Coletta
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - S Gaddis
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - K Lin
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - C D Mikulec
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - True Takata
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - M W Tomida
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - D Zhang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: College of Biology Hunan University Changsha410082 China
| | - D G Tang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: Department of Pharmacology and Therapeutics Roswell Park Cancer Institute BuffaloNew York14263 USA
| | - M R Estecio
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - J Shen
- Department of Epigenetics and Molecular Carcinogenesis.,Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Program in Genetics and Epigenetics MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences The University of Texas MD Anderson Cancer Center SmithvilleTexas78957 USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
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21
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Ford BR, Vignali PDA, Rittenhouse NL, Scharping NE, Peralta R, Lontos K, Frisch AT, Delgoffe GM, Poholek AC. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells. Sci Immunol 2022; 7:eabj9123. [PMID: 35930654 PMCID: PMC9851604 DOI: 10.1126/sciimmunol.abj9123] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Response rates to immunotherapy in solid tumors remain low due in part to the elevated prevalence of terminally exhausted T cells, a hypofunctional differentiation state induced through persistent antigen and stress signaling. However, the mechanisms promoting progression to terminal exhaustion in the tumor remain undefined. Using the low-input chromatin immunoprecipitation sequencing method CUT&RUN, we profiled the histone modification landscape of tumor-infiltrating CD8+ T cells throughout differentiation. We found that terminally exhausted T cells had unexpected chromatin features that limit their transcriptional potential. Terminally exhausted T cells had a substantial fraction of active chromatin, including active enhancers enriched for bZIP/AP-1 transcription factor motifs that lacked correlated gene expression, which was restored by immunotherapeutic costimulatory signaling. Reduced transcriptional potential was also driven by an increase in histone bivalency, which we linked directly to hypoxia exposure. Enforced expression of the hypoxia-insensitive histone demethylase Kdm6b was sufficient to overcome hypoxia, increase function, and promote antitumor immunity. Our study reveals the specific epigenetic changes mediated by histone modifications during T cell differentiation that support exhaustion in cancer, highlighting that their altered function is driven by improper costimulatory signals and environmental factors. These data suggest that even terminally exhausted T cells may remain competent for transcription in settings of increased costimulatory signaling and reduced hypoxia.
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Affiliation(s)
- B. Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paolo D. A. Vignali
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Natalie L. Rittenhouse
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicole E. Scharping
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ronal Peralta
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Konstantinos Lontos
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Andrew T. Frisch
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Greg M. Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
| | - Amanda C. Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
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22
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Zhang H, Hu Y, Liu D, Liu Z, Xie N, Liu S, Zhang J, Jiang Y, Li C, Wang Q, Chen X, Ye D, Sun D, Zhai Y, Yan X, Liu Y, Chen CD, Huang X, Eugene Chin Y, Shi Y, Wu B, Zhang X. The histone demethylase Kdm6b regulates the maturation and cytotoxicity of TCRαβ +CD8αα + intestinal intraepithelial lymphocytes. Cell Death Differ 2022; 29:1349-1363. [PMID: 34999729 PMCID: PMC9287323 DOI: 10.1038/s41418-021-00921-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
Intestinal intraepithelial lymphocytes (IELs) are distributed along the length of the intestine and are considered the frontline of immune surveillance. The precise molecular mechanisms, especially epigenetic regulation, of their development and function are poorly understood. The trimethylation of histone 3 at lysine 27 (H3K27Me3) is a kind of histone modifications and associated with gene repression. Kdm6b is an epigenetic enzyme responsible for the demethylation of H3K27Me3 and thus promotes gene expression. Here we identified Kdm6b as an important intracellular regulator of small intestinal IELs. Mice genetically deficient for Kdm6b showed greatly reduced numbers of TCRαβ+CD8αα+ IELs. In the absence of Kdm6b, TCRαβ+CD8αα+ IELs exhibited increased apoptosis, disturbed maturation and a compromised capability to lyse target cells. Both IL-15 and Kdm6b-mediated demethylation of histone 3 at lysine 27 are responsible for the maturation of TCRαβ+CD8αα+ IELs through upregulating the expression of Gzmb and Fasl. In addition, Kdm6b also regulates the expression of the gut-homing molecule CCR9 by controlling H3K27Me3 level at its promoter. However, Kdm6b is dispensable for the reactivity of thymic precursors of TCRαβ+CD8αα+ IELs (IELPs) to IL-15 and TGF-β. In conclusion, we showed that Kdm6b plays critical roles in the maturation and cytotoxic function of small intestinal TCRαβ+CD8αα+ IELs.
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Affiliation(s)
- Haohao Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yiming Hu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Dandan Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Zhi Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ningxia Xie
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
| | - Sanhong Liu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Jie Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yuhang Jiang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Cuifeng Li
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Qi Wang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Deji Ye
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Donglin Sun
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
| | - Yujia Zhai
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xinhui Yan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yongzhong Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xingxu Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China
| | - Y Eugene Chin
- Institutes of Biology and Medical Sciences, Soochow University Medical College, 215000, Suzhou, China
| | - Yufang Shi
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, 215000, Suzhou, China
| | - Baojin Wu
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
| | - Xiaoren Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University; Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes; State Key Laboratory of Respiratory Disease, 510000, Guangzhou, China.
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.
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23
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Sanchez A, Penault-Llorca F, Bignon YJ, Guy L, Bernard-Gallon D. Effects of GSK-J4 on JMJD3 Histone Demethylase in Mouse Prostate Cancer Xenografts. Cancer Genomics Proteomics 2022; 19:339-349. [PMID: 35430567 DOI: 10.21873/cgp.20324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Histone methylation status is required to control gene expression. H3K27me3 is an epigenetic tri-methylation modification to histone H3 controlled by the demethylase JMJD3. JMJD3 is dysregulated in a wide range of cancers and has been shown to control the expression of a specific growth-modulatory gene signature, making it an interesting candidate to better understand prostate tumor progression in vivo. This study aimed to identify the impact of JMJD3 inhibition by its inhibitor, GSK4, on prostate tumor growth in vivo. MATERIALS AND METHODS Prostate cancer cell lines were implanted into Balb/c nude male mice. The effects of the selective JMJD3 inhibitor GSK-J4 on tumor growth were analyzed by bioluminescence assays and H3K27me3-regulated changes in gene expression were analyzed by ChIP-qPCR and RT-qPCR. RESULTS JMJD3 inhibition contributed to an increase in tumor growth in androgen-independent (AR-) xenografts and a decrease in androgen-dependent (AR+). GSK-J4 treatment modulated H3K27me3 enrichment on the gene panel in DU-145-luc xenografts while it had little effect on PC3-luc and no effect on LNCaP-luc. Effects of JMJD3 inhibition affected the panel gene expression. CONCLUSION JMJD3 has a differential effect in prostate tumor progression according to AR status. Our results suggest that JMJD3 is able to play a role independently of its demethylase function in androgen-independent prostate cancer. The effects of GSK-J4 on AR+ prostate xenografts led to a decrease in tumor growth.
