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Zhang J, Hu G, Lu Y, Ren H, Huang Y, Wen Y, Ji B, Wang D, Wang H, Liu H, Ma N, Zhang L, Pan G, Qu Y, Wang H, Zhang W, Miao Z, Yao H. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment. Nat Commun 2024; 15:5524. [PMID: 38951485 PMCID: PMC11217373 DOI: 10.1038/s41467-024-49684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gongcheng Hu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yuli Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huawei Ren
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yin Huang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yulin Wen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Binrui Ji
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Diyang Wang
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Huisheng Liu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Ning Ma
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Guangjin Pan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Qu
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Hua Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Wei Zhang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Zhichao Miao
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Furst LM, Roussel EM, Leung RF, George AM, Best SA, Whittle JR, Firestein R, Faux MC, Eisenstat DD. The Landscape of Pediatric High-Grade Gliomas: The Virtues and Pitfalls of Pre-Clinical Models. BIOLOGY 2024; 13:424. [PMID: 38927304 PMCID: PMC11200883 DOI: 10.3390/biology13060424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Pediatric high-grade gliomas (pHGG) are malignant and usually fatal central nervous system (CNS) WHO Grade 4 tumors. The majority of pHGG consist of diffuse midline gliomas (DMG), H3.3 or H3.1 K27 altered, or diffuse hemispheric gliomas (DHG) (H3.3 G34-mutant). Due to diffuse tumor infiltration of eloquent brain areas, especially for DMG, surgery has often been limited and chemotherapy has not been effective, leaving fractionated radiation to the involved field as the current standard of care. pHGG has only been classified as molecularly distinct from adult HGG since 2012 through Next-Generation sequencing approaches, which have shown pHGG to be epigenetically regulated and specific tumor sub-types to be representative of dysregulated differentiating cells. To translate discovery research into novel therapies, improved pre-clinical models that more adequately represent the tumor biology of pHGG are required. This review will summarize the molecular characteristics of different pHGG sub-types, with a specific focus on histone K27M mutations and the dysregulated gene expression profiles arising from these mutations. Current and emerging pre-clinical models for pHGG will be discussed, including commonly used patient-derived cell lines and in vivo modeling techniques, encompassing patient-derived xenograft murine models and genetically engineered mouse models (GEMMs). Lastly, emerging techniques to model CNS tumors within a human brain environment using brain organoids through co-culture will be explored. As models that more reliably represent pHGG continue to be developed, targetable biological and genetic vulnerabilities in the disease will be more rapidly identified, leading to better treatments and improved clinical outcomes.
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Affiliation(s)
- Liam M. Furst
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Enola M. Roussel
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ryan F. Leung
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Ankita M. George
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Sarah A. Best
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3010, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - James R. Whittle
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3010, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ron Firestein
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia;
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Maree C. Faux
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Surgery, University of Melbourne, Parkville, VIC 3010, Australia
| | - David D. Eisenstat
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Children’s Cancer Centre, The Royal Children’s Hospital Melbourne, 50 Flemington Road, Parkville, VIC 3052, Australia
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3
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Hu G, Zheng Y, Zhang B, Zhao C, Xu L, Wei J, Jing J, Liu Y, Zeng T, Zhou Y. Histone methyltransferase SETD2 is required for proper hippocampal lamination and neuronal maturation. Mol Biol Cell 2024; 35:ar54. [PMID: 38446615 PMCID: PMC11064668 DOI: 10.1091/mbc.e23-12-0492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Proper formation of the hippocampus is crucial for the brain to execute memory and learning functions. However, many questions remain regarding how pyramidal neurons (PNs) of the hippocampus mature and precisely position. Here we revealed that Setd2, the methyltransferase for histone 3 lysine 36 trimethylation (H3K36me3), is essential for the precise localization and maturation of PNs in the hippocampal CA1. The ablation of Setd2 in neural progenitors leads to irregular lamination of the CA1 and increased numbers of PNs in the stratum oriens. Setd2 deletion in postmitotic neurons causes mislocalization and immaturity of CA1 PNs. Transcriptome analyses revealed that SETD2 maintains the expressions of clustered protocadherin (cPcdh) genes. Together, Setd2 is required for proper hippocampal lamination and maturation of CA1 PNs.
