1
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Yijian L, Weihan S, Lin Y, Heng Z, Yu W, Lin S, Shuo M, Mengyang L, Jianxun W. CircNCX1 modulates cardiomyocyte proliferation through promoting ubiquitination of BRG1. Cell Signal 2024; 120:111193. [PMID: 38679350 DOI: 10.1016/j.cellsig.2024.111193] [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: 01/23/2024] [Revised: 04/05/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
In mammal, the myocardium loss cannot be recovered spontaneously due to the negligible proliferation ability of mature mammalian cardiomyocyte. However, accumulated evidence has shown that terminally differentiated mammalian cardiomyocyte also has proliferation potency, which can be mediated by several mechanisms. Here, we reported that circNCX1, the most abundant circular RNA in mammalian hearts, can affect the proliferation of murine cardiomyocytes. The level of circNCX1 is significantly elevated during heart development. Forced expression of circNCX1 inhibits cardiomyocyte proliferation, while silencing of endogenous circNCX1 in cardiomyocyte shows reversed effect in vitro. Mechanistically, circNCX1 functions via negatively regulating transcription activator BRG1. It bridges BRG1 and FBXW7 to enhance the ubiquitination and degradation of BRG1, decreasing the expression of BMP10 to lead cell cycle arrest. In summary, our study first revealed that circNCX1 is a modulator of cardiomyocyte proliferation.
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Affiliation(s)
- Lu Yijian
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Sun Weihan
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Ye Lin
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Zhang Heng
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Wang Yu
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Song Lin
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Miao Shuo
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Li Mengyang
- School of Basic Medicine, Qingdao University, Qingdao 266071, China.
| | - Wang Jianxun
- School of Basic Medicine, Qingdao University, Qingdao 266071, China.
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2
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Wankhede D, Grover S, Hofman P. SMARCA4 alterations in non-small cell lung cancer: a systematic review and meta-analysis. J Clin Pathol 2024; 77:457-463. [PMID: 38702192 DOI: 10.1136/jcp-2024-209394] [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: 01/05/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
AIMS A mutation in the SMARCA4 gene which encodes BRG1, a common catalytic subunit of switch/sucrose non-fermentable chromatin-remodelling complexes, plays a vital role in carcinogenesis. SMARCA4 mutations are present in approximately 10% of non-small cell lung cancers (NSCLC), making it a crucial gene in NSCLC, but with varying prognostic associations. To explore this, we conducted a systematic review and meta-analysis on the prognostic significance of SMARCA4 mutations in NSCLC. METHODS Electronic database search was performed from inception to December 2022. Study characteristics and prognostic data were extracted from each eligible study. Depending on heterogeneity, pooled HR and 95% CI were derived using the random-effects or fixed-effects models. RESULTS 8 studies (11 cohorts) enrolling 8371 patients were eligible for inclusion. Data on overall survival (OS) and progression-free survival (PFS) were available from 8 (10 cohorts) and 1 (3 cohorts) studies, respectively. Comparing SMARCA4-mutated NSCLC patients with SMARCA4-wild-type NSCLC patients, the summary HRs for OS and PFS were 1.49 (95% CI 1.18 to 1.87; I2=84%) and 3.97 (95% CI 1.32 to 11.92; I2=79%), respectively. The results from the trim-and-fill method for publication bias and sensitivity analysis were inconsistent with the primary analyses. Three studies reported NSCLC prognosis for category I and II mutations separately; category I was significantly associated with OS. CONCLUSION Our findings suggest that SMARCA4 mutation negatively affects NSCLC OS and PFS. The prognostic effects of SMARCA4-co-occurring mutations and the predictive role of SMARCA4 mutation status in immunotherapy require further exploration.
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Affiliation(s)
- Durgesh Wankhede
- German Cancer Research Center, Heidelberg, Germany
- Faculty of Medicine, Univeristy of Heidelberg, Heidelberg, Germany
| | - Sandeep Grover
- Center for Human Genetics, Universitatsklinikum Giessen und Marburg - Standort Marburg, Marburg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, University Côte d'Azur, Nice, France
- Hospital-Integrated Biobank BB-0033-00025, Pasteur Hospital, Nice, France
- University Hospital Federation OncoAge, CHU de Nice, University Côte d'Azur, Nice, France
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3
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Kim J, Diaz LF, Miller MJ, Leadem B, Krivega I, Dean A. An enhancer RNA recruits KMT2A to regulate transcription of Myb. Cell Rep 2024; 43:114378. [PMID: 38889007 DOI: 10.1016/j.celrep.2024.114378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter. We identified a long non-coding RNA (Myrlin) originating from the -81-kb murine Myb enhancer. Myrlin and Myb are coordinately regulated during erythroid differentiation. Myrlin TSS deletion using CRISPR-Cas9 reduced Myrlin and Myb expression and LDB1 complex occupancy at the Myb enhancers, compromising enhancer contacts and reducing RNA Pol II occupancy in the locus. In contrast, CRISPRi silencing of Myrlin left LDB1 and the Myb enhancer hub unperturbed, although Myrlin and Myb expressions were downregulated, decoupling transcription and chromatin looping. Myrlin interacts with the KMT2A/MLL1 complex. Myrlin CRISPRi compromised KMT2A occupancy in the Myb locus, decreasing CDK9 and RNA Pol II binding and resulting in Pol II pausing in the Myb first exon/intron. Thus, Myrlin directly participates in activating Myb transcription by recruiting KMT2A.
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Affiliation(s)
- Juhyun Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Luis F Diaz
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Matthew J Miller
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; University of Iowa Medical School, Iowa City, IA 52242, USA
| | - Benjamin Leadem
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; GeneDx, Gaithersburg, MD 20877, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Sonothera, South San Francisco, CA 94080, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Kellett C, Bhogal RK, Botchkareva NV, Fessing MY. ATP-dependent chromatin remodeller brahma related gene 1 promotes keratinocyte migration and modulates cell Signalling during wound healing in human skin. Exp Dermatol 2024; 33:e15100. [PMID: 38840387 DOI: 10.1111/exd.15100] [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: 10/10/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
Skin wound healing is driven by proliferation, migration and differentiation of several cell types that are controlled by the alterations in the gene expression programmes. Brahma Gene 1 (BRG1) (also known as SMARCA4) is a core ATPase in the BRG1 Associated Factors (BAF) ATP-dependent chromatin remodelling complexes that alter DNA-histone interaction in chromatin at the specific gene regulatory elements resulting in increase or decrease of the target gene transcription. Using siRNA mediated suppression of BRG1 during wound healing in a human ex vivo and in vitro (scratch assay) models, we demonstrated that BRG1 is essential for efficient skin wound healing by promoting epidermal keratinocytes migration, but not their proliferation or survival. BRG1 controls changes in the expression of genes associated with gene transcription, response to wounding, cell migration and cell signalling. Altogether, our data revealed that BRG1 play positive role in skin repair by promoting keratinocyte migration and impacting the genes expression programmes associated with cell migration and cellular signalling.
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Affiliation(s)
- Carl Kellett
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
| | | | - Natalia V Botchkareva
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Michael Y Fessing
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
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5
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Gao CW, Lin W, Riddle RC, Chopra S, Kim J, Boukas L, Hansen KD, Björnsson HT, Fahrner JA. Growth deficiency in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1. PLoS Genet 2024; 20:e1011310. [PMID: 38857303 PMCID: PMC11192384 DOI: 10.1371/journal.pgen.1011310] [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: 10/16/2023] [Revised: 06/21/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
Growth deficiency is a characteristic feature of both Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), Mendelian disorders of the epigenetic machinery with similar phenotypes but distinct genetic etiologies. We previously described skeletal growth deficiency in a mouse model of KS1 and further established that a Kmt2d-/- chondrocyte model of KS1 exhibits precocious differentiation. Here we characterized growth deficiency in a mouse model of KS2, Kdm6atm1d/+. We show that Kdm6atm1d/+ mice have decreased femur and tibia length compared to controls and exhibit abnormalities in cortical and trabecular bone structure. Kdm6atm1d/+ growth plates are also shorter, due to decreases in hypertrophic chondrocyte size and hypertrophic zone height. Given these disturbances in the growth plate, we generated Kdm6a-/- chondrogenic cell lines. Similar to our prior in vitro model of KS1, we found that Kdm6a-/- cells undergo premature, enhanced differentiation towards chondrocytes compared to Kdm6a+/+ controls. RNA-seq showed that Kdm6a-/- cells have a distinct transcriptomic profile that indicates dysregulation of cartilage development. Finally, we performed RNA-seq simultaneously on Kmt2d-/-, Kdm6a-/-, and control lines at Days 7 and 14 of differentiation. This revealed surprising resemblance in gene expression between Kmt2d-/- and Kdm6a-/- at both time points and indicates that the similarity in phenotype between KS1 and KS2 also exists at the transcriptional level.
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Affiliation(s)
- Christine W. Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - WanYing Lin
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ryan C. Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, United States of America
| | - Sheetal Chopra
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jiyoung Kim
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, Maryland, United States of America
| | - Kasper D. Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hans T. Björnsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Landspítali University Hospital, Reykjavík, Iceland
| | - Jill A. Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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6
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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7
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Oh J, Park S, Kim J, Yeom S, Lee JM, Lee EJ, Cho YJ, Lee JS. Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6. BMC Biol 2024; 22:105. [PMID: 38702628 PMCID: PMC11069235 DOI: 10.1186/s12915-024-01903-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2, and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. RESULTS We investigated the genome-wide occupancy patterns of Rad6, Swd2, and Set1 under various genetic conditions, aiming to clarify the roles of Set1 and Rad6 for occupancy of Swd2. Swd2 peaks appear on both the 5' region and 3' region of genes, which are overlapped with its tightly bound two complexes, Set1 and cleavage and polyadenylation factor (CPF), respectively. In the absence of Rad6/H2Bub, Set1 predominantly localized to the 5' region of genes, while Swd2 lost all the chromatin binding. However, in the absence of Set1, Swd2 occupancy near the 5' region was impaired and rather increased in the 3' region. CONCLUSIONS This study highlights that the catalytic activity of Rad6 is essential for all the ways of Swd2's binding to the transcribed genes and Set1 redistributes the Swd2 to the 5' region for accomplishments of H3K4me3 in the genome-wide level.