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Affiliation(s)
- Anna Sanchez
- Department of Oncogenetics, Centre Jean Perrin, Clermont-Ferrand, France.,INSERM U 1240 Molecular Imagery and Theranostic Strategies (IMoST), Clermont-Ferrand, France
| | - Frédérique Penault-Llorca
- INSERM U 1240 Molecular Imagery and Theranostic Strategies (IMoST), Clermont-Ferrand, France.,Department of Biopathology, Centre Jean Perrin, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Department of Oncogenetics, Centre Jean Perrin, Clermont-Ferrand, France.,INSERM U 1240 Molecular Imagery and Theranostic Strategies (IMoST), Clermont-Ferrand, France
| | - Laurent Guy
- INSERM U 1240 Molecular Imagery and Theranostic Strategies (IMoST), Clermont-Ferrand, France.,Department of Urology, Gabriel Montpied Hospital, Clermont-Ferrand, France
| | - Dominique Bernard-Gallon
- Department of Oncogenetics, Centre Jean Perrin, Clermont-Ferrand, France; .,INSERM U 1240 Molecular Imagery and Theranostic Strategies (IMoST), Clermont-Ferrand, France
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24
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Adnan Awad S, Brück O, Shanmuganathan N, Jarvinen T, Lähteenmäki H, Klievink J, Ibrahim H, Kytölä S, Koskenvesa P, Hughes TP, Branford S, Kankainen M, Mustjoki S. Epigenetic modifier gene mutations in chronic myeloid leukemia (CML) at diagnosis are associated with risk of relapse upon treatment discontinuation. Blood Cancer J 2022; 12:69. [PMID: 35443743 PMCID: PMC9021312 DOI: 10.1038/s41408-022-00667-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Shady Adnan Awad
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland. .,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland. .,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland. .,Clinical Pathology Department, National Cancer Institute, Cairo University, Giza, Egypt.
| | - Oscar Brück
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Naranie Shanmuganathan
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia.,Department of Genetics and Molecular Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Timo Jarvinen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Hanna Lähteenmäki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Soili Kytölä
- HUS Diagnostic Center, HUSLAB, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Perttu Koskenvesa
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Timothy P Hughes
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Susan Branford
- Department of Genetics and Molecular Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Matti Kankainen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland. .,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland. .,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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25
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Kania AK, Price MJ, George-Alexander LE, Patterson DG, Hicks SL, Scharer CD, Boss JM. H3K27me3 Demethylase UTX Restrains Plasma Cell Formation. THE JOURNAL OF IMMUNOLOGY 2022; 208:1873-1885. [PMID: 35346967 PMCID: PMC9012698 DOI: 10.4049/jimmunol.2100948] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022]
Abstract
B cell differentiation is associated with substantial transcriptional, metabolic, and epigenetic remodeling, including redistribution of histone 3 lysine 27 trimethylation (H3K27me3), which is associated with a repressive chromatin state and gene silencing. Although the role of the methyltransferase EZH2 (Enhancer of zeste homolog 2) in B cell fate decisions has been well established, it is not known whether H3K27me3 demethylation is equally important. In this study, we showed that simultaneous genetic deletion of the two H3K27 demethylases UTX and JMJD3 (double-knockout [Utx fl/fl Jmjd3 fl/fl Cd19 cre/+] [dKO]) led to a significant increase in plasma cell (PC) formation after stimulation with the T cell-independent Ags LPS and NP-Ficoll. This phenotype occurred in a UTX-dependent manner as UTX single-knockout mice, but not JMJD3 single-knockout mice, mimicked the dKO. Although UTX- and JMJD3-deficient marginal zone B cells showed increased proliferation, dKO follicular B cells also showed increased PC formation. PCs from dKO mice upregulated genes associated with oxidative phosphorylation and exhibited increased spare respiratory capacity. Mechanistically, deletion of Utx and Jmjd3 resulted in higher levels of H3K27me3 at proapoptotic genes and resulted in reduced apoptosis of dKO PCs in vivo. Furthermore, UTX regulated chromatin accessibility at regions containing ETS and IFN regulatory factor (IRF) transcription factor family motifs, including motifs of known repressors of PC fate. Taken together, these data demonstrate that the H3K27me3 demethylases restrain B cell differentiation.
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Affiliation(s)
- Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Madeline J Price
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | | | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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26
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Guo T, Han X, He J, Feng J, Jing J, Janečková E, Lei J, Ho TV, Xu J, Chai Y. KDM6B interacts with TFDP1 to activate P53 signalling in regulating mouse palatogenesis. eLife 2022; 11:74595. [PMID: 35212626 PMCID: PMC9007587 DOI: 10.7554/elife.74595] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic regulation plays extensive roles in diseases and development. Disruption of epigenetic regulation not only increases the risk of cancer, but can also cause various developmental defects. However, the question of how epigenetic changes lead to tissue-specific responses during neural crest fate determination and differentiation remains understudied. Using palatogenesis as a model, we reveal the functional significance of Kdm6b, an H3K27me3 demethylase, in regulating mouse embryonic development. Our study shows that Kdm6b plays an essential role in cranial neural crest development, and loss of Kdm6b disturbs P53 pathway-mediated activity, leading to complete cleft palate along with cell proliferation and differentiation defects in mice. Furthermore, activity of H3K27me3 on the promoter of Trp53 is antagonistically controlled by Kdm6b, and Ezh2 in cranial neural crest cells. More importantly, without Kdm6b, the transcription factor TFDP1, which normally binds to the promoter of Trp53, cannot activate Trp53 expression in palatal mesenchymal cells. Furthermore, the function of Kdm6b in activating Trp53 in these cells cannot be compensated for by the closely related histone demethylase Kdm6a. Collectively, our results highlight the important role of the epigenetic regulator KDM6B and how it specifically interacts with TFDP1 to achieve its functional specificity in regulating Trp53 expression, and further provide mechanistic insights into the epigenetic regulatory network during organogenesis.