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Affiliation(s)
- Guangda Hu
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yue Zheng
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Bo Zhang
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chen Zhao
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Lichao Xu
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jiayi Wei
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jing Jing
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Ying Liu
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tao Zeng
- Department of Neurosurgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine; Shanghai 200072, China
| | - Yan Zhou
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
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4
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Mitchell B, Mu E, Currey L, Whitehead D, Walters S, Thor S, Kasherman M, Piper M. A protocol for high-resolution episcopic microscopy and 3D volumetric analyses of the adult mouse brain. Neurosci Lett 2024; 824:137675. [PMID: 38355003 DOI: 10.1016/j.neulet.2024.137675] [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: 09/15/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
The rapid evolution of different imaging modalities in the last two decades has enabled the investigation of the role of different genes in development and disease to be studied in a range of model organisms. However, selection of the appropriate imaging technique depends on a number of constraints, including cost, time, image resolution, size of the sample, computational complexity and processing power. Here, we use the adult mouse central nervous system to investigate whether High-Resolution Episcopic Microscopy (HREM) can provide an effective means to study the volume of individual subregions within the brain. We find that HREM can provide precise volume quantification of different structures within the mouse brain, albeit with limitations regarding the time involved for analysis and the necessity of some estimations.
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Affiliation(s)
- Benjamin Mitchell
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Mu
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Laura Currey
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Darryl Whitehead
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shaun Walters
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefan Thor
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maria Kasherman
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia; Katharina Gaus Light Microscopy Facility, Division of Research, Lowy Cancer Research Center C25, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Michael Piper
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia.
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5
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Zheng Y, Zhao C, Song Q, Xu L, Zhang B, Hu G, Kong X, Li S, Li X, Shen Y, Zhuang L, Wu M, Liu Y, Zhou Y. Histone methylation mediated by NSD1 is required for the establishment and maintenance of neuronal identities. Cell Rep 2023; 42:113496. [PMID: 37995181 DOI: 10.1016/j.celrep.2023.113496] [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: 06/07/2023] [Revised: 09/28/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Appropriate histone modifications emerge as essential cell fate regulators of neuronal identities across neocortical areas and layers. Here we showed that NSD1, the methyltransferase for di-methylated lysine 36 of histone H3 (H3K36me2), controls both area and layer identities of the neocortex. Nsd1-ablated neocortex showed an area shift of all four primary functional regions and aberrant wiring of cortico-thalamic-cortical projections. Nsd1 conditional knockout mice displayed defects in spatial memory, motor learning, and coordination, resembling patients with the Sotos syndrome carrying NSD1 mutations. On Nsd1 loss, superficial-layer pyramidal neurons (PNs) progressively mis-expressed markers for deep-layer PNs, and PNs remained immature both morphologically and electrophysiologically. Loss of Nsd1 in postmitotic PNs causes genome-wide loss of H3K36me2 and re-distribution of DNA methylation, which accounts for diminished expression of neocortical layer specifiers but ectopic expression of non-neural genes. Together, H3K36me2 mediated by NSD1 is required for the establishment and maintenance of region- and layer-specific neocortical identities.
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Affiliation(s)
- Yue Zheng
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Chen Zhao
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Qiulin Song
- Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China; Eye Center, Wuhan University Renmin Hospital, Wuhan 430071, China
| | - Lichao Xu
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Bo Zhang
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Guangda Hu
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Xiangfei Kong
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Shaowen Li
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Xiang Li
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Yin Shen
- Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China; Eye Center, Wuhan University Renmin Hospital, Wuhan 430071, China
| | - Lenan Zhuang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Min Wu
- Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China; College of Life Sciences, Taikang Center for Life and Medical Sciences of Wuhan University, Wuhan 430071, China.
| | - Ying Liu
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China.
| | - Yan Zhou
- Department of Neurosurgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Frontier Science Center of Immunology and Metabolism, Wuhan University, Wuhan 430071, China.
