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Chen K, Nan J, Xiong X. Genetic regulation of m 6A RNA methylation and its contribution in human complex diseases. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1591-1600. [PMID: 38764000 DOI: 10.1007/s11427-024-2609-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
N6-methyladenosine (m6A) has been established as the most prevalent chemical modification in message RNA (mRNA), playing an essential role in determining the fate of RNA molecules. Dysregulation of m6A has been revealed to lead to abnormal physiological conditions and cause various types of human diseases. Recent studies have delineated the genetic regulatory maps for m6A methylation by mapping the quantitative trait loci of m6A (m6A-QTLs), thereby building up the regulatory circuits linking genetic variants, m6A, and human complex traits. Here, we review the recent discoveries concerning the genetic regulatory maps of m6A, describing the methodological and technical details of m6A-QTL identification, and introducing the key findings of the cis- and trans-acting drivers of m6A. We further delve into the tissue- and ethnicity-specificity of m6A-QTL, the association with other molecular phenotypes in light of genetic regulation, the regulators underlying m6A genetics, and importantly, the functional roles of m6A in mediating human complex diseases. Lastly, we discuss potential research avenues that can accelerate the translation of m6A genetics studies toward the development of therapies for human genetic diseases.
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Affiliation(s)
- Kexuan Chen
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Jiuhong Nan
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China.
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China.
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Wang L, Gao P, Li C, Liu Q, Yao Z, Li Y, Zhang X, Sun J, Simintiras C, Welborn M, McMillin K, Oprescu S, Kuang S, Fu X. A single-cell atlas of bovine skeletal muscle reveals mechanisms regulating intramuscular adipogenesis and fibrogenesis. J Cachexia Sarcopenia Muscle 2023; 14:2152-2167. [PMID: 37439037 PMCID: PMC10570087 DOI: 10.1002/jcsm.13292] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/23/2023] [Accepted: 05/22/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis. METHODS Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate heterogeneities and differentiation processes of individual cell types and differences between cattle breeds. Experiments were conducted to validate the function and specificity of identified key regulatory and marker genes. Integrated analysis with multiple published human and non-human primate datasets was performed to identify common mechanisms. RESULTS A total of 32 708 cells and 21 clusters were identified, including fibro/adipogenic progenitor (FAP) and other resident and infiltrating cell types. We identified an endomysial adipogenic FAP subpopulation enriched for COL4A1 and CFD (log2FC = 3.19 and 1.92, respectively; P < 0.0001) and a perimysial fibrogenic FAP subpopulation enriched for COL1A1 and POSTN (log2FC = 1.83 and 0.87, respectively; P < 0.0001), both of which were likely derived from an unspecified subpopulation. Further analysis revealed more progressed adipogenic programming of Wagyu FAPs and more advanced fibrogenic programming of Brahman FAPs. Mechanistically, NAB2 drives CFD expression, which in turn promotes adipogenesis. CFD expression in FAPs of young cattle before the onset of intramuscular adipogenesis was predictive of IMF contents in adulthood (R2 = 0.885, P < 0.01). Similar adipogenic and fibrogenic FAPs were identified in humans and monkeys. In aged humans with metabolic syndrome and progressed Duchenne muscular dystrophy (DMD) patients, increased CFD expression was observed (P < 0.05 and P < 0.0001, respectively), which was positively correlated with adipogenic marker expression, including ADIPOQ (R2 = 0.303, P < 0.01; and R2 = 0.348, P < 0.01, respectively). The specificity of Postn/POSTN as a fibrogenic FAP marker was validated using a lineage-tracing mouse line. POSTN expression was elevated in Brahman FAPs (P < 0.0001) and DMD patients (P < 0.01) but not in aged humans. Strong interactions between vascular cells and FAPs were also identified. CONCLUSIONS Our study demonstrates the feasibility of beef cattle as a model for studying IMF and IMC. We illustrate the FAP programming during intramuscular adipogenesis and fibrogenesis and reveal the reliability of CFD as a predictor and biomarker of IMF accumulation in cattle and humans.