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Affiliation(s)
- Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jinzhi He
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jie Lei
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
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27
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Abstract
Epigenetic regulators are pivotal factors that influence and control T cell development. Recent findings continue to reveal additional elements of epigenetic modifications that play significant and crucial roles at different stages of T cell development. Through gaining a better understanding of the various epigenetic factors that influence the formation and survival of maturing T cells, new therapies can potentially be developed to combat diseases caused by dysregulated epigenetic chromatin modifications. In this review, we summarize the recent studies which shed light on the epigenetic regulation of T cell development especially at the critical stage of β-selection.
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Affiliation(s)
- Avik Dutta
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Paul E Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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28
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Stamos DB, Clubb LM, Mitra A, Chopp LB, Nie J, Ding Y, Das A, Venkataganesh H, Lee J, El-Khoury D, Li L, Bhandoola A, Bosselut R, Love PE. The histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development. J Exp Med 2021; 218:e20202012. [PMID: 34726730 PMCID: PMC8570297 DOI: 10.1084/jem.20202012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 08/27/2021] [Accepted: 09/30/2021] [Indexed: 11/27/2022] Open
Abstract
Analysis of the transcriptional profiles of developing thymocytes has shown that T lineage commitment is associated with loss of stem cell and early progenitor gene signatures and the acquisition of T cell gene signatures. Less well understood are the epigenetic alterations that accompany or enable these transcriptional changes. Here, we show that the histone demethylase Lsd1 (Kdm1a) performs a key role in extinguishing stem/progenitor transcriptional programs in addition to key repressive gene programs during thymocyte maturation. Deletion of Lsd1 caused a block in late T cell development and resulted in overexpression of interferon response genes as well as genes regulated by the Gfi1, Bcl6, and, most prominently, Bcl11b transcriptional repressors in CD4+CD8+ thymocytes. Transcriptional overexpression in Lsd1-deficient thymocytes was not always associated with increased H3K4 trimethylation at gene promoters, indicating that Lsd1 indirectly affects the expression of many genes. Together, these results identify a critical function for Lsd1 in the epigenetic regulation of multiple repressive gene signatures during T cell development.
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Affiliation(s)
- Daniel B. Stamos
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Lauren M. Clubb
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Apratim Mitra
- Bioinformatics and Scientific Programing Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Laura B. Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jan Lee
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Dalal El-Khoury
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - LiQi Li
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Paul E. Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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29
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Li F, Jing J, Movahed M, Cui X, Cao Q, Wu R, Chen Z, Yu L, Pan Y, Shi H, Shi H, Xue B. Epigenetic interaction between UTX and DNMT1 regulates diet-induced myogenic remodeling in brown fat. Nat Commun 2021; 12:6838. [PMID: 34824202 PMCID: PMC8617140 DOI: 10.1038/s41467-021-27141-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/05/2021] [Indexed: 02/04/2023] Open
Abstract
Brown adipocytes share the same developmental origin with skeletal muscle. Here we find that a brown adipocyte-to-myocyte remodeling also exists in mature brown adipocytes, and is induced by prolonged high fat diet (HFD) feeding, leading to brown fat dysfunction. This process is regulated by the interaction of epigenetic pathways involving histone and DNA methylation. In mature brown adipocytes, the histone demethylase UTX maintains persistent demethylation of the repressive mark H3K27me3 at Prdm16 promoter, leading to high Prdm16 expression. PRDM16 then recruits DNA methyltransferase DNMT1 to Myod1 promoter, causing Myod1 promoter hypermethylation and suppressing its expression. The interaction between PRDM16 and DNMT1 coordinately serves to maintain brown adipocyte identity while repressing myogenic remodeling in mature brown adipocytes, thus promoting their active brown adipocyte thermogenic function. Suppressing this interaction by HFD feeding induces brown adipocyte-to-myocyte remodeling, which limits brown adipocyte thermogenic capacity and compromises diet-induced thermogenesis, leading to the development of obesity.
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Affiliation(s)
- Fenfen Li
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Jia Jing
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Miranda Movahed
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Xin Cui
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Qiang Cao
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Rui Wu
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Ziyue Chen
- grid.256304.60000 0004 1936 7400Department of Computer Science, Georgia State University, Atlanta, GA 30303 USA
| | - Liqing Yu
- grid.411024.20000 0001 2175 4264Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Yi Pan
- grid.256304.60000 0004 1936 7400Department of Computer Science, Georgia State University, Atlanta, GA 30303 USA ,grid.458489.c0000 0001 0483 7922Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 P.R. China
| | - Huidong Shi
- grid.410427.40000 0001 2284 9329Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA 30912 USA ,grid.410427.40000 0001 2284 9329Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912 USA
| | - Hang Shi
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
| | - Bingzhong Xue
- grid.256304.60000 0004 1936 7400Department of Biology, Georgia State University, Atlanta, GA 30303 USA
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30
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Huppertz S, Senger K, Brown A, Leins H, Eiwen K, Mulaw MA, Geiger H, Becker M. KDM6A, a histone demethylase, regulates stress hematopoiesis and early B-cell differentiation. Exp Hematol 2021; 99:32-43.e13. [PMID: 34126175 DOI: 10.1016/j.exphem.2021.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Histone methylases and demethylases regulate gene expression programs in hematopoiesis. The molecular function of the demethylase KDM6A in normal hematopoiesis and, in particular, for the hematopoietic stem and progenitor cell (HSPC) compartment remains only partially understood. Female but not male Kdm6a-/- HSPCs were functionally impaired in adoptive transfer experiments as well as upon proliferative stress induced by 5-fluorouracil. Loss of Kdm6a affected primarily early B cells and erythroid and myeloid progenitor cells with respect to both number and function. Global gene expression analyses revealed a shared altered gene signature in Kdm6a-/- pro-B and pre-B cells that is also present in HSPCs, supporting that altered B-cell differentiation in Kdm6a-/- animals is already initiated in HSPCs. Interestingly, loss of KDM6A did not affect the global level of methylation of H3K27, its presumed target, in hematopoietic cells. Our data indicate a critical role for KDM6A in the regulation of hematopoietic differentiation and differentiation-specific gene expression programs, with a prominent role in early B-cell differentiation that is likely independent of H3K27 methylation status.