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6
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Rao H, Liu C, Wang A, Ma C, Xu Y, Ye T, Su W, Zhou P, Gao WQ, Li L, Ding X. SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer. Nat Commun 2023; 14:7572. [PMID: 37989747 PMCID: PMC10663509 DOI: 10.1038/s41467-023-43378-w] [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: 02/19/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain-containing 2 (SETD2) has been identified as an important tumor suppressor and an immunosuppressor in ccRCC. However, the role of SETD2 in ccRCC generation in PKD remains largely unexplored. Herein, we perform metabolomics, lipidomics, transcriptomics and proteomics within SETD2 loss induced PKD-ccRCC transition mouse model. Our analyses show that SETD2 loss causes extensive metabolic reprogramming events that eventually results in enhanced sphingomyelin biosynthesis and tumorigenesis. Clinical ccRCC patient specimens further confirm the abnormal metabolic reprogramming and sphingomyelin accumulation. Tumor symptom caused by Setd2 knockout is relieved by myriocin, a selective inhibitor of serine-palmitoyl-transferase and sphingomyelin biosynthesis. Our results reveal that SETD2 deficiency promotes large-scale metabolic reprogramming and sphingomyelin biosynthesis during PKD-ccRCC transition. This study introduces high-quality multi-omics resources and uncovers a regulatory mechanism of SETD2 on lipid metabolism during tumorigenesis.
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Affiliation(s)
- Hanyu Rao
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Changwei Liu
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Aiting Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Chunxiao Ma
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Xu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tianbao Ye
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqiong Su
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Peijun Zhou
- Division of Kidney Transplant, Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Li
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.
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7
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Mitchell B, Thor S, Piper M. Cellular and molecular functions of SETD2 in the central nervous system. J Cell Sci 2023; 136:jcs261406. [PMID: 37921122 DOI: 10.1242/jcs.261406] [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: 11/04/2023] Open
Abstract
The covalent modification of histones is critical for many biological functions in mammals, including gene regulation and chromatin structure. Posttranslational histone modifications are added and removed by specialised 'writer' and 'eraser' enzymes, respectively. One such writer protein implicated in a wide range of cellular processes is SET domain-containing 2 (SETD2), a histone methyltransferase that catalyses the trimethylation of lysine 36 on histone H3 (H3K36me3). Recently, SETD2 has also been found to modify proteins other than histones, including actin and tubulin. The emerging roles of SETD2 in the development and function of the mammalian central nervous system (CNS) are of particular interest as several SETD2 variants have been implicated in neurodevelopmental disorders, such as autism spectrum disorder and the overgrowth disorder Luscan-Lumish syndrome. Here, we summarise the numerous roles of SETD2 in mammalian cellular functions and development, with a focus on the CNS. We also provide an overview of the consequences of SETD2 variants in human disease and discuss future directions for understanding essential cellular functions of SETD2.
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Affiliation(s)
- Benjamin Mitchell
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefan Thor
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Michael Piper
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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8
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Parra A, Rabin R, Pappas J, Pascual P, Cazalla M, Arias P, Gallego-Zazo N, Santana A, Arroyo I, Artigas M, Pachajoa H, Alanay Y, Akgun-Dogan O, Ruaud L, Couque N, Levy J, Porras-Hurtado GL, Santos-Simarro F, Ballesta-Martinez MJ, Guillén-Navarro E, Muñoz-Hernández H, Nevado J, Tenorio-Castano J, Lapunzina P. Clinical Heterogeneity and Different Phenotypes in Patients with SETD2 Variants: 18 New Patients and Review of the Literature. Genes (Basel) 2023; 14:1179. [PMID: 37372360 DOI: 10.3390/genes14061179] [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: 05/11/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
SETD2 belongs to the family of histone methyltransferase proteins and has been associated with three nosologically distinct entities with different clinical and molecular features: Luscan-Lumish syndrome (LLS), intellectual developmental disorder, autosomal dominant 70 (MRD70), and Rabin-Pappas syndrome (RAPAS). LLS [MIM #616831] is an overgrowth disorder with multisystem involvement including intellectual disability, speech delay, autism spectrum disorder (ASD), macrocephaly, tall stature, and motor delay. RAPAS [MIM #6201551] is a recently reported multisystemic disorder characterized by severely impaired global and intellectual development, hypotonia, feeding difficulties with failure to thrive, microcephaly, and dysmorphic facial features. Other neurologic findings may include seizures, hearing loss, ophthalmologic defects, and brain imaging abnormalities. There is variable involvement of other organ systems, including skeletal, genitourinary, cardiac, and potentially endocrine. Three patients who carried the missense variant p.Arg1740Gln in SETD2 were reported with a moderately impaired intellectual disability, speech difficulties, and behavioral abnormalities. More variable findings included hypotonia and dysmorphic features. Due to the differences with the two previous phenotypes, this association was then named intellectual developmental disorder, autosomal dominant 70 [MIM 620157]. These three disorders seem to be allelic and are caused either by loss-of-function, gain-of-function, or missense variants in the SETD2 gene. Here we describe 18 new patients with variants in SETD2, most of them with the LLS phenotype, and reviewed 33 additional patients with variants in SETD2 that have been previously reported in the scientific literature. This article offers an expansion of the number of reported individuals with LLS and highlights the clinical features and the similarities and differences among the three phenotypes associated with SETD2.