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Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jueun Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Ji Min Lee
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
| | - Yong-Joon Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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8
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Santana JF, Spector BM, Suarez G, Luse D, Price D. NELF focuses sites of initiation and maintains promoter architecture. Nucleic Acids Res 2024; 52:2977-2994. [PMID: 38197272 PMCID: PMC11014283 DOI: 10.1093/nar/gkad1253] [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: 09/26/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits of NELFB, PAF1 and RTF1 to probe the effects of depletion of the factors on nascent transcripts using PRO-Seq and on chromatin architecture using DFF-ChIP. Although NELF is involved in promoter proximal pausing, depletion of NELFB had only a minimal effect on the level of paused transcripts and almost no effect on control of productive elongation. Instead, NELF depletion increased the utilization of downstream transcription start sites and caused a dramatic, genome-wide loss of H3K4me3 marked nucleosomes. Depletion of PAF1 and RTF1 both had major effects on productive transcript elongation in gene bodies and also caused initiation site changes like those seen with NELFB depletion. Our study confirmed that the first nucleosome encountered during initiation and early elongation is highly positioned with respect to the major TSS. In contrast, the positions of H3K4me3 marked nucleosomes in promoter regions are heterogeneous and are influenced by transcription. We propose a model defining NELF function and a general role of the H3K4me3 modification in blocking transcription initiation.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Benjamin M Spector
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Gustavo A Suarez
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - David H Price
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
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9
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Wang Q, Zeng S, Liang Y, Zhou R, Wang D. ASH2L mediates epidermal differentiation and hair follicle morphogenesis via H3K4me3 modification. J Invest Dermatol 2024:S0022-202X(24)00279-3. [PMID: 38582368 DOI: 10.1016/j.jid.2024.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
The processes of epidermal development in mammals are regulated by complex molecular mechanisms, such as histone modifications. Histone H3 lysine K4 (H3K4) methylation mediated by COMPASS methyltransferase is associated with gene activation, but its effect on epidermal lineage development remains unclear. Therefore, we constructed a mouse model of specific ASH2L (COMPASS methyltransferase core subunit) deletion in epidermal progenitor cells and investigated its effect on the development of mouse epidermal lineage. Furthermore, downstream target genes regulated by H3K4me3 were screened using RNA-sequencing combined with Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing. Deletion of ASH2L in epidermal progenitor cells caused thinning of the suprabasal layer of the epidermis and delayed hair follicle morphogenesis in newborn mice. These phenotypes may be related to the reduced proliferative capacity of epidermal and hair follicle progenitor cells. ASH2L depletion may also lead to depletion of the epidermal stem cell pools in late mouse development. Finally, genes related to hair follicle development (Shh, Edar and Fzd6), Notch signaling pathway (Notch2, Notch3, Hes5 and Nrarp) and ΔNp63 were identified as downstream target genes regulated by H3K4me3. Collectively, ASH2L-dependent H3K4me3 modification served as an upstream epigenetic regulator in epidermal differentiation and hair follicle morphogenesis in mice.
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Affiliation(s)
- Qirui Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Siyi Zeng
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Yimin Liang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Renpeng Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.
| | - Danru Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.
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10
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Wu Z, Gao H, Liu Z. COMPASS core subunits MpSet1 and MpSwd3 regulate Monascus pigments synthesis in Monascus purpureus. J Basic Microbiol 2024; 64:e2300686. [PMID: 38362934 DOI: 10.1002/jobm.202300686] [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: 11/15/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
In eukaryotes, methylation of histone H3 at lysine 4 (H3K4me) catalyzed by the complex of proteins associated with Set1 (COMPASS) is crucial for the transcriptional regulation of genes and the development of organisms. In Monascus, the functions of COMPASS in establishing H3K4me remain unclear. This study first identified the conserved COMPASS core subunits MpSet1 and MpSwd3 in Monascus purpureus and confirmed their roles in establishing H3K4me2/3. Loss of MpSet1 and MpSwd3 resulted in slower growth and development and inhibited the formation of cleistothecia, ascospores, and conidia. The loss of these core subunits also decreased the production of extracellular and intracellular Monascus pigments (MPs) by 94.2%, 93.5%, 82.7%, and 82.5%, respectively. In addition, RNA high-throughput sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) showed that the loss of MpSet1 and MpSwd3 altered the expression of 2646 and 2659 genes, respectively, and repressed the transcription of MPs synthesis-related genes. In addition, the ΔMpset1 and ΔMpswd3 strains demonstrated increased sensitivity to cell wall stress with the downregulation of chitin synthase-coding genes. These results indicated that the COMPASS core subunits MpSet1 and MpSwd3 help establish H3K4me2/3 for growth and development, spore formation, and pigment synthesis in Monascus. These core subunits also assist in maintaining cell wall integrity.
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Affiliation(s)
- Zhongling Wu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
| | - Hongyan Gao
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
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11
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D’Ambrosio A, Bressan D, Ferracci E, Carbone F, Mulè P, Rossi F, Barbieri C, Sorrenti E, Fiaccadori G, Detone T, Vezzoli E, Bianchi S, Sartori C, Corso S, Fukuda A, Bertalot G, Falqui A, Barbareschi M, Romanel A, Pasini D, Chiacchiera F. Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations. SCIENCE ADVANCES 2024; 10:eadh4435. [PMID: 38489371 PMCID: PMC10942108 DOI: 10.1126/sciadv.adh4435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Oncogenic mutations accumulating in many chromatin-associated proteins have been identified in different tumor types. With a mutation rate from 10 to 57%, ARID1A has been widely considered a tumor suppressor gene. However, whether this role is mainly due to its transcriptional-related activities or its ability to preserve genome integrity is still a matter of intense debate. Here, we show that ARID1A is largely dispensable for preserving enhancer-dependent transcriptional regulation, being ARID1B sufficient and required to compensate for ARID1A loss. We provide in vivo evidence that ARID1A is mainly required to preserve genomic integrity in adult tissues. ARID1A loss primarily results in DNA damage accumulation, interferon type I response activation, and chronic inflammation leading to tumor formation. Our data suggest that in healthy tissues, the increased genomic instability that follows ARID1A mutations and the selective pressure imposed by the microenvironment might result in the emergence of aggressive, possibly immune-resistant, tumors.
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Affiliation(s)
- Alessandro D’Ambrosio
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- SEMM, University of Milan, 20142 Milan, Italy
| | - Davide Bressan
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Elisa Ferracci
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Francesco Carbone
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
| | - Patrizia Mulè
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
| | - Federico Rossi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
| | - Caterina Barbieri
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
| | - Elisa Sorrenti
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Gaia Fiaccadori
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Thomas Detone
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
| | - Elena Vezzoli
- Department of Biomedical sciences for Health, University of Milan, 20133 Milan, Italy
| | - Salvatore Bianchi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Chiara Sartori
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
| | - Simona Corso
- Department of Oncology, University of Torino, 10060 Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Akihisa Fukuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Giovanni Bertalot
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
- Centre for Medical Sciences–CISMed, University of Trento, 38122 Trento, Italy
| | - Andrea Falqui
- Department of Physics, University of Milan, 20133 Milan, Italy
| | - Mattia Barbareschi
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
- Centre for Medical Sciences–CISMed, University of Trento, 38122 Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
- Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Fulvio Chiacchiera
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
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12
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Bonilla G, Morris A, Kundu S, Ducasse A, Jeffries NE, Chetal K, Yvanovich EE, Barghout R, Scadden D, Mansour MK, Kingston RE, Sykes DB, Mercier FE, Sadreyev RI. Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582846. [PMID: 38496490 PMCID: PMC10942317 DOI: 10.1101/2024.02.29.582846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Molecular mechanisms driving clonal aggressiveness in leukemia are not fully understood. We tracked and analyzed two mouse MLL-rearranged leukemic clones independently evolving towards higher aggressiveness. More aggressive subclones lost their growth differential ex vivo but restored it upon secondary transplantation, suggesting molecular memory of aggressiveness. Development of aggressiveness was associated with clone-specific gradual modulation of chromatin states and expression levels across the genome, with a surprising preferential trend of reversing the earlier changes between normal and leukemic progenitors. To focus on the core aggressiveness program, we identified genes with consistent changes of expression and chromatin marks that were maintained in vivo and ex vivo in both clones. Overexpressing selected core genes (Smad1 as aggressiveness driver, Irx5 and Plag1 as suppressors) affected leukemic progenitor growth in the predicted way and had convergent downstream effects on central transcription factors and repressive epigenetic modifiers, suggesting a broader regulatory network of leukemic aggressiveness.
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13
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Zhang B, Wang Z, Dai X, Gao J, Zhao J, Ma R, Chen Y, Sun Y, Ma H, Li S, Zhou C, Wang JP, Li W. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 241:1950-1972. [PMID: 38095236 DOI: 10.1111/nph.19481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Histone H3 lysine-4 trimethylation (H3K4me3) activating drought-responsive genes in plants for drought adaptation has long been established, but the underlying regulatory mechanisms are unknown. Here, using yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa, we unveiled in this adaptation a regulatory interplay between chromatin regulation and gene transactivation mediated by an epigenetic determinant, a PtrSDG2-1-PtrCOMPASS (complex proteins associated with Set1)-like H3K4me3 complex, PtrSDG2-1-PtrWDR5a-1-PtrRbBP5-1-PtrAsh2-2 (PtrSWRA). Under drought conditions, a transcription factor PtrAREB1-2 interacts with PtrSWRA, forming a PtrSWRA-PtrAREB1-2 pentamer, to recruit PtrSWRA to specific promoter elements of drought-tolerant genes, such as PtrHox2, PtrHox46, and PtrHox52, for depositing H3K4me3 to promote and maintain activated state of such genes for tolerance. CRISPR-edited defects in the pentamer impaired drought tolerance and elevated expression of PtrHox2, PtrHox46, or PtrHox52 improved the tolerance as well as growth in P. trichocarpa. Our findings revealed the identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency. Furthermore, our study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for elevating H3K4me3 marks for improved drought tolerance and growth/biomass production in plants.