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Affiliation(s)
- Sascha Huppertz
- Institute for Medical Radiology and Cell Research (MSZ), Center of Experimental Molecular Medicine (ZEMM), Würzburg University, Würzburg, Germany
| | - Katharina Senger
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Andreas Brown
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Hanna Leins
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Karina Eiwen
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Medhanie A Mulaw
- Institute of Experimental Cancer Research, Ulm University, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Matthias Becker
- Institute for Medical Radiology and Cell Research (MSZ), Center of Experimental Molecular Medicine (ZEMM), Würzburg University, Würzburg, Germany.
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31
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Duong P, Ma KH, Ramesh R, Moran JJ, Won S, Svaren J. H3K27 demethylases are dispensable for activation of Polycomb-regulated injury response genes in peripheral nerve. J Biol Chem 2021; 297:100852. [PMID: 34090875 PMCID: PMC8258988 DOI: 10.1016/j.jbc.2021.100852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
The induction of nerve injury response genes in Schwann cells depends on both transcriptional and epigenomic reprogramming. The nerve injury response program is regulated by the repressive histone mark H3K27 trimethylation (H3K27me3), deposited by Polycomb repressive complex 2 (PRC2). Loss of PRC2 function leads to early and augmented induction of the injury response gene network in peripheral nerves, suggesting H3K27 demethylases are required for derepression of Polycomb-regulated nerve injury genes. To determine the function of H3K27 demethylases in nerve injury, we generated Schwann cell-specific knockouts of H3K27 demethylase Kdm6b and double knockouts of Kdm6b/Kdm6a (encoding JMJD3 and UTX). We found that H3K27 demethylases are largely dispensable for Schwann cell development and myelination. In testing the function of H3K27 demethylases after injury, we found early induction of some nerve injury genes was diminished compared with control, but most injury genes were largely unaffected at 1 and 7 days post injury. Although it was proposed that H3K27 demethylases are required to activate expression of the cyclin-dependent kinase inhibitor Cdkn2a in response to injury, Schwann cell-specific deletion of H3K27 demethylases affected neither the expression of this gene nor Schwann cell proliferation after nerve injury. To further characterize the regulation of nerve injury response genes, we found that injury genes are associated with repressive histone H2AK119 ubiquitination catalyzed by PRC1, which declines after injury. Overall, our results indicate H3K27 demethylation is not required for induction of injury response genes and that other mechanisms likely are involved in activating Polycomb-repressed injury genes in peripheral nerve.
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Affiliation(s)
- Phu Duong
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ki H Ma
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Raghu Ramesh
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John J Moran
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Seongsik Won
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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32
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Crump NT, Hadjinicolaou AV, Xia M, Walsby-Tickle J, Gileadi U, Chen JL, Setshedi M, Olsen LR, Lau IJ, Godfrey L, Quek L, Yu Z, Ballabio E, Barnkob MB, Napolitani G, Salio M, Koohy H, Kessler BM, Taylor S, Vyas P, McCullagh JSO, Milne TA, Cerundolo V. Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation. Cell Rep 2021; 35:109101. [PMID: 33979616 PMCID: PMC8131582 DOI: 10.1016/j.celrep.2021.109101] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/01/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase, but it is unclear how these cancers, but not T cells, tolerate arginine depletion. In this study, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPβ binding to an enhancer within ASS1. T cells cannot induce ASS1, despite the presence of active ATF4 and CEBPβ, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation, which disrupts ATF4/CEBPβ binding and target gene transcription. We find that T cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andreas V Hadjinicolaou
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Meng Xia
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Uzi Gileadi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ji-Li Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mashiko Setshedi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lars R Olsen
- Section for Bioinformatics, DTU Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lynn Quek
- School of Cancer and Pharmaceutical Sciences, King's College London, SGDP Centre, Memory Lane, London SE5 8AF, UK
| | - Zhanru Yu
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mike B Barnkob
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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33
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Xu T, Schutte A, Jimenez L, Gonçalves ANA, Keller A, Pipkin ME, Nakaya HI, Pereira RM, Martinez GJ. Kdm6b Regulates the Generation of Effector CD8 + T Cells by Inducing Chromatin Accessibility in Effector-Associated Genes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:2170-2183. [PMID: 33863789 PMCID: PMC11139061 DOI: 10.4049/jimmunol.2001459] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/14/2022]
Abstract
The transcriptional and epigenetic regulation of CD8+ T cell differentiation is critical for balancing pathogen eradication and long-term immunity by effector and memory CTLs, respectively. In this study, we demonstrate that the lysine demethylase 6b (Kdm6b) is essential for the proper generation and function of effector CD8+ T cells during acute infection and tumor eradication. We found that cells lacking Kdm6b (by either T cell-specific knockout mice or knockdown using short hairpin RNA strategies) show an enhanced generation of memory precursor and early effector cells upon acute viral infection in a cell-intrinsic manner. We also demonstrate that Kdm6b is indispensable for proper effector functions and tumor protection, and that memory CD8+ T cells lacking Kdm6b displayed a defective recall response. Mechanistically, we identified that Kdm6b, through induction of chromatin accessibility in key effector-associated gene loci, allows for the proper generation of effector CTLs. Our results pinpoint the essential function of Kdm6b in allowing chromatin accessibility in effector-associated genes, and identify Kdm6b as a potential target for therapeutics in diseases with dysregulated effector responses.
