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Qiu W, Guo R, Yu H, Chen X, Chen Z, Ding D, Zhong J, Yang Y, Fang F. Single-cell atlas of human gingiva unveils a NETs-related neutrophil subpopulation regulating periodontal immunity. J Adv Res 2025; 72:287-301. [PMID: 39084404 DOI: 10.1016/j.jare.2024.07.028] [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: 04/25/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024] Open
Abstract
INTRODUCTION Exaggerated neutrophil recruitment and activation are the major features of pathological alterations in periodontitis, in which neutrophil extracellular traps (NETs) are considered to be responsible for inflammatory periodontal lesions. Despite the critical role of NETs in the development and progression of periodontitis, their specific functions and mechanisms remain unclear. OBJECTIVES To demonstrate the important functions and specific mechanisms of NETs involved in periodontal immunopathology. METHODS We performed single-cell RNA sequencing on gingival tissues from both healthy individuals and patients diagnosed with periodontitis. High-dimensional weighted gene co-expression network analysis and pseudotime analysis were then applied to characterize the heterogeneity of neutrophils. Animal models of periodontitis were treated with NETs inhibitors to investigate the effects of NETs in severe periodontitis. Additionally, we established a periodontitis prediction model based on NETs-related genes using six types of machine learning methods. Cell-cell communication analysis was used to identify ligand-receptor pairs among the major cell groups within the immune microenvironment. RESULTS We constructed a single-cell atlas of the periodontal microenvironment and obtained nine major cell populations. We further identified a NETs-related subgroup (NrNeu) in neutrophils. An in vivo inhibition experiment confirmed the involvement of NETs in gingival inflammatory infiltration and alveolar bone absorption in severe periodontitis. We further screened three key NETs-related genes (PTGS2, MME and SLC2A3) and verified that they have the potential to predict periodontitis. Moreover, our findings revealed that gingival fibroblasts had the most interactions with NrNeu and that they might facilitate the production of NETs through the MIF-CD74/CXCR4 axis in periodontitis. CONCLUSION This study highlights the pathogenic role of NETs in periodontal immunity and elucidates the specific regulatory relationship by which gingival fibroblasts activate NETs, which provides new insights into the clinical diagnosis and treatment of periodontitis.
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Affiliation(s)
- Wei Qiu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Ruiming Guo
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hongwen Yu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoxin Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zehao Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Dian Ding
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jindou Zhong
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yumeng Yang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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Luglio A, Maggi E, Riviello FN, Conforti A, Sorrentino U, Zuccarello D. Hereditary Neuromuscular Disorders in Reproductive Medicine. Genes (Basel) 2024; 15:1409. [PMID: 39596609 PMCID: PMC11593801 DOI: 10.3390/genes15111409] [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: 09/26/2024] [Revised: 10/25/2024] [Accepted: 10/29/2024] [Indexed: 11/28/2024] Open
Abstract
Neuromuscular disorders (NMDs) encompass a broad range of hereditary and acquired conditions that affect motor units, significantly impacting patients' quality of life and reproductive health. This narrative review aims to explore in detail the reproductive challenges associated with major hereditary NMDs, including Charcot-Marie-Tooth disease (CMT), dystrophinopathies, Myotonic Dystrophy (DM), Facioscapulohumeral Muscular Dystrophy (FSHD), Spinal Muscular Atrophy (SMA), Limb-Girdle Muscular Dystrophy (LGMD), and Amyotrophic Lateral Sclerosis (ALS). Specifically, it discusses the stages of diagnosis and genetic testing, recurrence risk estimation, options for preimplantation genetic testing (PGT) and prenatal diagnosis (PND), the reciprocal influence between pregnancy and disease, potential obstetric complications, and risks to the newborn.