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Affiliation(s)
- Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfeng Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Rong Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yanjie Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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14
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Glancy E, Choy N, Eckersley-Maslin MA. Bivalent chromatin: a developmental balancing act tipped in cancer. Biochem Soc Trans 2024; 52:217-229. [PMID: 38385532 PMCID: PMC10903468 DOI: 10.1042/bst20230426] [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: 11/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Bivalent chromatin is defined by the co-occurrence of otherwise opposing H3K4me3 and H3K27me3 modifications and is typically located at unmethylated promoters of lowly transcribed genes. In embryonic stem cells, bivalent chromatin has been proposed to poise developmental genes for future activation, silencing or stable repression upon lineage commitment. Normally, bivalent chromatin is kept in tight balance in cells, in part through the activity of the MLL/COMPASS-like and Polycomb repressive complexes that deposit the H3K4me3 and H3K27me3 modifications, respectively, but also emerging novel regulators including DPPA2/4, QSER1, BEND3, TET1 and METTL14. In cancers, both the deregulation of existing domains and the creation of de novo bivalent states is associated with either the activation or silencing of transcriptional programmes. This may facilitate diverse aspects of cancer pathology including epithelial-to-mesenchymal plasticity, chemoresistance and immune evasion. Here, we review current methods for detecting bivalent chromatin and discuss the factors involved in the formation and fine-tuning of bivalent domains. Finally, we examine how the deregulation of chromatin bivalency in the context of cancer could facilitate and/or reflect cancer cell adaptation. We propose a model in which bivalent chromatin represents a dynamic balance between otherwise opposing states, where the underlying DNA sequence is primed for the future activation or repression. Shifting this balance in any direction disrupts the tight equilibrium and tips cells into an altered epigenetic and phenotypic space, facilitating both developmental and cancer processes.
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Affiliation(s)
- Eleanor Glancy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Natalie Choy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melanie A. Eckersley-Maslin
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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15
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Seneviratne JA, Ho WWH, Glancy E, Eckersley-Maslin MA. A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin. Epigenetics Chromatin 2024; 17:3. [PMID: 38336688 PMCID: PMC10858499 DOI: 10.1186/s13072-024-00527-9] [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: 09/18/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome occurs predominantly at promoters that are poised for future transcriptional upregulation or terminal silencing. We know little of the dynamics, resolution, and regulation of this chromatin state outside of embryonic stem cells where it was first described. This is partly due to the technical challenges distinguishing bone-fide bivalent chromatin, where both marks are on the same nucleosome, from allelic or sample heterogeneity where there is a mix of H3K4me3-only and H3K27me3-only mononucleosomes. RESULTS Here, we present a robust and sensitive method to accurately map bivalent chromatin genome-wide, along with controls, from as little as 2 million cells. We optimized and refined the sequential ChIP protocol which uses two sequential overnight immunoprecipitation reactions to robustly purify nucleosomes that are truly bivalent and contain both H3K4me3 and H3K27me3 modifications. Our method generates high quality genome-wide maps with strong peak enrichment and low background, which can be analyzed using standard bioinformatic packages. Using this method, we detect 8,789 bivalent regions in mouse embryonic stem cells corresponding to 3,918 predominantly CpG rich and developmentally regulated gene promoters. Furthermore, profiling Dppa2/4 knockout mouse embryonic stem cells, which lose both H3K4me3 and H3K27me3 at approximately 10% of bivalent promoters, demonstrated the ability of our method to capture bivalent chromatin dynamics. CONCLUSIONS Our optimized sequential reChIP method enables high-resolution genome-wide assessment of bivalent chromatin together with all required controls in as little as 2 million cells. We share a detailed protocol and guidelines that will enable bivalent chromatin landscapes to be generated in a range of cellular contexts, greatly enhancing our understanding of bivalent chromatin and epigenetic plasticity beyond embryonic stem cells.
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Affiliation(s)
- Janith A Seneviratne
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - William W H Ho
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
| | - Eleanor Glancy
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Melanie A Eckersley-Maslin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia.
- Department of Anatomy and Physiology, The University of Melbourne, Victoria, 3010, Australia.
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16
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Niederhuber MJ, Leatham-Jensen M, McKay DJ. The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development. Genetics 2024; 226:iyad196. [PMID: 37949841 PMCID: PMC10847718 DOI: 10.1093/genetics/iyad196] [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: 10/05/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodelers are known to work together to control enhancer accessibility, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of nucleosome remodelers in control of dynamic enhancer activity. We find that the Drosophila Switch/Sucrose Non-Fermenting complex, BAP, is required for repression of a temporally dynamic enhancer, brdisc. Contrary to expectations, we find that the BAP-specific subunit Osa is dispensable for mediating changes in chromatin accessibility between the early and late stages of wing development. Instead, we find that Osa is required to constrain the levels of brdisc activity when the enhancer is normally active. Genome-wide profiling reveals that Osa directly binds brdisc as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. Transgenic reporter analyses demonstrate that Osa is required for activation and for constraint of different sets of target enhancers in the same cells. Moreover, Osa loss results in hyperactivation of the Notch ligand Delta and development of ectopic sensory structures patterned by Notch signaling early in development. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.
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Affiliation(s)
- Matthew J Niederhuber
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mary Leatham-Jensen
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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17
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Wang Z, Ren B. Role of H3K4 monomethylation in gene regulation. Curr Opin Genet Dev 2024; 84:102153. [PMID: 38278054 PMCID: PMC11065453 DOI: 10.1016/j.gde.2024.102153] [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: 10/13/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/28/2024]
Abstract
Methylation of histone H3 on the lysine-4 residue (H3K4me) is found throughout the eukaryotic domain, and its initial discovery as a conserved epigenetic mark of active transcription from yeast to mammalian cells has contributed to the histone code hypothesis. However, recent studies have raised questions on whether the different forms of H3K4me play a direct role in gene regulation or are simply by-products of the transcription process. Here, we review the often-conflicting experimental evidence, focusing on the monomethylation of lysine 4 on histone H3 that has been linked to the transcriptional state of enhancers in metazoans. We suggest that this epigenetic mark acts in a context-dependent manner to directly facilitate the transcriptional output of the genome and the establishment of cellular identity.
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Affiliation(s)
- Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA. https://twitter.com/@ZhaoningWang
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA; Institute of Genomic Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
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18
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Yang Q, Zhang Q, Yi S, Zhang S, Yi S, Zhou X, Qin Z, Chen B, Luo J. Novel germline variants in KMT2C in Chinese patients with Kleefstra syndrome-2. Front Neurol 2024; 15:1340458. [PMID: 38356881 PMCID: PMC10864639 DOI: 10.3389/fneur.2024.1340458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Kleefstra syndrome (KLEFS) refers to a rare inherited neurodevelopmental disorder characterized by intellectual disability (ID), language and motor delays, behavioral abnormalities, abnormal facial appearance, and other variable clinical features. KLEFS is subdivided into two subtypes: Kleefstra syndrome-1 (KLEFS1, OMIM: 610253), caused by a heterozygous microdeletion encompassing the Euchromatic Histone Lysine Methyltransferase 1 (EHMT1) gene on chromosome 9q34.3 or pathogenic variants in the EHMT1 gene, and Kleefstra syndrome-2 (KLEFS2, OMIM: 617768), caused by pathogenic variants in the KMT2C gene. More than 100 cases of KLEFS1 have been reported with pathogenic variants in the EHMT1 gene. However, only 13 patients with KLEFS2 have been reported to date. In the present study, five unrelated Chinese patients were diagnosed with KLEFS2 caused by KMT2C variants through whole-exome sequencing (WES). We identified five different variants of the KMT2C gene in these patients: c.9166C>T (p.Gln3056*), c.9232_9247delCAGCGATCAGAACCGT (p.Gln3078fs*13), c.5068dupA (p.Arg1690fs*10), c.10815_10819delAAGAA (p.Lys3605fs*7), and c.6911_6912insA (p.Met2304fs*8). All five patients had a clinical profile similar to that of patients with KLEFS2. To analyze the correlation between the genotype and phenotype of KLEFS2, we examined 18 variants and their associated phenotypes in 18 patients with KLEFS2. Patients carrying KMT2C variants presented with a wide range of phenotypic defects and an extremely variable phenotype. We concluded that the core phenotypes associated with KMT2C variants were intellectual disability, facial dysmorphisms, language and motor delays, behavioral abnormalities, hypotonia, short stature, and weight loss. Additionally, sex may be one factor influencing the outcome. Our findings expand the phenotypic and genetic spectrum of KLEFS2 and help to clarify the genotype-phenotype correlation.
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Affiliation(s)
- Qi Yang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sheng Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shujie Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xunzhao Zhou
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Biyan Chen
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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19
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Lei Y, Yu Y, Fu W, Zhu T, Wu C, Zhang Z, Yu Z, Song X, Xu J, Liang Z, Lü P, Li C. BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants. Nat Commun 2024; 15:935. [PMID: 38296999 PMCID: PMC10830565 DOI: 10.1038/s41467-024-45250-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: 06/29/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machineries that establish and maintain chromatin accessibility and gene expression by regulating chromatin structure. However, how the remodeling activities of SWI/SNF complexes are regulated in eukaryotes remains elusive. B-cell lymphoma/leukemia protein 7 A/B/C (BCL7A/B/C) have been reported as subunits of SWI/SNF complexes for decades in animals and recently in plants; however, the role of BCL7 subunits in SWI/SNF function remains undefined. Here, we identify a unique role for plant BCL7A and BCL7B homologous subunits in potentiating the genome-wide chromatin remodeling activities of SWI/SNF complexes in plants. BCL7A/B require the catalytic ATPase BRAHMA (BRM) to assemble with the signature subunits of the BRM-Associated SWI/SNF complexes (BAS) and for genomic binding at a subset of target genes. Loss of BCL7A and BCL7B diminishes BAS-mediated genome-wide chromatin accessibility without changing the stability and genomic targeting of the BAS complex, highlighting the specialized role of BCL7A/B in regulating remodeling activity. We further show that BCL7A/B fine-tune the remodeling activity of BAS complexes to generate accessible chromatin at the juvenility resetting region (JRR) of the microRNAs MIR156A/C for plant juvenile identity maintenance. In summary, our work uncovers the function of previously elusive SWI/SNF subunits in multicellular eukaryotes and provides insights into the mechanisms whereby plants memorize the juvenile identity through SWI/SNF-mediated control of chromatin accessibility.