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Affiliation(s)
- Leshan Wang
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Peidong Gao
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Chaoyang Li
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Qianglin Liu
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Zeyang Yao
- Department of Computer ScienceOld Dominion UniversityNorfolkVAUSA
| | - Yuxia Li
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Xujia Zhang
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Jiangwen Sun
- Department of Computer ScienceOld Dominion UniversityNorfolkVAUSA
| | | | - Matthew Welborn
- School of Veterinary MedicineLouisiana State UniversityBaton RougeLAUSA
| | - Kenneth McMillin
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
| | | | - Shihuan Kuang
- Department of Animal SciencesPurdue UniversityWest LafayetteINUSA
| | - Xing Fu
- School of Animal ScienceLouisiana State University Agricultural CenterBaton RougeLAUSA
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Wu X, Dong W, Kong M, Ren H, Wang J, Shang L, Zhu Z, Zhu W, Shi X. Down-Regulation of CXXC5 De-Represses MYCL1 to Promote Hepatic Stellate Cell Activation. Front Cell Dev Biol 2021; 9:680344. [PMID: 34621736 PMCID: PMC8490686 DOI: 10.3389/fcell.2021.680344] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022] Open
Abstract
Liver fibrosis is mediated by myofibroblasts, a specialized cell type involved in wound healing and extracellular matrix production. Hepatic stellate cells (HSC) are the major source of myofibroblasts in the fibrotic livers. In the present study we investigated the involvement of CXXC-type zinc-finger protein 5 (CXXC5) in HSC activation and the underlying mechanism. Down-regulation of CXXC5 was observed in activated HSCs compared to quiescent HSCs both in vivo and in vitro. In accordance, over-expression of CXXC5 suppressed HSC activation. RNA-seq analysis revealed that CXXC5 influenced multiple signaling pathways to regulate HSC activation. The proto-oncogene MYCL1 was identified as a novel target for CXXC5. CXXC5 bound to the proximal MYCL1 promoter to repress MYCL1 transcription in quiescent HSCs. Loss of CXXC5 expression during HSC activation led to the removal of CpG methylation and acquisition of acetylated histone H3K9/H3K27 on the MYCL1 promoter resulting in MYCL1 trans-activation. Finally, MYCL1 knockdown attenuated HSC activation whereas MYCL1 over-expression partially relieved the blockade of HSC activation by CXXC5. In conclusion, our data unveil a novel transcriptional mechanism contributing to HSC activation and liver fibrosis.
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Affiliation(s)
- Xiaoyan Wu
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China.,Hepatobiliary Institute of Nanjing University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China.,Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, and Center for Experimental Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Wenhui Dong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, and Center for Experimental Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Ming Kong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, and Center for Experimental Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Haozhen Ren
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China.,Hepatobiliary Institute of Nanjing University, Nanjing, China
| | - Jinglin Wang
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China.,Hepatobiliary Institute of Nanjing University, Nanjing, China
| | - Longcheng Shang
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhengyi Zhu
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Wei Zhu
- Department of Anesthesiology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaolei Shi
- Department of Hepatobiliary Surgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China.,Hepatobiliary Institute of Nanjing University, Nanjing, China
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Genetic drivers of m 6A methylation in human brain, lung, heart and muscle. Nat Genet 2021; 53:1156-1165. [PMID: 34211177 DOI: 10.1038/s41588-021-00890-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 05/18/2021] [Indexed: 01/22/2023]
Abstract
The most prevalent post-transcriptional mRNA modification, N6-methyladenosine (m6A), plays diverse RNA-regulatory roles, but its genetic control in human tissues remains uncharted. Here we report 129 transcriptome-wide m6A profiles, covering 91 individuals and 4 tissues (brain, lung, muscle and heart) from GTEx/eGTEx. We integrate these with interindividual genetic and expression variation, revealing 8,843 tissue-specific and 469 tissue-shared m6A quantitative trait loci (QTLs), which are modestly enriched in, but mostly orthogonal to, expression QTLs. We integrate m6A QTLs with disease genetics, identifying 184 GWAS-colocalized m6A QTL, including brain m6A QTLs underlying neuroticism, depression, schizophrenia and anxiety; lung m6A QTLs underlying expiratory flow and asthma; and muscle/heart m6A QTLs underlying coronary artery disease. Last, we predict novel m6A regulators that show preferential binding in m6A QTLs, protein interactions with known m6A regulators and expression correlation with the m6A levels of their targets. Our results provide important insights and resources for understanding both cis and trans regulation of epitranscriptomic modifications, their interindividual variation and their roles in human disease.