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Affiliation(s)
- Alejandro Parra
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, NY 10016, USA
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, NY 10016, USA
- Clinical Genetics, NYU Orthopedic Hospital, New York, NY 10010, USA
| | - Patricia Pascual
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Mario Cazalla
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
| | - Pedro Arias
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Natalia Gallego-Zazo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Alfredo Santana
- Clinical Genetics Unit, Complejo Hospitalario Universitario Insular-Materno Infantil de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
| | - Ignacio Arroyo
- Pediatrics Department, San Pedro de Alcántara Hospital, 10003 Cáceres, Spain
| | - Mercè Artigas
- Genetics Unit, Hospital de Navarra, 31008 Pamplona, Spain
| | - Harry Pachajoa
- Fundación Valle del Lili, Universidad Icesi, 760032 Cali, Colombia
| | - Yasemin Alanay
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Ozlem Akgun-Dogan
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Lyse Ruaud
- Department of Genetics, APHP-Robert Debré University Hospital, 75019 Paris, France
- INSERM UMR1141, Neurodiderot, University of Paris Cité, 75019 Paris, France
| | - Nathalie Couque
- Department of Genetics, APHP-Robert Debré University Hospital, 75019 Paris, France
- Laboratoire de Biologie Médicale Multisites Seqoia-FMG2025, 75014 Paris, France
| | - Jonathan Levy
- Department of Genetics, APHP-Robert Debré University Hospital, 75019 Paris, France
- Laboratoire de Biologie Médicale Multisites Seqoia-FMG2025, 75014 Paris, France
| | | | - Fernando Santos-Simarro
- Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitario Son Espases, Idisba, 07120 Palma de Mallorca, Spain
| | - Maria Juliana Ballesta-Martinez
- Sección de Genética Médica, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB), 30120 Murcia, Spain
| | - Encarna Guillén-Navarro
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB), 30120 Murcia, Spain
| | - Hugo Muñoz-Hernández
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Jair Tenorio-Castano
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, 28046 Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, 28046 Madrid, Spain
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9
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Zhang Z, Yang L, Li Y, Sun D, Chen R, Dou S, Liu T, Zhang S, Zhou Q, Xie L. Interference of sympathetic overactivation restores limbal stem/progenitor cells function and accelerates corneal epithelial wound healing in diabetic mice. Biomed Pharmacother 2023; 161:114523. [PMID: 36931034 DOI: 10.1016/j.biopha.2023.114523] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Diabetic keratopathy (DK), the diabetic complication in the cornea, is characterized by the delayed epithelial regeneration and sensory nerve degeneration. The involvement of limbal stem/progenitor cells (LSPCs) dysfunction has been reported, however the pathogenic mechanisms remain unclear. Here, we confirmed the dysfunction of LSPCs in diabetic mouse and human corneas. The sympathetic nerve in the cornea was adjacent to LSPCs, and the sympathetic overactivation was found in diabetic mice. Surgical and pharmacological ablation of sympathetic nerves rescued the LSPCs function and promoted corneal epithelial regeneration in diabetic mice. In contrast, both topical norepinephrine (NE) application and chemogenetic sympathetic overactivation directly impaired the stemness and proliferation characteristics of LSPCs, as well as the normal epithelial regeneration. Moreover, we identified that β2-adrenoceptor (Adrb2) was the predominant adrenergic receptor expressed in LSPCs by corneal limbal single-cell sequencing and real time PCR (RT-PCR) analysis of sorted LSPCs. The Adrb2 knockout mice exhibited the enhancement of epithelial regeneration and LSPCs function, compared with the wild-type mice. Similarly, topical application of the Adrb2 specific antagonist ICI 118, 551 effectively accelerated diabetic corneal epithelial regeneration with the restored LSPCs function. Mechanistically, sonic hedgehog (Shh) activity mediated the downstream effects of NE-Adrb2 signaling pathway in regulating LSPCs and epithelial regeneration. Taken together, our data revealed the involvement of sympathetic overactivation in the impairment of diabetic LSPCs function and corneal epithelial regeneration through the NE-Adrb2-Shh signaling pathway. The interference of sympathetic overactivation may provide novel treatment strategies for diabetic keratopathy.