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Affiliation(s)
- Tianhao Xu
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
- Discipline of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Alexander Schutte
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Leandro Jimenez
- Department of Clinical Analyses and Toxicology, School of Pharmaceutical Sciences, University of Sao Paulo, Brazil
| | - Andre N A Gonçalves
- Department of Clinical Analyses and Toxicology, School of Pharmaceutical Sciences, University of Sao Paulo, Brazil
| | - Ashleigh Keller
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Helder I Nakaya
- Department of Clinical Analyses and Toxicology, School of Pharmaceutical Sciences, University of Sao Paulo, Brazil
| | - Renata M Pereira
- Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gustavo J Martinez
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL;
- Discipline of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
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34
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Keenan CR. Heterochromatin and Polycomb as regulators of haematopoiesis. Biochem Soc Trans 2021; 49:805-814. [PMID: 33929498 PMCID: PMC8106494 DOI: 10.1042/bst20200737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/23/2022]
Abstract
Haematopoiesis is the process by which multipotent haematopoietic stem cells are transformed into each and every type of terminally differentiated blood cell. Epigenetic silencing is critical for this process by regulating the transcription of cell-cycle genes critical for self-renewal and differentiation, as well as restricting alternative fate genes to allow lineage commitment and appropriate differentiation. There are two distinct forms of transcriptionally repressed chromatin: H3K9me3-marked heterochromatin and H3K27me3/H2AK119ub1-marked Polycomb (often referred to as facultative heterochromatin). This review will discuss the role of these distinct epigenetic silencing mechanisms in regulating normal haematopoiesis, how these contribute to age-related haematopoietic dysfunction, and the rationale for therapeutic targeting of these pathways in the treatment of haematological malignancies.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
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35
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Howson LJ, Li J, von Borstel A, Barugahare A, Mak JYW, Fairlie DP, McCluskey J, Turner SJ, Davey MS, Rossjohn J. Mucosal-Associated Invariant T Cell Effector Function Is an Intrinsic Cell Property That Can Be Augmented by the Metabolic Cofactor α-Ketoglutarate. THE JOURNAL OF IMMUNOLOGY 2021; 206:1425-1435. [PMID: 33597151 DOI: 10.4049/jimmunol.2001048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are an innate-like population of unconventional T cells that respond rapidly to microbial metabolite Ags or cytokine stimulation. Because of this reactivity and surface expression of CD45RO+, CD45RA-, and CD127+, they are described as effector memory cells. Yet, there is heterogeneity in MAIT cell effector response. It is unclear what factors control MAIT cell effector capacity, whether it is fixed or can be modified and if this differs based on whether activation is TCR dependent or independent. To address this, we have taken a systematic approach to examine human MAIT cell effector capacity across healthy individuals in response to ligand and cytokine stimulation. We demonstrate the heterogenous nature of MAIT cell effector capacity and that the ability to produce an effector response is not directly attributable to TCR clonotype or coreceptor expression. Global gene transcription analysis revealed that the MAIT cell effector capacity produced in response to TCR stimulation is associated with increased expression of the epigenetic regulator lysine demethylase 6B (KDM6B). Addition of a KDM6B inhibitor did not alter MAIT cell effector function to Ag or cytokine stimulation. However, addition of the KDM6B cofactor α-ketoglutarate greatly enhanced MAIT cell effector capacity to TCR-dependent stimulation in a partially KDM6B-dependent manner. These results demonstrate that the TCR-dependent effector response of MAIT cells is epigenetically regulated and dependent on the availability of metabolic cofactors.
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Affiliation(s)
- Lauren J Howson
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
| | - Jasmine Li
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Anouk von Borstel
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Adele Barugahare
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3000, Australia
| | - Stephen J Turner
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Martin S Davey
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
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36
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Mitchell JE, Lund MM, Starmer J, Ge K, Magnuson T, Shpargel KB, Whitmire JK. UTX promotes CD8 + T cell-mediated antiviral defenses but reduces T cell durability. Cell Rep 2021; 35:108966. [PMID: 33852868 PMCID: PMC8112613 DOI: 10.1016/j.celrep.2021.108966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 12/22/2020] [Accepted: 03/17/2021] [Indexed: 11/29/2022] Open
Abstract
Persistent virus infections can cause pathogenesis that is debilitating or lethal. During these infections, virus-specific T cells fail to protect due to weakened antiviral activity or failure to persist. These outcomes are governed by histone modifications, although it is unknown which enzymes contribute to T cell loss or impaired function over time. In this study, we show that T cell receptor-stimulated CD8+ T cells increase their expression of UTX (ubiquitously transcribed tetratricopeptide repeat, X chromosome) to enhance gene expression. During chronic lymphocytic choriomeningitis virus (LCMV) infection in mice, UTX binds to enhancers and transcription start sites of effector genes, allowing for improved cytotoxic T lymphocyte (CTL)-mediated protection, independent of its trimethylation of histone 3 lysine 27 (H3K27me3) demethylase activity. UTX also limits the frequency and durability of virus-specific CD8+ T cells, which correspond to increased expression of inhibitory receptors. Thus, UTX guides gene expression patterns in CD8+ T cells, advancing early antiviral defenses while reducing the longevity of CD8+ T cell responses. T cells fail to eliminate chronic virus infections due to alterations in gene expression that undermine their activity. In this study, Mitchell et al. identify a histone-modifying enzyme that promotes effector gene expression and CTL activity early on yet reduces T cell survival, leading to infection persistence.
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Affiliation(s)
- Joseph E Mitchell
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Microbiology & Immunology, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Makayla M Lund
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Josh Starmer
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry Magnuson
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Karl B Shpargel
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
| | - Jason K Whitmire
- Department of Genetics, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Microbiology & Immunology, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
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37
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The Functions of the Demethylase JMJD3 in Cancer. Int J Mol Sci 2021; 22:ijms22020968. [PMID: 33478063 PMCID: PMC7835890 DOI: 10.3390/ijms22020968] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 12/09/2022] Open
Abstract
Cancer is a major cause of death worldwide. Epigenetic changes in response to external (diet, sports activities, etc.) and internal events are increasingly implicated in tumor initiation and progression. In this review, we focused on post-translational changes in histones and, more particularly, the tri methylation of lysine from histone 3 (H3K27me3) mark, a repressive epigenetic mark often under- or overexpressed in a wide range of cancers. Two actors regulate H3K27 methylation: Jumonji Domain-Containing Protein 3 demethylase (JMJD3) and Enhancer of zeste homolog 2 (EZH2) methyltransferase. A number of studies have highlighted the deregulation of these actors, which is why this scientific review will focus on the role of JMJD3 and, consequently, H3K27me3 in cancer development. Data on JMJD3’s involvement in cancer are classified by cancer type: nervous system, prostate, blood, colorectal, breast, lung, liver, ovarian, and gastric cancers.