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Affiliation(s)
- Agnese Luglio
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | | | | | - Alessandro Conforti
- Department of Neuroscience, Reproductive Science and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy
| | - Ugo Sorrentino
- Department of Women’s and Children’s Health, University Hospital of Padova, Via Giustiniani 3, 35128 Padova, Italy
| | - Daniela Zuccarello
- Unit of Medical Genetics and Genomics, San Bortolo Hospital, ULSS n.8 “Berica”, 36100 Vicenza, Italy;
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Kokitsu-Nakata NM, Segarra VCD, Tonello C, Brandão MM, Alonso N, Zechi-Ceide RM. Hemiarhinia caused by a missense variation in SMCHD1: A mild phenotype in the clinical spectrum of Bosma arhinia microphthalmia syndrome. Am J Med Genet A 2024; 194:e63640. [PMID: 38808953 DOI: 10.1002/ajmg.a.63640] [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: 11/04/2022] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/30/2024]
Abstract
Bosma arhinia microphthalmia syndrome (BAMS, OMIM #603457) is a rare autosomal dominant disorder caused by heterozygous variation in the SMCHD1 gene on chromosome 18p11. Clinically, it is characterized by microphthalmia, absence or hypoplasia of nose, choanal atresia, anosmia, palatal abnormalities, hypogonadotropic hypogonadism, and cryptorchidism. Here we report a Brazilian patient with a likely pathogenic variation in SMCHD1 gene (c.1418A>T; p.Glu473Val) presenting hemiarhinia associated with short stature and hypogonadotropic hypogonadism. Due to the clinical variability of BAMS, we considered that hemiarhinia, without microphthalmia, in the present case, can be considered a mild form of BAMS and could be considered for screening of SMCHD1 gene variation.
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Affiliation(s)
- Nancy Mizue Kokitsu-Nakata
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
- Craniofacial Team, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
| | - Vinicius Contrucci Dantas Segarra
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
| | - Cristiano Tonello
- Craniofacial Team, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
| | - Michele Madeira Brandão
- Craniofacial Team, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
| | - Nivaldo Alonso
- Craniofacial Team, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
| | - Roseli Maria Zechi-Ceide
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies (HRAC), University of São Paulo (USP), Bauru, Brazil
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Santanasto AJ, Acharya S, Wojczynski MK, Cvejkus RK, Lin S, Brent MR, Anema JA, Wang L, Thyagarajan B, Christensen K, Daw EW, Zmuda JM. Whole Genome Linkage and Association Analyses Identify DLG Associated Protein-1 as a Novel Positional and Biological Candidate Gene for Muscle Strength: The Long Life Family Study. J Gerontol A Biol Sci Med Sci 2024; 79:glae144. [PMID: 38808484 PMCID: PMC11226997 DOI: 10.1093/gerona/glae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Grip strength is a robust indicator of overall health, is moderately heritable, and predicts longevity in older adults. METHODS Using genome-wide linkage analysis, we identified a novel locus on chromosome 18p (mega-basepair region: 3.4-4.0) linked to grip strength in 3 755 individuals from 582 families aged 64 ± 12 years (range 30-110 years; 55% women). There were 26 families that contributed to the linkage peak (cumulative logarithm of the odds [LOD] score = 10.94), with 6 families (119 individuals) accounting for most of the linkage signal (LOD = 6.4). In these 6 families, using whole genome sequencing data, we performed association analyses between the 7 312 single nucleotide (SNVs) and insertion deletion (INDELs) variants in the linkage region and grip strength. Models were adjusted for age, age2, sex, height, field center, and population substructure. RESULTS We found significant associations between genetic variants (8 SNVs and 4 INDELs, p < 5 × 10-5) in the Disks Large-associated Protein 1 (DLGAP1) gene and grip strength. Haplotypes constructed using these variants explained up to 98.1% of the LOD score. Finally, RNAseq data showed that these variants were significantly associated with the expression of nearby Myosin Light Chain 12A (MYL12A), Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1), Erythrocyte Membrane Protein Band 4.1 Like 3 (EPB41L3) genes (p < .0004). CONCLUSIONS The DLGAP1 gene plays an important role in the postsynaptic density of neurons; thus, it is both a novel positional and biological candidate gene for follow-up studies aimed at uncovering genetic determinants of muscle strength.