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Affiliation(s)
- Yawen Lei
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Caihong Wu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhihao Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zewang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Peitao Lü
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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20
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Merlini A, Rabino M, Brusco S, Pavese V, Masci D, Sangiolo D, Bironzo P, Scagliotti GV, Novello S, D'Ambrosio L. Epigenetic determinants in soft tissue sarcomas: molecular mechanisms and therapeutic targets. Expert Opin Ther Targets 2024; 28:17-28. [PMID: 38234142 DOI: 10.1080/14728222.2024.2306344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/12/2024] [Indexed: 01/19/2024]
Abstract
INTRODUCTION Soft tissue sarcomas are a group of rare, mesenchymal tumors characterized by dismal prognosis in advanced/metastatic stages. Knowledge of their molecular determinants is still rather limited. However, in recent years, epigenetic regulation - the modification of gene expression/function without DNA sequence variation - has emerged as a key player both in sarcomagenesis and sarcoma progression. AREAS COVERED Herein, we describe and review the main epigenetic mechanisms involved in chromatin remodeling and their role as disease drivers in different soft tissue sarcoma histotypes, focusing on epithelioid sarcoma, synovial sarcoma, and malignant peripheral nerve sheath tumors. Focusing on chromatin-remodeling complexes, we provide an in-depth on the role of BAF complex alterations in these soft tissue sarcoma histotypes. In parallel, we highlight current state-of-the-art and future perspectives in the development of rational, innovative treatments leveraging on epigenetic dysregulation in soft tissue sarcomas. EXPERT OPINION Therapeutic options for metastatic/advanced sarcomas are to date very limited and largely represented by cytotoxic agents, with only modest results. In the continuous attempt to find novel targets and innovative, effective drugs, epigenetic mechanisms represent an emerging and promising field of research, especially for malignant peripheral nerve sheath tumors, epithelioid and synovial sarcoma.
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Affiliation(s)
| | - Martina Rabino
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Silvia Brusco
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Division of Molecular Pathology, The Institute of Cancer Research Royal Cancer Hospital, London, UK
| | - Valeria Pavese
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Debora Masci
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Dario Sangiolo
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Paolo Bironzo
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - Giorgio Vittorio Scagliotti
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - Lorenzo D'Ambrosio
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
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21
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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22
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Ertl H. SWI/SNF function compensated by another chromatin remodeller. Nat Rev Genet 2024; 25:5. [PMID: 38012269 DOI: 10.1038/s41576-023-00680-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
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Gruenbacher S, Jaritz M, Hill L, Schäfer M, Busslinger M. Essential role of the Pax5 C-terminal domain in controlling B cell commitment and development. J Exp Med 2023; 220:e20230260. [PMID: 37725138 PMCID: PMC10509461 DOI: 10.1084/jem.20230260] [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: 02/10/2023] [Revised: 07/28/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
The B cell regulator Pax5 consists of multiple domains whose function we analyzed in vivo by deletion in Pax5. While B lymphopoiesis was minimally affected in mice with homozygous deletion of the octapeptide or partial homeodomain, both sequences were required for optimal B cell development. Deletion of the C-terminal regulatory domain 1 (CRD1) interfered with B cell development, while elimination of CRD2 modestly affected B-lymphopoiesis. Deletion of CRD1 and CRD2 arrested B cell development at an uncommitted pro-B cell stage. Most Pax5-regulated genes required CRD1 or both CRD1 and CRD2 for their activation or repression as these domains induced or eliminated open chromatin at Pax5-activated or Pax5-repressed genes, respectively. Co-immunoprecipitation experiments demonstrated that the activating function of CRD1 is mediated through interaction with the chromatin-remodeling BAF, H3K4-methylating Set1A-COMPASS, and H4K16-acetylating NSL complexes, while its repressing function depends on recruitment of the Sin3-HDAC and MiDAC complexes. These data provide novel molecular insight into how different Pax5 domains regulate gene expression to promote B cell commitment and development.
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Affiliation(s)
- Sarah Gruenbacher
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Louisa Hill
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Markus Schäfer
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
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24
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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Hu X, Wang Y, Zhang X, Li C, Zhang X, Yang D, Liu Y, Li L. DNA methylation of HOX genes and its clinical implications in cancer. Exp Mol Pathol 2023; 134:104871. [PMID: 37696326 DOI: 10.1016/j.yexmp.2023.104871] [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: 03/29/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Homeobox (HOX) genes encode highly conserved transcription factors that play vital roles in embryonic development. DNA methylation is a pivotal regulatory epigenetic signaling mark responsible for regulating gene expression. Abnormal DNA methylation is largely associated with the aberrant expression of HOX genes, which is implicated in a broad range of human diseases, including cancer. Numerous studies have clarified the mechanisms of DNA methylation in both physiological and pathological processes. In this review, we focus on how DNA methylation regulates HOX genes and briefly discuss drug development approaches targeting these mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China; Laboratory of Precision Medicine, Zhangqiu District People's Hospital of Jinan, Jinan 250200, Shandong, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Chensheng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Xikun Zhang
- Department of Minimally Invasive Interventional, The Third Affiliated Hospital of Shandong First Medical University, Jinan 250031, Shandong, China
| | - Dongxia Yang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Yuanyuan Liu
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Lianlian Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China; Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
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Mori S, Oya S, Takahashi M, Takashima K, Inagaki S, Kakutani T. Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis. EMBO J 2023; 42:e113798. [PMID: 37849386 PMCID: PMC10690457 DOI: 10.15252/embj.2023113798] [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: 02/17/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is significantly attenuated in the ldl3 mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 demethylation in plants as chromatin records of transcriptional activity, which ensures robust gene control.
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Affiliation(s)
- Shusei Mori
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Satoyo Oya
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | | | | | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- National Institute of GeneticsShizuokaJapan
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Zhou Y, Jin J, Ji Y, Zhang J, Fu N, Chen M, Wang J, Qin K, Jiang Y, Cheng D, Deng X, Shen B. TP53 missense mutation reveals gain-of-function properties in small-sized KRAS transformed pancreatic ductal adenocarcinoma. J Transl Med 2023; 21:872. [PMID: 38037073 PMCID: PMC10691048 DOI: 10.1186/s12967-023-04742-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Although the molecular features of pancreatic ductal adenocarcinoma (PDAC) have been well described, the impact of detailed gene mutation subtypes on disease progression remained unclear. This study aimed to evaluate the impact of different TP53 mutation subtypes on clinical characteristics and outcomes of patients with PDAC. METHODS We included 639 patients treated with PDAC in Ruijin Hospital affiliated to Shanghai Jiaotong University School of Medicine between Jan 2019 and Jun 2021. The genomic alterations of PDAC were analyzed, and the association of TP53 mutation subtypes and other core gene pathway alterations with patients' clinical characteristics were evaluated by Chi-squared test, Kaplan-Meier method and Cox regression model. RESULTS TP53 missense mutation was significantly associated with poor differentiation in KRASmut PDAC (50.7% vs. 36.1%, P = 0.001). In small-sized (≤ 2 cm) KRASmut tumors, significantly higher LNs involvement (54.8% vs. 23.5%, P = 0.010) and distal metastic rate (20.5% vs. 2.9%, P = 0.030) were observed in those with TP53 missense mutation instead of truncating mutation. Compared with TP53 truncating mutation, missense mutation was significantly associated with reduced DFS (6.6 [5.6-7.6] vs. 9.2 [5.2-13.3] months, HR 0.368 [0.200-0.677], P = 0.005) and OS (9.6 [8.0-11.1] vs. 18.3 [6.7-30.0] months, HR 0.457 [0.248-0.842], P = 0.012) in patients who failed to receive chemotherapy, while higher OS (24.2 [20.8-27.7] vs. 23.8 [19.0-28.5] months, HR 1.461 [1.005-2.124], P = 0.047) was observed in TP53missense cases after chemotherapy. CONCLUSIONS TP53 missense mutation was associated with poor tumor differentiation, and revealed gain-of-function properties in small-sized KRAS transformed PDAC. Nonetheless, it was not associated with insensitivity to chemotherapy, highlighting the neoadjuvant therapy before surgery as the potential optimized strategy for the treatment of a subset of patients.