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38
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Vahedi G. Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors. Immunol Rev 2021; 300:167-180. [PMID: 33452686 DOI: 10.1111/imr.12942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022]
Abstract
An extraordinary degree of condensation is required to fit the eukaryotic genome inside the nucleus. This compaction is attained by first coiling the DNA around structures called nucleosomes. Mammalian genomes are further folded into sophisticated three-dimensional (3D) configurations, enabling the genetic code to dictate a diverse range of cell fates. Recent advances in molecular and computational technologies have enabled the query of higher-order chromatin architecture at an unprecedented resolution and scale. In T lymphocytes, similar to other developmental programs, the hierarchical genome organization is shaped by a highly coordinated division of labor among different classes of sequence-specific transcription factors. In this review, we will summarize the general principles of 1D and 3D genome organization, introduce the common experimental and computational techniques to measure the multilayer chromatin organization, and discuss the pervasive role of transcription factors on chromatin organization in T lymphocytes.
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Affiliation(s)
- Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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39
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KDM6B is an androgen regulated gene and plays oncogenic roles by demethylating H3K27me3 at cyclin D1 promoter in prostate cancer. Cell Death Dis 2021; 12:2. [PMID: 33414463 PMCID: PMC7791132 DOI: 10.1038/s41419-020-03354-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Lysine (K)-specific demethylase 6B (KDM6B), a stress-inducible H3K27me3 demethylase, plays oncogenic or antitumoral roles in malignant tumors depending on the type of tumor cell. However, how this histone modifier affects the progression of prostate cancer (PCa) is still unknown. Here we analyzed sequenced gene expression data and tissue microarray to explore the expression features and prognostic value of KDM6B in PCa. Further, we performed in vitro cell biological experiments and in vivo nude mouse models to reveal the biological function, upstream and downstream regulation mechanism of KDM6B. In addition, we investigated the effects of a KDM6B inhibitor, GSK-J4, on PCa cells. We showed that KDM6B overexpression was observed in PCa, and elevated KDM6B expression was associated with high Gleason Score, low serum prostate-specific antigen level and shorted recurrence-free survival. Moreover, KDM6B prompted proliferation, migration, invasion and cell cycle progression and suppressed apoptosis in PCa cells. GSK-J4 administration could significantly suppress the biological function of KDM6B in PCa cells. KDM6B is involved in the development of castration-resistant prostate cancer (CRPC), and combination of MDV3100 plus GSK-J4 is effective for CRPC and MDV3100-resistant CRPC. Mechanism exploration revealed that androgen receptor can decrease the transcription of KDM6B and that KDM6B demethylates H3K27me3 at the cyclin D1 promoter and cooperates with smad2/3 to prompt the expression of cyclin D1. In conclusion, our study demonstrates that KDM6B is an androgen receptor regulated gene and plays oncogenic roles by promoting cyclin D1 transcription in PCa and GSK-J4 has the potential to be a promising agent for the treatment of PCa.
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40
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Sawada Y, Gallo RL. Role of Epigenetics in the Regulation of Immune Functions of the Skin. J Invest Dermatol 2020; 141:1157-1166. [PMID: 33256976 DOI: 10.1016/j.jid.2020.10.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/16/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
This review is intended to illuminate the emerging understanding of epigenetic modifications that regulate both adaptive and innate immunity in the skin. Host defense of the epidermis and dermis involves the interplay of many cell types to enable homeostasis; tolerance to the external environment; and appropriate response to transient microbial, chemical, and physical insults. To understand this process, the study of cutaneous immunology has focused on immune responses that reflect both adaptive learned and genetically programmed innate defense systems. However, recent advances have begun to reveal that epigenetic modifications of chromatin structure also have a major influence on the skin immune system. This deeper understanding of how enzymatic changes in chromatin structure can modify the skin immune system and may explain how environmental exposures during life, and the microbiome, lead to both short-term and long-term changes in cutaneous allergic and other inflammatory processes. Understanding the mechanisms responsible for alterations in gene and chromatin structure within skin immunocytes could provide key insights into the pathogenesis of inflammatory skin diseases that have thus far evaded understanding by dermatologists.
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Affiliation(s)
- Yu Sawada
- Department of Dermatology, University of California, San Diego, San Diego, California, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, San Diego, California, USA.
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41
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Liu Z, Zhang H, Hu Y, Liu D, Li L, Li C, Wang Q, Huo J, Liu H, Xie N, Huang X, Liu Y, Chen CD, Shi Y, Zhang X. Critical role of histone H3 lysine 27 demethylase Kdm6b in the homeostasis and function of medullary thymic epithelial cells. Cell Death Differ 2020; 27:2843-2855. [PMID: 32346138 PMCID: PMC7493893 DOI: 10.1038/s41418-020-0546-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/26/2023] Open
Abstract
Medullary thymic epithelial cells (mTECs) play a central role in the establishment of T cell central immunological tolerance by promiscuously expressing tissue-restricted antigens (TRAs) and presenting them to developing T cells, leading to deletion of T cells responding to self-antigens. However, molecular mechanisms especially epigenetic regulation of mTEC homeostasis and TRA expression remain elusive. Here we show that the H3K27 demethylase Kdm6b is essential to maintain the postnatal thymic medulla by promoting mTEC survival and regulating the expression of TRA genes. Moreover, mice lacking Kdm6b developed pathological autoimmune disorders. Mechanically, Kdm6b exerted its function by reducing repressive H3K27 trimethylation (H3K27me3) at the promoters of anti-apoptotic gene Bcl2 and a set of Aire-dependent TRA genes. Thus, our findings reveal a dual role of Kdm6b in the regulation of mTEC-mediated T cell central tolerance.
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Affiliation(s)
- Zhi Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Haohao Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiming Hu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dandan Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lingling Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cuifeng Li
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qi Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Junhaohui Huo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hanshao Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ningxia Xie
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xingxu Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China
| | - Yongzhong Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yufang Shi
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoren Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou, 510000, China.