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Affiliation(s)
- Adam J Santanasto
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sandeep Acharya
- Division of Computational and Data Sciences, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ryan K Cvejkus
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shiow Lin
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Michael R Brent
- Division of Computational and Data Sciences, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jason A Anema
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kaare Christensen
- Epidemiology Unit, Institute of Public Health, The Danish Aging Research Center, University of Southern Denmark, Odense, Denmark
| | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Zmuda
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Xu T, Yue F, He J, Zhang H, Liu R. Prenatal detection of distal 18p deletion by chromosomal microarray analysis: Three case reports and literature review. Medicine (Baltimore) 2024; 103:e39046. [PMID: 39058883 PMCID: PMC11272248 DOI: 10.1097/md.0000000000039046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Chromosome 18p deletion syndrome is caused by total or partial deletion of the short arm of chromosome 18 and associated with cognitive impairment, growth retardation and mild facial dysmorphism. However, most studies on the genotype-phenotype correlations in the 18p region are diagnosed postnatally. Prenatal reports involving 18p deletions are limited. METHODS Three pregnant women opted for invasive prenatal testing due to noninvasive prenatal testing indicating high risk for chromosome 18 abnormalities. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed simultaneously. The pregnancy outcomes for all cases were followed up. Meanwhile, we also made a literature review on prenatal phenotypes of 18p deletions. RESULTS G-banding analysis showed that 2 fetuses presented abnormal karyotypes: 45,XN,der(18)t(18;21)(p11; q11),-21 (case 2) and 46,XN,18p- (case 3). The karyotype of case 1 was normal. Meanwhile, CMA detected 4.37 Mb (case 1), 7.26 Mb (case 2) and 14.97 Mb (case 3) deletions in chromosome 18p region. All 3 pregnancies were terminated finally according to genetic counseling based upon abnormal CMA results. CONCLUSION Prenatal diagnosis of 18p deletion syndrome is full of challenges due to the phenotypic diversity, incomplete penetrance and lack of prenatal phenotypes. Increased nuchal translucency and holoprosencephaly are common prenatal phenotypes of distal 18p deletion. For fetuses carrying 18p deletions with atypical sonographic phenotypes, noninvasive prenatal testing could be adopted as an effective approach.
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Affiliation(s)
- Tangfei Xu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Fagui Yue
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Jing He
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ruizhi Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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Huang Z, Cui W, Ratnayake I, Tawil R, Pfeifer GP. SMCHD1 maintains heterochromatin and genome compartments in human myoblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602392. [PMID: 39026812 PMCID: PMC11257445 DOI: 10.1101/2024.07.07.602392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Mammalian genomes are subdivided into euchromatic A compartments that contain mostly active chromatin, and inactive, heterochromatic B compartments. However, it is unknown how A and B genome compartments are established and maintained. Here we studied SMCHD1, an SMC-like protein in human male myoblasts. SMCHD1 colocalizes with Lamin B1 and the heterochromatin mark H3K9me3. Loss of SMCHD1 leads to extensive heterochromatin depletion at the nuclear lamina and acquisition of active chromatin states along all chromosomes. In absence of SMCHD1, long range intra-chromosomal and inter-chromosomal contacts between B compartments are lost while many new TADs and loops are formed. Inactivation of SMCHD1 promotes numerous B to A compartment transitions accompanied by activation of silenced genes. SMCHD1 functions as an anchor for heterochromatin domains ensuring that these domains are inaccessible to epigenome modification enzymes that typically operate in active chromatin. Therefore, A compartments are formed by default when not prevented by SMCHD1.
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Wang C, Liu Y, Xiong J, Xie K, Wang T, Hu Y, Fu H, Zhang B, Huang X, Bao H, Cai H, Dong B, Li Z. Genome-wide CRISPR screenings identified SMCHD1 as a host-restricting factor for AAV transduction. PLoS Pathog 2024; 20:e1012344. [PMID: 38976714 PMCID: PMC11257396 DOI: 10.1371/journal.ppat.1012344] [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: 01/23/2024] [Revised: 07/18/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
AAV-mediated gene therapy typically requires a high dose of viral transduction, risking acute immune responses and patient safety, part of which is due to limited understanding of the host-viral interactions, especially post-transduction viral genome processing. Here, through a genome-wide CRISPR screen, we identified SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain 1), an epigenetic modifier, as a critical broad-spectrum restricting host factor for post-entry AAV transgene expression. SMCHD1 knock-down by RNAi and CRISPRi or knock-out by CRISPR all resulted in significantly enhanced transgene expression across multiple viral serotypes, as well as for both single-strand and self-complementary AAV genome types. Mechanistically, upon viral transduction, SMCHD1 effectively repressed AAV transcription by the formation of an LRIF1-HP1-containing protein complex and directly binding with the AAV genome to maintain a heterochromatin-like state. SMCHD1-KO or LRIF1-KD could disrupt such a complex and thus result in AAV transcriptional activation. Together, our results highlight the host factor-induced chromatin remodeling as a critical inhibitory mechanism for AAV transduction and may shed light on further improvement in AAV-based gene therapy.