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Affiliation(s)
- Zhenzhen Zhang
- Medical College of Qingdao University, Qingdao, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Lingling Yang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Ya Li
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Di Sun
- School of Ophthalmology, Shandong First Medical University, Jinan, China
| | - Rong Chen
- School of Ophthalmology, Shandong First Medical University, Jinan, China
| | - Shengqian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Ting Liu
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Sai Zhang
- School of Ophthalmology, Shandong First Medical University, Jinan, China
| | - Qingjun Zhou
- Medical College of Qingdao University, Qingdao, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China; School of Ophthalmology, Shandong First Medical University, Jinan, China.
| | - Lixin Xie
- Medical College of Qingdao University, Qingdao, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China; School of Ophthalmology, Shandong First Medical University, Jinan, China.
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10
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Wu Y, Liu F, Wan R, Jiao B. A novel SETD2 variant causing global development delay without overgrowth in a Chinese 3-year-old boy. Front Genet 2023; 14:1153284. [PMID: 37025455 PMCID: PMC10072282 DOI: 10.3389/fgene.2023.1153284] [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: 01/29/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Background: Luscan-Lumish syndrome is characterized by macrocephaly, postnatal overgrowth, intellectual disability (ID), developmental delay (DD), which is caused by heterozygous SETD2 (SET domain containing 2) mutations. The incidence of Luscan-Lumish syndrome is unclear. The study was conducted to provide a novel pathogenic SETD2 variant causing atypical Luscan-Lumish syndrome and review all the published SETD2 mutations and corresponding symptoms, comprehensively understanding the phenotypes and genotypes of SETD2 mutations. Methods: Peripheral blood samples of the proband and his parents were collected for next-generation sequencing including whole-exome sequencing (WES), copy number variation (CNV) detection and mitochondrial DNA sequencing. Identified variant was verified by Sanger sequencing. Conservative analysis and structural analysis were performed to investigate the effect of mutation. Public databases such as PubMed, Clinvar and Human Gene Mutation Database (HGMD) were used to collect all cases with SETD2 mutations. Results: A novel pathogenic SETD2 variant (c.5835_c.5836insAGAA, p. A1946Rfs*2) was identified in a Chinese 3-year-old boy, who had speech and motor delay without overgrowth. Conservative analysis and structural analysis showed that the novel pathogenic variant would loss the conserved domains in the C-terminal region and result in loss of function of SETD2 protein. Frameshift mutations and non-sense mutations account for 68.5% of the total 51 SETD2 point mutations, suggesting that Luscan-Lumish syndrome is likely due to loss of function of SETD2. But we failed to find an association between genotype and phenotype of SETD2 mutations. Conclusion: Our findings expand the genotype-phenotype knowledge of SETD2-associated neurological disorder and provide new evidence for further genetic counselling.
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Affiliation(s)
- Yuanyuan Wu
- Department of Reproduction and Genetics, Bethune International Peace Hospital, Shijiazhuang, China
| | - Fang Liu
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, China
| | - Ruihua Wan
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, China
| | - Baoquan Jiao
- Department of Reproduction and Genetics, Bethune International Peace Hospital, Shijiazhuang, China
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11
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Ritchie FD, Lizarraga SB. The role of histone methyltransferases in neurocognitive disorders associated with brain size abnormalities. Front Neurosci 2023; 17:989109. [PMID: 36845425 PMCID: PMC9950662 DOI: 10.3389/fnins.2023.989109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Brain size is controlled by several factors during neuronal development, including neural progenitor proliferation, neuronal arborization, gliogenesis, cell death, and synaptogenesis. Multiple neurodevelopmental disorders have co-morbid brain size abnormalities, such as microcephaly and macrocephaly. Mutations in histone methyltransferases that modify histone H3 on Lysine 36 and Lysine 4 (H3K36 and H3K4) have been identified in neurodevelopmental disorders involving both microcephaly and macrocephaly. H3K36 and H3K4 methylation are both associated with transcriptional activation and are proposed to sterically hinder the repressive activity of the Polycomb Repressor Complex 2 (PRC2). During neuronal development, tri-methylation of H3K27 (H3K27me3) by PRC2 leads to genome wide transcriptional repression of genes that regulate cell fate transitions and neuronal arborization. Here we provide a review of neurodevelopmental processes and disorders associated with H3K36 and H3K4 histone methyltransferases, with emphasis on processes that contribute to brain size abnormalities. Additionally, we discuss how the counteracting activities of H3K36 and H3K4 modifying enzymes vs. PRC2 could contribute to brain size abnormalities which is an underexplored mechanism in relation to brain size control.