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Affiliation(s)
- Yiran Zhou
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiabin Jin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuchen Ji
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqiang Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ningzhen Fu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mengmin Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dongfeng Cheng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Ozyerli-Goknar E, Kala EY, Aksu AC, Bulut I, Cingöz A, Nizamuddin S, Biniossek M, Seker-Polat F, Morova T, Aztekin C, Kung SHY, Syed H, Tuncbag N, Gönen M, Philpott M, Cribbs AP, Acilan C, Lack NA, Onder TT, Timmers HTM, Bagci-Onder T. Epigenetic-focused CRISPR/Cas9 screen identifies (absent, small, or homeotic)2-like protein (ASH2L) as a regulator of glioblastoma cell survival. Cell Commun Signal 2023; 21:328. [PMID: 37974198 PMCID: PMC10652464 DOI: 10.1186/s12964-023-01335-6] [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: 05/02/2023] [Accepted: 09/26/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Glioblastoma is the most common and aggressive primary brain tumor with extremely poor prognosis, highlighting an urgent need for developing novel treatment options. Identifying epigenetic vulnerabilities of cancer cells can provide excellent therapeutic intervention points for various types of cancers. METHOD In this study, we investigated epigenetic regulators of glioblastoma cell survival through CRISPR/Cas9 based genetic ablation screens using a customized sgRNA library EpiDoKOL, which targets critical functional domains of chromatin modifiers. RESULTS Screens conducted in multiple cell lines revealed ASH2L, a histone lysine methyltransferase complex subunit, as a major regulator of glioblastoma cell viability. ASH2L depletion led to cell cycle arrest and apoptosis. RNA sequencing and greenCUT&RUN together identified a set of cell cycle regulatory genes, such as TRA2B, BARD1, KIF20B, ARID4A and SMARCC1 that were downregulated upon ASH2L depletion. Mass spectrometry analysis revealed the interaction partners of ASH2L in glioblastoma cell lines as SET1/MLL family members including SETD1A, SETD1B, MLL1 and MLL2. We further showed that glioblastoma cells had a differential dependency on expression of SET1/MLL family members for survival. The growth of ASH2L-depleted glioblastoma cells was markedly slower than controls in orthotopic in vivo models. TCGA analysis showed high ASH2L expression in glioblastoma compared to low grade gliomas and immunohistochemical analysis revealed significant ASH2L expression in glioblastoma tissues, attesting to its clinical relevance. Therefore, high throughput, robust and affordable screens with focused libraries, such as EpiDoKOL, holds great promise to enable rapid discovery of novel epigenetic regulators of cancer cell survival, such as ASH2L. CONCLUSION Together, we suggest that targeting ASH2L could serve as a new therapeutic opportunity for glioblastoma. Video Abstract.
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Affiliation(s)
- Ezgi Ozyerli-Goknar
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Freiburg, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Ezgi Yagmur Kala
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Ali Cenk Aksu
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Ipek Bulut
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Ahmet Cingöz
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Sheikh Nizamuddin
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Freiburg, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Martin Biniossek
- Institute for Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Fidan Seker-Polat
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Tunc Morova
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Can Aztekin
- Koç University School of Medicine, Istanbul, Türkiye
| | - Sonia H Y Kung
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Hamzah Syed
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Biostatistics, Bioinformatics and Data Management Lab, KUTTAM, Istanbul, Türkiye
| | - Nurcan Tuncbag
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Department of Chemical and Biological Engineering, Koç University, Istanbul, Türkiye
| | - Mehmet Gönen
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Department of Industrial Engineering, Koç University, Istanbul, Türkiye
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ceyda Acilan
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
| | - Nathan A Lack
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Tamer T Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
| | - H T Marc Timmers
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Freiburg, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Tugba Bagci-Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye.
- Koç University School of Medicine, Istanbul, Türkiye.
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Giudice V, Serio B, Errichiello S, Ferrara I, Galdiero A, Bertolini A, Visconti R, De Novellis D, Guariglia R, Luponio S, Morini D, Della Corte AM, Sessa AM, Verdesca F, Langella M, Izzo B, Selleri C. Subclones with variants of uncertain clinical significance might contribute to ineffective hemopoiesis and leukemia predisposition. Eur J Haematol 2023; 111:729-741. [PMID: 37501402 DOI: 10.1111/ejh.14069] [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: 05/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Splicing modifications, genomic instability, and hypomethylation are central mechanisms promoting myelodysplasia and acute myeloid leukemia (AML). In this real-life retrospective study, to elucidate pathophysiology of clonal hemopoiesis in hematological malignancies, we investigated clinical significance of mutations in leukemia-related genes of known pathogenetic significance and of variants of uncertain clinical significance (VUS) in a cohort of patients with MDS and AML. METHODS A total of 59 consecutive subjects diagnosed with MDS, 48 with AML, and 17 with clonal cytopenia with unknown significance were screened for somatic mutations in AML-related genes by next-generation sequencing. RESULTS We showed that TET2, SETBP1, ASXL1, EZH2, RUNX1, SRSF2, DNMT3A, and IDH1/2 were commonly mutated. MDS patients also showed a high genetic complexity, especially for SETBP1. Moreover, the presence of SETBP1 wild-type or two or more simultaneous VUS variants identified a subgroup of AML and MDS patients with better outcome, while the presence of single SETBP1 VUS variant was related to a worse prognosis, regardless TET2 mutational status. CONCLUSIONS In conclusions, we linked both pathogenic and VUS variants in AML-related genes to clonal hematopoiesis; therefore, we proposed to consider those variants as prognostic markers in leukemia and myelodysplasia. However, further studies in larger prospective cohorts are required to validate our results.
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Affiliation(s)
- Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Santa Errichiello
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Idalucia Ferrara
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Alessandra Galdiero
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Angela Bertolini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Roberta Visconti
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Danilo De Novellis
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Roberto Guariglia
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Serena Luponio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Denise Morini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Della Corte
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Sessa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Francesco Verdesca
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Maddalena Langella
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
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Rodriguez JD, Reeves M, Wang HL, Chavez J, Rastogi R, Chavez S, Chadha M, Hill EJ, Corces VG, Schmeichel K, Katz DJ. Ectopic transcription due to inappropriately inherited histone methylation may interfere with the ongoing function of terminally differentiated cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564525. [PMID: 37961655 PMCID: PMC10634925 DOI: 10.1101/2023.10.29.564525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Many human neurodevelopmental disorders are caused by de novo mutations in histone modifying enzymes. These patients have craniofacial defects, developmental delay, intellectual disability and behavioral abnormalities, but it remains unclear how the mutations lead to such developmental defects. Here we take advantage of the invariant C. elegans lineage along with a unique double mutant in the H3K4me1/2 demethylase SPR-5/LSD1/KDM1A and the H3K9 methyltransferase MET-2/SETDB1 to address this question. We demonstrate that spr-5; met-2 double mutant worms have a severe chemotaxis defect that is dependent upon the ectopic expression of germline genes in somatic tissues. In addition, by performing single-cell RNAseq, we find that germline genes begin to be ectopically expression widely in spr-5; met-2 embryos. However, surprisingly we found that spr-5; met-2 mutants have no somatic lineage defects prior to the 200-cell stage of embryogenesis. This suggests that the altered chemotaxis behavior may be due to ongoing defect in terminally differentiated cells rather than a defect in development. To test this directly, we used RNAi to shut off the ectopic expression of germline genes in L2 spr-5; met-2 larvae, which have a fully formed nervous system. Remarkably, we find that shutting off the ectopic germline expression rescues normal chemotaxis behavior in the same adult worms that previously had a chemotaxis defect at the L2 stage. This suggests that ongoing ectopic transcription can block normal behavior in a fully intact nervous system. These data raise the possibility that intellectual disability and altered behavior in neurodevelopmental syndromes, caused by mutations in histone modifying enzymes, could be due to ongoing ectopic transcription and may be reversible.
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Mayayo-Peralta I, Gregoricchio S, Schuurman K, Yavuz S, Zaalberg A, Kojic A, Abbott N, Geverts B, Beerthuijzen S, Siefert J, Severson TM, van Baalen M, Hoekman L, Lieftink C, Altelaar M, Beijersbergen RL, Houtsmuller A, Prekovic S, Zwart W. PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription. Nucleic Acids Res 2023; 51:9576-9593. [PMID: 37070193 PMCID: PMC10570044 DOI: 10.1093/nar/gkad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
How steroid hormone receptors (SHRs) regulate transcriptional activity remains partly understood. Upon activation, SHRs bind the genome together with a co-regulator repertoire, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited co-regulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we functionally dissected the Glucocorticoid Receptor (GR) complex. We describe a functional cross-talk between PAXIP1 and the cohesin subunit STAG2, critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on chromatin, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. In lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.
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Affiliation(s)
- Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Selçuk Yavuz
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
| | - Anniek Zaalberg
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aleksandar Kojic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Suzanne Beerthuijzen
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joseph Siefert
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martijn van Baalen
- Flow Cytometry Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherland
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
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Kim J, Diaz LF, Miller MJ, Leadem B, Krivega I, Dean A. An enhancer RNA recruits MLL1 to regulate transcription of Myb. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559528. [PMID: 37808852 PMCID: PMC10557664 DOI: 10.1101/2023.09.26.559528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter. We identified a long non-coding RNA (Myrlin) originating from the -81 kb murine Myb enhancer. Myrlin and Myb are coordinately regulated during erythroid differentiation. Myrlin TSS deletion using CRISPR/Cas9 reduced Myrlin and Myb expression and LDB1 complex occupancy at the Myb enhancers, compromising enhancer contacts and reducing RNA Pol II occupancy in the locus. In contrast, CRISPRi silencing of Myrlin left LDB1 and the Myb enhancer hub unperturbed, although Myrlin and Myb expression were downregulated, decoupling transcription and chromatin looping. Myrlin interacts with the MLL1 complex. Myrlin CRISPRi compromised MLL1 occupancy in the Myb locus, decreasing CDK9 and RNA Pol II binding and resulting in Pol II pausing in the Myb first exon/intron. Thus, Myrlin directly participates in activating Myb transcription by recruiting MLL1.