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Affiliation(s)
- Chenlu Wang
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Liu
- National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jingfei Xiong
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Xie
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tianshu Wang
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Hu
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huancheng Fu
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Baiquan Zhang
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaochao Huang
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hui Bao
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyang Cai
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Biao Dong
- National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Sichuan Real and Best Biotech Co., Ltd., Chengdu, China
| | - Zhonghan Li
- Center of Growth Metabolism and Aging, State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
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Yang JL, Gu H, Yuan ZZ, Xie XH, Yang YF, Tan ZP. Identification of a pathogenic SMCHD1 variant in a Chinese patient with bosma arhinia microphthalmia syndrome: a case report. BMC Med Genomics 2024; 17:136. [PMID: 38773541 PMCID: PMC11110391 DOI: 10.1186/s12920-024-01907-6] [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: 10/03/2023] [Accepted: 05/13/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Bosma arhinia microphthalmia syndrome (BAMS; MIM603457) is a rare genetic disorder, predominantly autosomal dominant. It is a multi-system developmental disorder characterized by severe hypoplasia of the nose and eyes, and reproductive system defects. BAMS is extremely rare in the world and no cases have been reported in Chinese population so far. Pathogenic variants in the SMCHD1 gene (MIM614982) cause BAMS, while the underlying molecular mechanisms requires further investigation. CASE PRESENTATION In this study, a Chinese girl who has suffered from congenital absence of nose and microphthalmia was enrolled and subsequently submitted to a comprehensive clinical and genetic evaluation. Whole-exome sequencing (WES) was employed to identify the genetic entity of thisgirl. A heterozygous pathogenic variant, NM_015295, c.1025G > C; p. (Trp342Ser) of SMCHD1 was identified. By performing very detailed physical and genetic examinations, the patient was diagnosed as BAMS. CONCLUSION This report is the first description of a variant in SMCHD1 in a Chinese patient affected with BAMS.Our study not only furnished valuable genetic data for counseling of BAMS, but also confirmed the diagnosis of BAMS, which may help the management and prognosis for this patient.
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Affiliation(s)
- Jun-Lin Yang
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Heng Gu
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zhuang-Zhuang Yuan
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Xiao-Hui Xie
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yi-Feng Yang
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zhi-Ping Tan
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China.
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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Kim T, Martínez-Bonet M, Wang Q, Hackert N, Sparks JA, Baglaenko Y, Koh B, Darbousset R, Laza-Briviesca R, Chen X, Aguiar VRC, Chiu DJ, Westra HJ, Gutierrez-Arcelus M, Weirauch MT, Raychaudhuri S, Rao DA, Nigrovic PA. Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development. Nat Commun 2024; 15:2150. [PMID: 38459032 PMCID: PMC10923805 DOI: 10.1038/s41467-024-46457-8] [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: 01/27/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells and, in rheumatoid arthritis patients, of blood and joint fluid Tph cells as well as circulating plasmablasts. Correspondingly, ICOS ligation and carriage of the rs117701653 risk allele accelerate T cell differentiation into CXCR5-PD-1high Tph cells producing IL-21 and CXCL13. Thus, mechanistic dissection of a functional non-coding variant in human autoimmunity discloses a previously undefined pathway through which ICOS regulates Tph development and abundance.
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Affiliation(s)
- Taehyeung Kim
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marta Martínez-Bonet
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory of Immune-regulation, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Qiang Wang
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicolaj Hackert
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuriy Baglaenko
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Byunghee Koh
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Roxane Darbousset
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Raquel Laza-Briviesca
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Vitor R C Aguiar
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Darren J Chiu
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Harm-Jan Westra
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, The Netherlands
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Divisions of Human Genetics, Biomedical Informatics, and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
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Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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11
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Tian X, Zhou Y, Wang S, Gao M, Xia Y, Li Y, Zhong Y, Xu W, Bai L, Fu B, Zhou Y, Lee HR, Deng H, Lan K, Feng P, Zhang J. Genome-Wide CRISPR-Cas9 Screen Identifies SMCHD1 as a Restriction Factor for Herpesviruses. mBio 2023; 14:e0054923. [PMID: 37010434 PMCID: PMC10128004 DOI: 10.1128/mbio.00549-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 04/04/2023] Open
Abstract
Intrinsic immunity is the frontline of host defense against invading pathogens. To combat viral infection, mammalian hosts deploy cell-intrinsic effectors to block viral replication prior to the onset of innate and adaptive immunity. In this study, SMCHD1 is identified as a pivotal cellular factor that restricts Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation through a genome-wide CRISPR-Cas9 knockout screen. Genome-wide chromatin profiling revealed that SMCHD1 associates with the KSHV genome, most prominently the origin of lytic DNA replication (ORI-Lyt). SMCHD1 mutants defective in DNA binding could not bind ORI-Lyt and failed to restrict KSHV lytic replication. Moreover, SMCHD1 functioned as a pan-herpesvirus restriction factor that potently suppressed a wide range of herpesviruses, including alpha, beta, and gamma subfamilies. SMCHD1 deficiency facilitated the replication of a murine herpesvirus in vivo. These findings uncovered SMCHD1 as a restriction factor against herpesviruses, and this could be harnessed for the development of antiviral therapies to limit viral infection. IMPORTANCE Intrinsic immunity represents the frontline of host defense against invading pathogens. However, our understanding of cell-intrinsic antiviral effectors remains limited. In this study, we identified SMCHD1 as a cell-intrinsic restriction factor that controlled KSHV lytic reactivation. Moreover, SMCHD1 restricted the replication of a wide range of herpesviruses by targeting the origins of viral DNA replication (ORIs), and SMCHD1 deficiency facilitated the replication of a murine herpesvirus in vivo. This study helps us to better understand intrinsic antiviral immunity, which may be harnessed to develop new therapeutics for the treatment of herpesvirus infection and the related diseases.