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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42
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Das P, Taube JH. Regulating Methylation at H3K27: A Trick or Treat for Cancer Cell Plasticity. Cancers (Basel) 2020; 12:E2792. [PMID: 33003334 PMCID: PMC7600873 DOI: 10.3390/cancers12102792] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Properly timed addition and removal of histone 3 lysine 27 tri-methylation (H3K27me3) is critical for enabling proper differentiation throughout all stages of development and, likewise, can guide carcinoma cells into altered differentiation states which correspond to poor prognoses and treatment evasion. In early embryonic stages, H3K27me3 is invoked to silence genes and restrict cell fate. Not surprisingly, mutation or altered functionality in the enzymes that regulate this pathway results in aberrant methylation or demethylation that can lead to malignancy. Likewise, changes in expression or activity of these enzymes impact cellular plasticity, metastasis, and treatment evasion. This review focuses on current knowledge regarding methylation and de-methylation of H3K27 in cancer initiation and cancer cell plasticity.
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Affiliation(s)
| | - Joseph H. Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA;
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43
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Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
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Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
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44
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Abstract
Lysine demethylase 6A (KDM6A), also known as UTX, belongs to the KDM6 family of histone H3 lysine 27 (H3K27) demethylases, which also includes UTY and KDM6B (JMJD3). The KDM6A protein contains six tetratricopeptide repeat (TPR) domains and an enzymatic Jumonji C (JmjC) domain that catalyzes the removal of di- and trimethylation on H3K27. KDM6A physically associates with histone H3 lysine 4 monomethyltransferases MLL3 (KMT2C) and MLL4 (KMT2D). Since its identification as an H3K27 demethylase in 2007, studies have reported KDM6A's critical roles in cell differentiation, development, and cancer. KDM6A is important for differentiation of embryonic stem cells and development of various tissues. Mutations of KDM6A cause Kabuki syndrome. KDM6A is frequently mutated in cancers and functions as a tumor suppressor. KDM6A is redundant with UTY and functions largely independently of its demethylase activity. It regulates gene expression, likely through the associated transcription factors and MLL3/4 on enhancers. However, KDM6A enzymatic activity is required in certain cellular contexts. Functional redundancy between H3K27 demethylase activities of KDM6A and KDM6B in vivo has yet to be determined. Further understanding of KDM6A functions and working mechanisms will provide more insights into enhancer regulation and may help generate novel therapeutic approaches to treat KDM6A-related diseases.
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45
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Zhang Y, Wang Y, Zhou X, Wang J, Shi M, Wang J, Li F, Chen Q. Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B. Mol Cell Biochem 2020; 472:157-171. [PMID: 32594337 DOI: 10.1007/s11010-020-03794-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/13/2020] [Indexed: 12/25/2022]
Abstract
Adipose-derived stem cells (ADSCs) are an ideal source of cells for intervertebral disc (IVD) regeneration, but the effect of an increased osmotic microenvironment on ADSC differentiation remains unclear. Here, we aimed to elucidate whether hyperosmolarity facilitates ADSC nucleus pulposus (NP)-like differentiation and whether histone demethylase KDM4B is involved in this process. ADSCs were cultured under standard and increased osmolarity conditions for 1-3 weeks, followed by analysis for proliferation and viability. Differentiation was then quantified by gene and protein analysis. Finally, KDM4B knockdown ADSCs were generated using lentiviral vectors. The results showed that increasing the osmolarity of the differentiation medium to 400 mOsm significantly increased NP-like gene expression and the synthesis of extracellular matrix (ECM) components during ADSC differentiation; however, further increasing the osmolarity to 500 mOsm suppressed the NP-like differentiation of ADSCs. KDM4B, as well as the IVD formation regulators forkhead box (Fox)a1/2 and sonic hedgehog (Shh), were found to be significantly upregulated at 400 mOsm. KDM4B knockdown reduced Foxa1/2, Shh, and NP-associated markers' expression, as well as the synthesis of ECM components. The reduction in NP-like differentiation caused by KDM4B knockdown was partially rescued by Purmorphamine, a specific agonist of Shh. Moreover, we found that KDM4B can directly bind to the promoter region of Foxa1/2 and decrease the content of H3K9me3/2. In conclusion, our results indicate that a potential optimal osmolarity window might exist for successful ADSC differentiation. KDM4B plays an essential role in regulating the osmolarity-induced NP-like differentiation of ADSCs by interacting with Foxa1/2-Shh signaling.
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Affiliation(s)
- Yujie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Yanyan Wang
- Department of Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Xiaopeng Zhou
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Jingkai Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Mingmin Shi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Jian Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Fangcai Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
| | - Qixin Chen
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
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Tang QY, Zhang SF, Dai SK, Liu C, Wang YY, Du HZ, Teng ZQ, Liu CM. UTX Regulates Human Neural Differentiation and Dendritic Morphology by Resolving Bivalent Promoters. Stem Cell Reports 2020; 15:439-453. [PMID: 32679064 PMCID: PMC7419705 DOI: 10.1016/j.stemcr.2020.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023] Open
Abstract
UTX, a H3K27me3 demethylase, plays an important role in mouse brain development. However, so little is known about the function of UTX in human neural differentiation and dendritic morphology. In this study, we generated UTX-null human embryonic stem cells using CRISPR/Cas9, and differentiated them into neural progenitor cells and neurons to investigate the effects of UTX loss of function on human neural development. The results showed that the number of differentiated neurons significantly reduced after loss of UTX, and that the dendritic morphology of UTX KO neurons tended to be simplified. The electrophysiological recordings showed that most of the UTX KO neurons were immature. Finally, RNA sequencing identified dozens of differentially expressed genes involved in neural differentiation and synaptic function in UTX KO neurons and our results demonstrated that UTX regulated these critical genes by resolving bivalent promoters. In summary, we establish a reference for the important role of UTX in human neural differentiation and dendritic morphology. Loss of UTX in hESCs reduces their neural differentiation potential The dendritic morphology of UTX KO neurons tends to be simplified UTX regulates human neural development depending on its demethylation UTX regulates the expression of genes by resolving bivalent promoters
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Affiliation(s)
- Qing-Yuan Tang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Feng Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Cong Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying-Ying Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Zhen Du
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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Zhang Y, Chen Y, Ma R, Jiang Y, Liu J, Lin Y, Chen S, Xia M, Zou F, Zhang J, Pan T, Wang L, Wei L, Zhang H. UHRF1 Controls Thymocyte Fate Decisions through the Epigenetic Regulation of EGR1 Expression. THE JOURNAL OF IMMUNOLOGY 2020; 204:3248-3261. [DOI: 10.4049/jimmunol.1901471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
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48
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Emamgolizadeh Gurt Tapeh B, Mosayyebi B, Samei M, Beyrampour Basmenj H, Mohammadi A, Alivand MR, Hassanpour P, Solali S. microRNAs involved in T-cell development, selection, activation, and hemostasis. J Cell Physiol 2020; 235:8461-8471. [PMID: 32324267 DOI: 10.1002/jcp.29689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) characterized by small, noncoding RNAs have a fundamental role in the regulation of gene expression at the post-transcriptional level. Additionally, miRNAs have recently been identified as potential regulators of various genes involved in the pathogenesis of the autoimmune and inflammatory disease. So far, the interaction between miRNAs and T lymphocytes in the immune response as a new and significant topic has not been emphasized substantially. The role of miRNAs in different biological processes including apoptosis, immune checkpoints and the activation of immune cells is still unclear. Aberrant miRNA expression profile affects various aspects of T-cell function. Accordingly, in this literature review, we summarized the role of significant miRNAs in T-cell development processes. Consequently, we demonstrated precise mechanisms that candidate miRNAs interfere in Immune response mediated by different types of T cells. We believe that a good understanding of the interaction between miRNAs and immune response contributes to the new therapeutic strategies in relation to disease with an immunological origin.