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Affiliation(s)
- Juhyun Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luis F. Diaz
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Oregon Health and Sciences University, Portland, OR 97239
| | - Matthew J. Miller
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- University of Iowa Medical School, Iowa City, IA 52242
| | - Benjamin Leadem
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- GeneDx, Gaithersburg, MD 20877
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Sonothera, South San Francisco, CA 94080
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Bhattacharya A, Fushimi A, Wang K, Yamashita N, Morimoto Y, Ishikawa S, Daimon T, Liu T, Liu S, Long MD, Kufe D. MUC1-C intersects chronic inflammation with epigenetic reprogramming by regulating the set1a compass complex in cancer progression. Commun Biol 2023; 6:1030. [PMID: 37821650 PMCID: PMC10567710 DOI: 10.1038/s42003-023-05395-9] [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: 04/19/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
Chronic inflammation promotes epigenetic reprogramming in cancer progression by pathways that remain unclear. The oncogenic MUC1-C protein is activated by the inflammatory NF-κB pathway in cancer cells. There is no known involvement of MUC1-C in regulation of the COMPASS family of H3K4 methyltransferases. We find that MUC1-C regulates (i) bulk H3K4 methylation levels, and (ii) the COMPASS SET1A/SETD1A and WDR5 genes by an NF-κB-mediated mechanism. The importance of MUC1-C in regulating the SET1A COMPASS complex is supported by the demonstration that MUC1-C and WDR5 drive expression of FOS, ATF3 and other AP-1 family members. In a feedforward loop, MUC1-C, WDR5 and AP-1 contribute to activation of genes encoding TRAF1, RELB and other effectors in the chronic NF-κB inflammatory response. We also show that MUC1-C, NF-κB, WDR5 and AP-1 are necessary for expression of the (i) KLF4 master regulator of the pluripotency network and (ii) NOTCH1 effector of stemness. In this way, MUC1-C/NF-κB complexes recruit SET1A/WDR5 and AP-1 to enhancer-like signatures in the KLF4 and NOTCH1 genes with increases in H3K4me3 levels, chromatin accessibility and transcription. These findings indicate that MUC1-C regulates the SET1A COMPASS complex and the induction of genes that integrate NF-κB-mediated chronic inflammation with cancer progression.
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Affiliation(s)
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Keyi Wang
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nami Yamashita
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Satoshi Ishikawa
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tatsuaki Daimon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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Gilan O, Talarmain L, Bell CC, Neville D, Knezevic K, Ferguson DT, Boudes M, Chan YC, Davidovich C, Lam EYN, Dawson MA. CRISPR-ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia. Nat Struct Mol Biol 2023; 30:1592-1606. [PMID: 37679565 DOI: 10.1038/s41594-023-01087-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
Chromatin regulation involves the selective recruitment of chromatin factors to facilitate DNA repair, replication and transcription. Here we demonstrate the utility of coupling unbiased functional genomics with chromatin immunoprecipitation (CRISPR-ChIP) to identify the factors associated with active chromatin modifications in mammalian cells. Specifically, an integrated reporter containing a cis-regulatory element of interest and a single guide RNA provide a chromatinized template for a direct readout for regulators of histone modifications associated with actively transcribed genes such as H3K4me3 and H3K79me2. With CRISPR-ChIP, we identify all the nonredundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukemia cells driven by MLL translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units: an oncogenic DOT1L complex directed by the MLL fusion protein in a Menin-dependent manner and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia.
| | - Laure Talarmain
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Neville
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel T Ferguson
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- EMBL-Australia, Clayton, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Clinical Haematology, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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Moreta-Moraleda C, Queralt C, Vendrell-Ayats C, Forcales S, Martínez-Balibrea E. Chromatin factors: Ready to roll as biomarkers in metastatic colorectal cancer? Pharmacol Res 2023; 196:106924. [PMID: 37709185 DOI: 10.1016/j.phrs.2023.106924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent cancer globally and stands as the fourth leading cause of cancer-related fatalities in 2020. Survival rates for metastatic disease have slightly improved in recent decades, with clinical trials showing median overall survival of approximately 24-30 months. This progress can be attributed to the integration of chemotherapeutic treatments alongside targeted therapies and immunotherapy. Despite these modest improvements, the primary obstacle to successful treatment for advanced CRC lies in the development of chemoresistance, whether inherent or acquired, which remains the major cause of treatment failure. Epigenetics has emerged as a hallmark of cancer, contributing to master transcription regulation and genome stability maintenance. As a result, epigenetic factors are starting to appear as potential clinical biomarkers for diagnosis, prognosis, and prediction of treatment response in CRC.In recent years, numerous studies have investigated the influence of DNA methylation, histone modifications, and chromatin remodelers on responses to chemotherapeutic treatments. While there is accumulating evidence indicating their significant involvement in various types of cancers, the exact relationship between chromatin landscapes and treatment modulation in CRC remains elusive. This review aims to provide a comprehensive summary of the most pertinent and extensively researched epigenetic-associated mechanisms described between 2015 and 2022 and their potential usefulness as predictive biomarkers in the metastatic disease.
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Affiliation(s)
- Cristina Moreta-Moraleda
- Immunology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, c/Feixa Llarga s/n, 08917 L'Hospitalet de Llobregat, Barcelona, Spain; Group of Inflammation, Immunity and Cancer, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), The Bellvitge Biomedical Research Institute ( IDIBELL), Hospital Duran i Reynals 3a Planta, Av. Gran Via de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Spain
| | - Cristina Queralt
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain
| | - Carla Vendrell-Ayats
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain; CARE Program, Germans Trias I Pujol Research Institute (IGTP), Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain
| | - Sonia Forcales
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, c/Feixa Llarga s/n, 08917 L'Hospitalet de Llobregat, Barcelona, Spain; Group of Inflammation, Immunity and Cancer, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), The Bellvitge Biomedical Research Institute ( IDIBELL), Hospital Duran i Reynals 3a Planta, Av. Gran Via de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Spain.
| | - Eva Martínez-Balibrea
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain; CARE Program, Germans Trias I Pujol Research Institute (IGTP), Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain.
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Tsukahara T, Kethireddy S, Bonefas K, Chen A, Sutton BLM, Dou Y, Iwase S, Sutton MA. Division of labor among H3K4 Methyltransferases Defines Distinct Facets of Homeostatic Plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558734. [PMID: 37790395 PMCID: PMC10542164 DOI: 10.1101/2023.09.20.558734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Heterozygous mutations in any of the six H3K4 methyltransferases (KMT2s) result in monogenic neurodevelopmental disorders, indicating nonredundant yet poorly understood roles of this enzyme family in neurodevelopment. Recent evidence suggests that histone methyltransferase activity may not be central to KMT2 functions; however, the enzymatic activity is evolutionarily conserved, implicating the presence of selective pressure to maintain the catalytic activity. Here, we show that H3K4 methylation is dynamically regulated during prolonged alteration of neuronal activity. The perturbation of H3K4me by the H3.3K4M mutant blocks synaptic scaling, a form of homeostatic plasticity that buffers the impact of prolonged reductions or increases in network activity. Unexpectedly, we found that the six individual enzymes are all necessary for synaptic scaling and that the roles of KMT2 enzymes segregate into evolutionary-defined subfamilies: KMT2A and KMT2B (fly-Trx homologs) for synaptic downscaling, KMT2C and KMT2D (Trr homologs) for upscaling, and KMT2F and KMT2G (dSet homologs) for both directions. Selective blocking of KMT2A enzymatic activity by a small molecule and targeted disruption of the enzymatic domain both blocked the synaptic downscaling and interfered with the activity-dependent transcriptional program. Furthermore, our study revealed specific phases of synaptic downscaling, i.e., induction and maintenance, in which KMT2A and KMT2B play distinct roles. These results suggest that mammalian brains have co-opted intricate H3K4me installation to achieve stability of the expanding neuronal circuits.
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Affiliation(s)
- Takao Tsukahara
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Saini Kethireddy
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan
| | - Katherine Bonefas
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Alex Chen
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Brendan LM Sutton
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Yali Dou
- Department of Medicine and Department of Biochemistry and Molecular Medicine, Keck School of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Shigeki Iwase
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Michael A. Sutton
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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He H, Li J, Wang W, Cheng J, Zhou J, Li Q, Jin J, Chen L. The SIRT7-mediated deacetylation of CHD1L amplifies HIF-2α-dependent signal that drives renal cell carcinoma progression and sunitinib resistance. Cell Biosci 2023; 13:166. [PMID: 37691108 PMCID: PMC10493023 DOI: 10.1186/s13578-023-01113-4] [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: 03/26/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Aberrant interplay between epigenetic reprogramming and hypoxia signaling contributes to renal cell carcinoma progression and drug resistance, which is an essential hallmark. How the chromatin remodelers enhance RCC malignancy remains to be poorly understood. We aimed to elucidate the roles of CHD1L in determining hypoxia signaling activation and sunitinib resistance. METHODS The qRT-PCR, western blotting, and immunohistochemistry technologies were used to detect CHD1L expressions. Lentivirus transfection was used to generate stable CHD1L-KD cells. The roles of SIRT7/CHD1L were evaluated by CCK-8, wound healing, transwell assays, xenograft models, and tail-vein metastasis models. Co-immunoprecipitation, Chromatin Immunoprecipitation (ChIP), and luciferase reporter assays were conducted to explore epigenetic regulations. RESULTS We screened and validated that CHD1L is up-regulated in RCC and correlates with poorer prognosis of patients. CHD1L overexpression notably enhances cell proliferation, migration, and self-renewal capacities in vitro and in vivo. Mechanistically, SIRT7 physically interacts with CHDL1 and mediates the deacetylation of CHD1L. Wild-type SIRT7, but not H187Y dead mutant, stabilizes CHD1L protein levels via attenuating its ubiquitination levels. SIRT7 is increased in RCC and correlates with hazardous RCC clinical characteristics. SIRT7 depends on CHD1L to exert its tumor-promoting functions. Accumulated CHD1L amplifies HIF-2α-driven transcriptional programs via interacting with HIF-2α. CHD1L recruits BRD4 and increases the RNA polymerase II S2P loading. CHD1L ablation notably abolishes HIF-2α binding and subsequent transcriptional activation. CHD1L overexpression mediates the sunitinib resistance via sustaining VEGFA and targeting CHD1L reverses this effect. Specific CHD1L inhibitor (CHD1Li) shows a synergistic effect with sunitinib and strengthens its pharmaceutical effect. CONCLUSIONS These results uncover a CHD1L-mediated epigenetic mechanism of HIF-2α activation and downstream sunitinib resistance. The SIRT7-CHD1L-HIF-2α axis is highlighted to predict RCC prognosis and endows potential targets.