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12
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Zhan A, Luo Y, Qin H, Lin W, Tian L. Hypomagnetic Field Exposure Affecting Gut Microbiota, Reactive Oxygen Species Levels, and Colonic Cell Proliferation in Mice. Bioelectromagnetics 2022; 43:462-475. [PMID: 36434792 DOI: 10.1002/bem.22427] [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: 05/19/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
The gut microbiota has been considered one of the key factors in host health, which is influenced by many environmental factors. The geomagnetic field (GMF) represents one of the important environmental conditions for living organisms. Previous studies have shown that the elimination of GMF, the so-called hypomagnetic field (HMF), could affect the physiological functions and resistance to antibiotics of some microorganisms. However, whether long-term HMF exposure could alter the gut microbiota to some extent in mammals remains unclear. Here, we investigated the effects of long-term (8- and 12-week) HMF exposure on the gut microbiota in C57BL/6J mice. Our results clearly showed that 8-week HMF significantly affected the diversity and function of the mouse gut microbiota. Compared with the GMF group, the concentrations of short-chain fatty acids tended to decrease in the HMF group. Immunofluorescence analysis showed that HMF promoted colonic cell proliferation, concomitant with an increased level of reactive oxygen species (ROS). To our knowledge, this is the first in vivo finding that long-term HMF exposure could affect the mouse gut microbiota, ROS levels, and colonic cell proliferation in the colon. Moreover, the changes in gut microbiota can be restored by returning mice to the GMF environment, thus the possible harm to the microbiota caused by HMF exposure can be alleviated. © 2022 Bioelectromagnetics Society.
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Affiliation(s)
- Aisheng Zhan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yukai Luo
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huafeng Qin
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Lanxiang Tian
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
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13
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Wang J, Wang A, Tian K, Hua X, Zhang B, Zheng Y, Kong X, Li W, Xu L, Wang J, Li Z, Liu Y, Zhou Y. A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors. Cell Discov 2022; 8:74. [PMID: 35915089 PMCID: PMC9343459 DOI: 10.1038/s41421-022-00421-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
β-catenin-dependent canonical Wnt signaling plays a plethora of roles in neocortex (Ncx) development, but its function in regulating the abundance of intermediate progenitors (IPs) is elusive. Here we identified neCtnnb1, an evolutionarily conserved cis-regulatory element with typical enhancer features in developing Ncx. neCtnnb1 locates 55 kilobase upstream of and spatially close to the promoter of Ctnnb1, the gene encoding β-catenin. CRISPR/Cas9-mediated activation or interference of the neCtnnb1 locus enhanced or inhibited transcription of Ctnnb1. neCtnnb1 drove transcription predominantly in the subventricular zone of developing Ncx. Knock-out of neCtnnb1 in mice resulted in compromised expression of Ctnnb1 and the Wnt reporter in developing Ncx. Importantly, knock-out of neCtnnb1 lead to reduced production and transit-amplification of IPs, which subsequently generated fewer upper-layer Ncx projection neurons (PNs). In contrast, enhancing the canonical Wnt signaling by stabilizing β-catenin in neCtnnb1-active cells promoted the production of IPs and upper-layer Ncx PNs. ASH2L was identified as the key trans-acting factor that associates with neCtnnb1 and Ctnnb1’s promoter to maintain Ctnnb1’s transcription in both mouse and human Ncx progenitors. These findings advance understanding of transcriptional regulation of Ctnnb1, and provide insights into mechanisms underlying Ncx expansion during development.
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Affiliation(s)
- Junbao Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Andi Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Kuan Tian
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Xiaojiao Hua
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Bo Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Yue Zheng
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Xiangfei Kong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Wei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Lichao Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Juan Wang
- Department of Neurology, Wuhan Central Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Ying Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China.
| | - Yan Zhou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China.