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Affiliation(s)
- Behnam Emamgolizadeh Gurt Tapeh
- Division of Hematology and Transfusion Medicine, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashir Mosayyebi
- Department of Medical Biotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdieh Samei
- Department of Immunology, Gorgan University of Medical Sciences, Gorgan, Iran
| | | | - Ali Mohammadi
- Department of cancer and inflammation, University of Southern Denmark, Odense, Denmark
| | - Mohammad R Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parviz Hassanpour
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Solali
- Division of Hematology and Transfusion Medicine, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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49
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Umutoni D, Iwagawa T, Baba Y, Tsuhako A, Honda H, Aihara M, Watanabe S. H3K27me3 demethylase UTX regulates the differentiation of a subset of bipolar cells in the mouse retina. Genes Cells 2020; 25:402-412. [PMID: 32215989 DOI: 10.1111/gtc.12767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/08/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Di- and trimethylation of lysine 27 on histone 3 (H3K27me2/3) is a critical gene repression mechanism. We previously showed that down-regulation of the H3K27 demethylase, Jumonji domain-containing protein 3 (JMJD3), resulted in a reduced number of protein kinase C (PKC)α-positive rod ON-bipolar cells. In this work, we focused on the role of another H3K27 demethylase, ubiquitously transcribed tetratricopeptide repeat X chromosome (UTX), in retinal development. UTX was expressed in the retinal progenitor cells of the embryonic mouse retina and was observed in the inner nuclear layer during late retinal development and in the mature retina. The short hairpin RNA-mediated knockdown of Utx in a mouse retinal explant led to a reduced number of PKCα-positive rod ON-bipolar cells. However, other retinal subtypes were unaffected by this knockdown. Using a retina-specific knockout of Utx in mice, the in vivo effects of UTX down-regulation were examined. Again, the number of PKCα-positive rod ON-bipolar cells was reduced, and no other apparent phenotypes, including retinal progenitor proliferation, apoptosis or differentiation, were observed. Finally, we examined retina-specific Utx and Jmjd3 double-knockout mice and found that although the number of rod ON-bipolar cells was reduced, no additional effects from the loss of Utx and Jmjd3 were observed. Taken together, our data show that UTX contributes to retinal differentiation in a lineage-specific manner.
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Affiliation(s)
- Daisy Umutoni
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Ophthalmology, University of Tokyo, Tokyo, Japan
| | - Toshiro Iwagawa
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yukihiro Baba
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Asano Tsuhako
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Makoto Aihara
- Department of Ophthalmology, University of Tokyo, Tokyo, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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50
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Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism. Proc Natl Acad Sci U S A 2020; 117:6056-6066. [PMID: 32123118 PMCID: PMC7084125 DOI: 10.1073/pnas.1919893117] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
T cells control many immune functions, with Th17 cells critical in regulating inflammation. Following activation, T cells undergo metabolic reprogramming and utilize glycolysis to increase the ATP availability. Epigenetic mechanisms controlling metabolic functions in T cells are currently not well-defined. Here, we establish an epigenetic link between the histone H3K27me3 demethylases KDM6A/B and the coordination of a metabolic response. Inhibition of KDM6A/B leads to global increases in the repressive H3K27me3 histone mark, resulting in down-regulation of key transcription factors, followed by metabolic reprogramming and anergy. This work suggests a critical role of H3K27 demethylase enzymes in maintaining Th17 functions by controlling metabolic switches. Short-term treatment with KDM6 enzyme inhibitors may be useful in the therapy of chronic inflammatory diseases. T helper (Th) cells are CD4+ effector T cells that play a critical role in immunity by shaping the inflammatory cytokine environment in a variety of physiological and pathological situations. Using a combined chemico-genetic approach, we identify histone H3K27 demethylases KDM6A and KDM6B as central regulators of human Th subsets. The prototypic KDM6 inhibitor GSK-J4 increases genome-wide levels of the repressive H3K27me3 chromatin mark and leads to suppression of the key transcription factor RORγt during Th17 differentiation. In mature Th17 cells, GSK-J4 induces an altered transcriptional program with a profound metabolic reprogramming and concomitant suppression of IL-17 cytokine levels and reduced proliferation. Single-cell analysis reveals a specific shift from highly inflammatory cell subsets toward a resting state upon demethylase inhibition. The root cause of the observed antiinflammatory phenotype in stimulated Th17 cells is reduced expression of key metabolic transcription factors, such as PPRC1. Overall, this leads to reduced mitochondrial biogenesis, resulting in a metabolic switch with concomitant antiinflammatory effects. These data are consistent with an effect of GSK-J4 on Th17 T cell differentiation pathways directly related to proliferation and include regulation of effector cytokine profiles. This suggests that inhibiting KDM6 demethylases may be an effective, even in the short term, therapeutic target for autoimmune diseases, including ankylosing spondylitis.
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