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Affiliation(s)
- Hongchao He
- Department of Urology, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jie Li
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Wei Wang
- Department of Clinical Laboratory, Lianshui County People's Hospital, Huai'an, 223400, China
| | - Jie Cheng
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Xuhui Central Hospital, Shanghai, 200031, China
| | - Jian Zhou
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Xuhui Central Hospital, Shanghai, 200031, China
| | - Qunyi Li
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Juan Jin
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, 310000, Zhejiang, China.
| | - Li Chen
- Department of Pharmacy, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China.
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Fountain DM, Sauka-Spengler T. The SWI/SNF Complex in Neural Crest Cell Development and Disease. Annu Rev Genomics Hum Genet 2023; 24:203-223. [PMID: 37624665 DOI: 10.1146/annurev-genom-011723-082913] [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] [Indexed: 08/27/2023]
Abstract
While the neural crest cell population gives rise to an extraordinary array of derivatives, including elements of the craniofacial skeleton, skin pigmentation, and peripheral nervous system, it is today increasingly recognized that Schwann cell precursors are also multipotent. Two mammalian paralogs of the SWI/SNF (switch/sucrose nonfermentable) chromatin-remodeling complexes, BAF (Brg1-associated factors) and PBAF (polybromo-associated BAF), are critical for neural crest specification during normal mammalian development. There is increasing evidence that pathogenic variants in components of the BAF and PBAF complexes play central roles in the pathogenesis of neural crest-derived tumors. Transgenic mouse models demonstrate a temporal window early in development where pathogenic variants in Smarcb1 result in the formation of aggressive, poorly differentiated tumors, such as rhabdoid tumors. By contrast, later in development, homozygous inactivation of Smarcb1 requires additional pathogenic variants in tumor suppressor genes to drive the development of differentiated adult neoplasms derived from the neural crest, which have a comparatively good prognosis in humans.
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Affiliation(s)
- Daniel M Fountain
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom; ,
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom; ,
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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39
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Batbayar G, Ishimura A, Lyu H, Wanna-Udom S, Meguro-Horike M, Terashima M, Horike SI, Takino T, Suzuki T. ASH2L, a COMPASS core subunit, is involved in the cell invasion and migration of triple-negative breast cancer cells through the epigenetic control of histone H3 lysine 4 methylation. Biochem Biophys Res Commun 2023; 669:19-29. [PMID: 37262949 DOI: 10.1016/j.bbrc.2023.05.061] [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: 05/07/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023]
Abstract
ASH2L (Absent-Small-Homeotic-2-Like protein) is a core subunit of the COMPASS (COMplex of Proteins ASsociated with Set1) complex, the most notable writer of the methylation of histone H3 lysine 4 (H3K4). The COMPASS complex regulates active promoters or enhancers for gene expression, and its dysfunction is associated with aberrant development and disease. Here, we demonstrated that ASH2L mediated the cell invasion and migration activity of triple-negative breast cancer cells through the interaction with the COMPASS components and the target genomic regions. Transcriptome analysis indicated a potential correlation between ASH2L and the genes involved in inflammatory/immune responses. Among them, we found that the intrinsic expression of IL1B (interleukin 1 beta), an essential proinflammatory gene, was directly regulated by ASH2L. These results revealed a novel role of ASH2L on the maintenance of breast cancer malignancy possibly through H3K4 methylation of the target inflammatory/immune responsive genes.
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Affiliation(s)
- Gerelsuren Batbayar
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Ishikawa, Japan
| | - Akihiko Ishimura
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Ishikawa, Japan
| | - Hanbing Lyu
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Ishikawa, Japan
| | - Sasithorn Wanna-Udom
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Thailand
| | - Makiko Meguro-Horike
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Takara-machi, Kanazawa, 920-0934, Ishikawa, Japan
| | - Minoru Terashima
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Ishikawa, Japan
| | - Shin-Ichi Horike
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Takara-machi, Kanazawa, 920-0934, Ishikawa, Japan
| | - Takahisa Takino
- Division of Education for Global Standard, Institute of Liberal Arts and Science, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Ishikawa, Japan
| | - Takeshi Suzuki
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Ishikawa, Japan.
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40
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Lee RS, Sad K, Fawwal DV, Spangle JM. Emerging Role of Epigenetic Modifiers in Breast Cancer Pathogenesis and Therapeutic Response. Cancers (Basel) 2023; 15:4005. [PMID: 37568822 PMCID: PMC10417282 DOI: 10.3390/cancers15154005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023] Open
Abstract
Breast cancer pathogenesis, treatment, and patient outcomes are shaped by tumor-intrinsic genomic alterations that divide breast tumors into molecular subtypes. These molecular subtypes often dictate viable therapeutic interventions and, ultimately, patient outcomes. However, heterogeneity in therapeutic response may be a result of underlying epigenetic features that may further stratify breast cancer patient outcomes. In this review, we examine non-genetic mechanisms that drive functional changes to chromatin in breast cancer to contribute to cell and tumor fitness and highlight how epigenetic activity may inform the therapeutic response. We conclude by providing perspectives on the future of therapeutic targeting of epigenetic enzymes, an approach that holds untapped potential to improve breast cancer patient outcomes.
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Affiliation(s)
- Richard Sean Lee
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
- Department of Biology, Emory College, Atlanta, GA 30322, USA
| | - Kirti Sad
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
| | - Dorelle V. Fawwal
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30311, USA
| | - Jennifer Marie Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
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41
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Brauer B, Merino-Veliz N, Ahumada-Marchant C, Arriagada G, Bustos FJ. KMT2C knockout generates ASD-like behaviors in mice. Front Cell Dev Biol 2023; 11:1227723. [PMID: 37538398 PMCID: PMC10394233 DOI: 10.3389/fcell.2023.1227723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
Neurodevelopmental disorders have been associated with genetic mutations that affect cellular function, including chromatin regulation and epigenetic modifications. Recent studies in humans have identified mutations in KMT2C, an enzyme responsible for modifying histone tails and depositing H3K4me1 and H3K4me3, as being associated with Kleefstra syndrome 2 and autism spectrum disorder (ASD). However, the precise role of KMT2C mutations in brain disorders remains poorly understood. Here we employed CRISPR/Cas9 gene editing to analyze the effects of KMT2C brain specific knockout on animal behavior. Knocking out KMT2C expression in cortical neurons and the mouse brain resulted in decreased KMT2C levels. Importantly, KMT2C brain specific knockout animals exhibited repetitive behaviors, social deficits, and intellectual disability resembling ASD. Our findings shed light on the involvement of KMT2C in neurodevelopmental processes and establish a valuable model for elucidating the cellular and molecular mechanisms underlying KMT2C mutations and their relationship to Kleefstra syndrome 2 and ASD.
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42
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Albert TK, Kerl K. A histone tale that enCOMPASSes pausing: new insights into the functional repertoire of H3K4me3. Signal Transduct Target Ther 2023; 8:270. [PMID: 37443139 PMCID: PMC10345018 DOI: 10.1038/s41392-023-01529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/11/2023] [Accepted: 05/24/2023] [Indexed: 07/15/2023] Open
Affiliation(s)
- Thomas K Albert
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany.
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43
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Mätlik K, Govek EE, Paul MR, Allis CD, Hatten ME. Histone bivalency regulates the timing of cerebellar granule cell development. Genes Dev 2023; 37:570-589. [PMID: 37491148 PMCID: PMC10499015 DOI: 10.1101/gad.350594.123] [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: 03/02/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature neurons. Here we used RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron: the mouse cerebellar granule cell (GC). We found that in proliferating GC progenitors (GCPs), H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Expressing a fluorescent sensor for bivalent domains revealed subnuclear bivalent foci in proliferating GCPs. Inhibiting H3K27 methyltransferases EZH1 and EZH2 in vitro and in organotypic cerebellar slices dramatically altered the expression of bivalent genes, induced the down-regulation of migration-related genes and up-regulation of synaptic genes, inhibited glial-guided migration, and accelerated terminal differentiation. Thus, histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.
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Affiliation(s)
- Kärt Mätlik
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, Rockefeller University, New York, New York 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, New York, New York 10065, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA;
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44
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Liu R, Chen X, Zhao F, Jiang Y, Lu Z, Ji H, Feng Y, Li J, Zhang H, Zheng J, Zhang J, Zhao Y. The COMPASS Complex Regulates Fungal Development and Virulence through Histone Crosstalk in the Fungal Pathogen Cryptococcus neoformans. J Fungi (Basel) 2023; 9:672. [PMID: 37367608 DOI: 10.3390/jof9060672] [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: 05/17/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023] Open
Abstract
The Complex of Proteins Associated with Set1 (COMPASS) methylates lysine K4 on histone H3 (H3K4) and is conserved from yeast to humans. Its subunits and regulatory roles in the meningitis-causing fungal pathogen Cryptococcus neoformans remain unknown. Here we identified the core subunits of the COMPASS complex in C. neoformans and C. deneoformans and confirmed their conserved roles in H3K4 methylation. Through AlphaFold modeling, we found that Set1, Bre2, Swd1, and Swd3 form the catalytic core of the COMPASS complex and regulate the cryptococcal yeast-to-hypha transition, thermal tolerance, and virulence. The COMPASS complex-mediated histone H3K4 methylation requires H2B mono-ubiquitination by Rad6/Bre1 and the Paf1 complex in order to activate the expression of genes specific for the yeast-to-hypha transition in C. deneoformans. Taken together, our findings demonstrate that putative COMPASS subunits function as a unified complex, contributing to cryptococcal development and virulence.
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Affiliation(s)
- Ruoyan Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoyu Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fujie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yixuan Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhenguo Lu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Heng Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Youbao Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
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45
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Rajan A, Anhezini L, Rives-Quinto N, Chhabra JY, Neville MC, Larson ED, Goodwin SF, Harrison MM, Lee CY. Low-level repressive histone marks fine-tune gene transcription in neural stem cells. eLife 2023; 12:e86127. [PMID: 37314324 PMCID: PMC10344426 DOI: 10.7554/elife.86127] [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: 01/11/2023] [Accepted: 06/11/2023] [Indexed: 06/15/2023] Open
Abstract
Coordinated regulation of gene activity by transcriptional and translational mechanisms poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC (FruC) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fruC function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruC negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fruC loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes gene transcription in stem cells, a mechanism likely conserved from flies to humans.