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Astori A, Matherat G, Munoz I, Gautier EF, Surdez D, Zermati Y, Verdier F, Zaidi S, Feuillet V, Kadi A, Lauret E, Delattre O, Lefèvre C, Fontenay M, Ségal-Bendirdjian E, Dusanter-Fourt I, Bouscary D, Hermine O, Mayeux P, Pendino F. The epigenetic regulator RINF (CXXC5) maintains <i>SMAD7</i> expression in human immature erythroid cells and sustains red blood cells expansion. Haematologica 2020; 107:268-283. [PMID: 33241676 PMCID: PMC8719099 DOI: 10.3324/haematol.2020.263558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 11/16/2022] Open
Abstract
The gene CXXC5, encoding a retinoid-inducible nuclear factor (RINF), is located within a region at 5q31.2 commonly deleted in myelodysplastic syndrome and adult acute myeloid leukemia. RINF may act as an epigenetic regulator and has been proposed as a tumor suppressor in hematopoietic malignancies. However, functional studies in normal hematopoiesis are lacking, and its mechanism of action is unknown. Here, we evaluated the consequences of RINF silencing on cytokine-induced erythroid differentiation of human primary CD34+ progenitors. We found that RINF is expressed in immature erythroid cells and that RINF-knockdown accelerated erythropoietin-driven maturation, leading to a significant reduction (~45%) in the number of red blood cells, without affecting cell viability. The phenotype induced by RINF-silencing was dependent on tumor growth factor b (TGFb) and mediated by SMAD7, a TGFb-signaling inhibitor. RINF upregulates SMAD7 expression by direct binding to its promoter and we found a close correlation between RINF and SMAD7 mRNA levels both in CD34+ cells isolated from bone marrow of healthy donors and myelodysplastic syndrome patients with del(5q). Importantly, RINF knockdown attenuated SMAD7 expression in primary cells and ectopic SMAD7 expression was sufficient to prevent the RINF knockdown-dependent erythroid phenotype. Finally, RINF silencing affects 5’-hydroxymethylation of human erythroblasts, in agreement with its recently described role as a TET2-anchoring platform in mouse. Collectively, our data bring insight into how the epigenetic factor RINF, as a transcriptional regulator of SMAD7, may fine-tune cell sensitivity to TGFb superfamily cytokines and thus play an important role in both normal and pathological erythropoiesis.
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Affiliation(s)
- Audrey Astori
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Gabriel Matherat
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Isabelle Munoz
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Emilie-Fleur Gautier
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Didier Surdez
- Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris
| | - Yaël Zermati
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris
| | - Frédérique Verdier
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris
| | - Sakina Zaidi
- Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris
| | - Vincent Feuillet
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris
| | - Amir Kadi
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris
| | - Evelyne Lauret
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Olivier Delattre
- Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris
| | - Carine Lefèvre
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Service d'Hématologie Biologique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris, Paris
| | | | - Isabelle Dusanter-Fourt
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Didier Bouscary
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Olivier Hermine
- Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; Université de Paris, Institut Imagine, INSERM, CNRS, F-75015, Paris
| | - Patrick Mayeux
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Frédéric Pendino
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris.
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