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14
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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15
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Tocco C, Bertacchi M, Studer M. Structural and Functional Aspects of the Neurodevelopmental Gene NR2F1: From Animal Models to Human Pathology. Front Mol Neurosci 2022; 14:767965. [PMID: 34975398 PMCID: PMC8715095 DOI: 10.3389/fnmol.2021.767965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023] Open
Abstract
The assembly and maturation of the mammalian brain result from an intricate cascade of highly coordinated developmental events, such as cell proliferation, migration, and differentiation. Any impairment of this delicate multi-factorial process can lead to complex neurodevelopmental diseases, sharing common pathogenic mechanisms and molecular pathways resulting in multiple clinical signs. A recently described monogenic neurodevelopmental syndrome named Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) is caused by NR2F1 haploinsufficiency. The NR2F1 gene, coding for a transcriptional regulator belonging to the steroid/thyroid hormone receptor superfamily, is known to play key roles in several brain developmental processes, from proliferation and differentiation of neural progenitors to migration and identity acquisition of neocortical neurons. In a clinical context, the disruption of these cellular processes could underlie the pathogenesis of several symptoms affecting BBSOAS patients, such as intellectual disability, visual impairment, epilepsy, and autistic traits. In this review, we will introduce NR2F1 protein structure, molecular functioning, and expression profile in the developing mouse brain. Then, we will focus on Nr2f1 several functions during cortical development, from neocortical area and cell-type specification to maturation of network activity, hippocampal development governing learning behaviors, assembly of the visual system, and finally establishment of cortico-spinal descending tracts regulating motor execution. Whenever possible, we will link experimental findings in animal or cellular models to corresponding features of the human pathology. Finally, we will highlight some of the unresolved questions on the diverse functions played by Nr2f1 during brain development, in order to propose future research directions. All in all, we believe that understanding BBSOAS mechanisms will contribute to further unveiling pathophysiological mechanisms shared by several neurodevelopmental disorders and eventually lead to effective treatments.
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Affiliation(s)
- Chiara Tocco
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
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16
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Wang A, Wang J, Tian K, Huo D, Ye H, Li S, Zhao C, Zhang B, Zheng Y, Xu L, Hua X, Wang K, Wu QF, Wu X, Zeng T, Liu Y, Zhou Y. An epigenetic circuit controls neurogenic programs during neocortex development. Development 2021; 148:273471. [PMID: 35020876 DOI: 10.1242/dev.199772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022]
Abstract
The production and expansion of intermediate progenitors (IPs) are essential for neocortical neurogenesis during development and over evolution. Here, we have characterized an epigenetic circuit that precisely controls neurogenic programs, particularly properties of IPs, during neocortical development. The circuit comprises a long non-coding RNA (LncBAR) and the BAF (SWI/SNF) chromatin-remodeling complex, which transcriptionally maintains the expression of Zbtb20. LncBAR knockout neocortex contains more deep-layer but fewer upper-layer projection neurons. Intriguingly, loss of LncBAR promotes IP production, but paradoxically prolongs the duration of the cell cycle of IPs during mid-later neocortical neurogenesis. Moreover, in LncBAR knockout mice, depletion of the neural progenitor pool at embryonic stage results in fewer adult neural progenitor cells in the subventricular zone of lateral ventricles, leading to a failure in adult neurogenesis to replenish the olfactory bulb. LncBAR binds to BRG1, the core enzymatic component of the BAF chromatin-remodeling complex. LncBAR depletion enhances association of BRG1 with the genomic locus of, and suppresses the expression of, Zbtb20, a transcription factor gene known to regulate both embryonic and adult neurogenesis. ZBTB20 overexpression in LncBAR-knockout neural precursors reverses compromised cell cycle progressions of IPs.
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Affiliation(s)
- Andi Wang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Junbao Wang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Kuan Tian
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Dawei Huo
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China200072
| | - Hanzhe Ye
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Si Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China 300070
| | - Chen Zhao
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Bo Zhang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Yue Zheng
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Lichao Xu
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Xiaojiao Hua
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Kun Wang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China 300070
| | - Tao Zeng
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China200072
| | - Ying Liu
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
| | - Yan Zhou
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, China430071
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Abstract
Neurodevelopmental disorders (NDDs) affect about 1% of the population and can be caused by mutations in genes that affect the epigenetic code. There is limited functional understanding of most of these epigenetic modifiers, and we suggest that associated NDDs are caused, in part, by deficits in epigenetic priming, a prepatterning step that alters the genome in preparation to make cells competent to signaling cues. We provide evidence from high-resolution epigenetic and transcriptomic mapping studies to demonstrate how a failure to adequately prime the genome for neural induction could lead to impairment of terminally differentiated cells. This idea provides a framework for NDD pathogenesis and treatment.
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