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Affiliation(s)
- Arjun Rajan
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Noemi Rives-Quinto
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jay Y Chhabra
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Megan C Neville
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
- Department of Cell and Developmental Biology, University of Michigan Medical SchoolAnn ArborUnited States
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical SchoolAnn ArborUnited States
- Rogel Cancer Center, University of Michigan Medical SchoolAnn ArborUnited States
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46
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Estell C, Davidson L, Eaton JD, Kimura H, Gold VAM, West S. A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription. Mol Cell 2023:S1097-2765(23)00385-4. [PMID: 37329883 DOI: 10.1016/j.molcel.2023.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The transcriptional termination of unstable non-coding RNAs (ncRNAs) is poorly understood compared to coding transcripts. We recently identified ZC3H4-WDR82 ("restrictor") as restricting human ncRNA transcription, but how it does this is unknown. Here, we show that ZC3H4 additionally associates with ARS2 and the nuclear exosome targeting complex. The domains of ZC3H4 that contact ARS2 and WDR82 are required for ncRNA restriction, suggesting their presence in a functional complex. Consistently, ZC3H4, WDR82, and ARS2 co-transcriptionally control an overlapping population of ncRNAs. ZC3H4 is proximal to the negative elongation factor, PNUTS, which we show enables restrictor function and is required to terminate the transcription of all major RNA polymerase II transcript classes. In contrast to short ncRNAs, longer protein-coding transcription is supported by U1 snRNA, which shields transcripts from restrictor and PNUTS at hundreds of genes. These data provide important insights into the mechanism and control of transcription by restrictor and PNUTS.
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Affiliation(s)
- Chris Estell
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Lee Davidson
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Joshua D Eaton
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Hiroshi Kimura
- Cell Biology Centre, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Steven West
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom.
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47
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Rots D, Jakub TE, Keung C, Jackson A, Banka S, Pfundt R, de Vries BBA, van Jaarsveld RH, Hopman SMJ, van Binsbergen E, Valenzuela I, Hempel M, Bierhals T, Kortüm F, Lecoquierre F, Goldenberg A, Hertz JM, Andersen CB, Kibæk M, Prijoles EJ, Stevenson RE, Everman DB, Patterson WG, Meng L, Gijavanekar C, De Dios K, Lakhani S, Levy T, Wagner M, Wieczorek D, Benke PJ, Lopez Garcia MS, Perrier R, Sousa SB, Almeida PM, Simões MJ, Isidor B, Deb W, Schmanski AA, Abdul-Rahman O, Philippe C, Bruel AL, Faivre L, Vitobello A, Thauvin C, Smits JJ, Garavelli L, Caraffi SG, Peluso F, Davis-Keppen L, Platt D, Royer E, Leeuwen L, Sinnema M, Stegmann APA, Stumpel CTRM, Tiller GE, Bosch DGM, Potgieter ST, Joss S, Splitt M, Holden S, Prapa M, Foulds N, Douzgou S, Puura K, Waltes R, Chiocchetti AG, Freitag CM, Satterstrom FK, De Rubeis S, Buxbaum J, Gelb BD, Branko A, Kushima I, Howe J, Scherer SW, Arado A, Baldo C, Patat O, Bénédicte D, Lopergolo D, Santorelli FM, Haack TB, Dufke A, Bertrand M, Falb RJ, Rieß A, Krieg P, Spranger S, Bedeschi MF, Iascone M, Josephi-Taylor S, Roscioli T, Buckley MF, Liebelt J, Dagli AI, Aten E, Hurst ACE, Hicks A, Suri M, Aliu E, Naik S, Sidlow R, Coursimault J, Nicolas G, Küpper H, Petit F, Ibrahim V, Top D, Di Cara F, Louie RJ, Stolerman E, Brunner HG, Vissers LELM, Kramer JM, Kleefstra T. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder. Am J Hum Genet 2023; 110:963-978. [PMID: 37196654 PMCID: PMC10257005 DOI: 10.1016/j.ajhg.2023.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.
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Affiliation(s)
- Dmitrijs Rots
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Taryn E Jakub
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Crystal Keung
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Adam Jackson
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Rolph Pfundt
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | | | | | - Saskia M J Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irene Valenzuela
- Hospital Universitari Vall D'Hebron, Clinical and Molecular Genetics Unit, Barcelona, Catalonia, Spain
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francois Lecoquierre
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Alice Goldenberg
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Jens Michael Hertz
- Odense University Hospital, Department of Clinical Genetics, Odense, Denmark; University of Southern Denmark, Department of Clinical Research, Odense, Denmark
| | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | | | | | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Karl De Dios
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Tess Levy
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Division of Pediatric Neurology, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Munich, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Paul J Benke
- Division of Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | | | - Renee Perrier
- Department of Medical Genetics, Alberta Children's Hospital and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Pedro M Almeida
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria José Simões
- CBR Genomics, Cantanhede, Portugal; Genoinseq, Next-Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Wallid Deb
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Andrew A Schmanski
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Christel Thauvin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jeroen J Smits
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Stefano G Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Francesca Peluso
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Laura Davis-Keppen
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Dylan Platt
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Erin Royer
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Lisette Leeuwen
- University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Margje Sinnema
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Alexander P A Stegmann
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Constance T R M Stumpel
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - George E Tiller
- Kaiser Permanente, Department of Genetics, Los Angeles, CA, USA
| | | | | | - Shelagh Joss
- West of Scotland Regional Genetics Service, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, International Centre for Life, Newcastle Upon Tyne NE1 3BZ, UK
| | - Simon Holden
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matina Prapa
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kaija Puura
- Department of Child Psychiatry, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia De Rubeis
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph Buxbaum
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksic Branko
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Jennifer Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Alessia Arado
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Olivier Patat
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Demeer Bénédicte
- Service de Génétique Clinique, Centre de référence maladies rares, CHU d'Amiens-site Sud, Amiens, France
| | - Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 2, 53100 Siena, Italy; IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Filippo M Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Peter Krieg
- Department of Pediatrics, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | | | - Maria Iascone
- Laboratory of Medical Genetics, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW 2031, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2031, Australia
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Aditi I Dagli
- Orlando Health Arnold Palmer Hospital for Children, Division of Genetics, Orlando, FL, USA
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alesha Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ermal Aliu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sunil Naik
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Richard Sidlow
- Valley Children's Hospital, Valley Children's Place, Madera, CA 93636, USA
| | - Juliette Coursimault
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Gaël Nicolas
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Hanna Küpper
- Neuropediatric Department, University Hospital Tübingen, Tübingen, Germany
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | - Veyan Ibrahim
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Deniz Top
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | | | | | - Han G Brunner
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | | | - Jamie M Kramer
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada.
| | - Tjitske Kleefstra
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Center for Neuropsychiatry, Vincent van Gogh, Venray, the Netherlands; Department of Clinical Genetics, ErasmusMC, Rotterdam, the Netherlands.
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Xu H, Lin S, Zhou Z, Li D, Zhang X, Yu M, Zhao R, Wang Y, Qian J, Li X, Li B, Wei C, Chen K, Yoshimura T, Wang JM, Huang J. New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine. Cell Mol Immunol 2023:10.1038/s41423-023-01032-x. [PMID: 37198402 DOI: 10.1038/s41423-023-01032-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Over the past thirty years, the importance of chemokines and their seven-transmembrane G protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine interactions with receptors trigger signaling pathway activity to form a network fundamental to diverse immune processes, including host homeostasis and responses to disease. Genetic and nongenetic regulation of both the expression and structure of chemokines and receptors conveys chemokine functional heterogeneity. Imbalances and defects in the system contribute to the pathogenesis of a variety of diseases, including cancer, immune and inflammatory diseases, and metabolic and neurological disorders, which render the system a focus of studies aiming to discover therapies and important biomarkers. The integrated view of chemokine biology underpinning divergence and plasticity has provided insights into immune dysfunction in disease states, including, among others, coronavirus disease 2019 (COVID-19). In this review, by reporting the latest advances in chemokine biology and results from analyses of a plethora of sequencing-based datasets, we outline recent advances in the understanding of the genetic variations and nongenetic heterogeneity of chemokines and receptors and provide an updated view of their contribution to the pathophysiological network, focusing on chemokine-mediated inflammation and cancer. Clarification of the molecular basis of dynamic chemokine-receptor interactions will help advance the understanding of chemokine biology to achieve precision medicine application in the clinic.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China
| | - Ziyun Zhou
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Duoduo Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xiting Zhang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Muhan Yu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Ruoyi Zhao
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Yiheng Wang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Junru Qian
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xinyi Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Bohan Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Chuhan Wei
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China.
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China.
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
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Hu S, Song A, Peng L, Tang N, Qiao Z, Wang Z, Lan F, Chen FX. H3K4me2/3 modulate the stability of RNA polymerase II pausing. Cell Res 2023; 33:403-406. [PMID: 36922644 PMCID: PMC10156655 DOI: 10.1038/s41422-023-00794-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Affiliation(s)
- Shibin Hu
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Aixia Song
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Linna Peng
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Nan Tang
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhibin Qiao
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhenning Wang
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Fei Lan
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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50
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Morse K, Swerdlow S, Ünal E. Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538572. [PMID: 37162931 PMCID: PMC10168381 DOI: 10.1101/2023.04.27.538572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well understood. Using an unbiased genetic approach followed by integrated genomic analysis, we uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes. To our knowledge, this study is the first to observe Swi/Snf's direct involvement in gene repression via a cis transcriptional interference mechanism.
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Affiliation(s)
- Kaitlin Morse
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Sarah Swerdlow
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
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