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Affiliation(s)
- Xuezhang Tian
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yaru Zhou
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Shaowei Wang
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Ming Gao
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yanlin Xia
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Yangyang Li
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Yunhong Zhong
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Wenhao Xu
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Lei Bai
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Bishi Fu
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yu Zhou
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
- Department of Lab Medicine, College of Medicine, Korea University, Seoul, South Korea
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Lan
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Junjie Zhang
- State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
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12
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Esmaeili S, Xian CJ. Phenotypic and cytogenetic features of an Iranian child with tetrasomy 18p syndrome: A case report. World J Med Genet 2023; 11:1-7. [DOI: 10.5496/wjmg.v11.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/16/2023] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Tetrasomy 18p is a rare chromosome abnormality disorder known to have considerable variability in clinical features and gathering data from different cases will help clinicians and researchers learn about its genotype-phenotype relationship and diagnosis.
CASE SUMMARY Herein, we have reviewed the literature on phenotypic features of this disorder and described the phenotypic and cytogenetic features of a girl of early childhood with tetrasomy 18p for the first time from Iran. This patient showed a strong sense of smell (a unique feature not reported previously for this syndrome), had clenched hand, pes planus, forward head posture in walking and hirsutism (dysmorphic features less reported), and showed 10 clinical features that are generally observed in previously reported cases, including developmental delay/intellectual disability, triangular face, smooth philtrum, feeding difficulties, hypotonia, epicanthus, strabismus, history of constipation, growth retardation and foot anomalies. G-banding chromosome analysis from peripheral blood revealed an abnormal female karyotype with a small marker chromosome (47,XX, +mar), and oligo-array comparative genomic hybridization displayed a gain of 14Mb of the 18p arm containing 56 Online Mendelian Inheritance in Man (OMIM) genes in this patient. Overall, this patient seems to have mild phenotypes.
CONCLUSION This Iranian tetrasomy 18p child displays a uniquely strong sense of smell, some less reported dysmorphic features and ten features generally reported.
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Affiliation(s)
- Sara Esmaeili
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5001, SA, Australia
| | - Cory J Xian
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5001, SA, Australia
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13
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Latham KE. Preimplantation embryo gene expression: 56 years of discovery, and counting. Mol Reprod Dev 2023; 90:169-200. [PMID: 36812478 DOI: 10.1002/mrd.23676] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
The biology of preimplantation embryo gene expression began 56 years ago with studies of the effects of protein synthesis inhibition and discovery of changes in embryo metabolism and related enzyme activities. The field accelerated rapidly with the emergence of embryo culture systems and progressively evolving methodologies that have allowed early questions to be re-addressed in new ways and in greater detail, leading to deeper understanding and progressively more targeted studies to discover ever more fine details. The advent of technologies for assisted reproduction, preimplantation genetic testing, stem cell manipulations, artificial gametes, and genetic manipulation, particularly in experimental animal models and livestock species, has further elevated the desire to understand preimplantation development in greater detail. The questions that drove enquiry from the earliest years of the field remain drivers of enquiry today. Our understanding of the crucial roles of oocyte-expressed RNA and proteins in early embryos, temporal patterns of embryonic gene expression, and mechanisms controlling embryonic gene expression has increased exponentially over the past five and a half decades as new analytical methods emerged. This review combines early and recent discoveries on gene regulation and expression in mature oocytes and preimplantation stage embryos to provide a comprehensive understanding of preimplantation embryo biology and to anticipate exciting future advances that will build upon and extend what has been discovered so far.
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Affiliation(s)
- Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA.,Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, Michigan, USA.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
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14
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Benetti N, Gouil Q, Tapia Del Fierro A, Beck T, Breslin K, Keniry A, McGlinn E, Blewitt ME. Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo. Nat Commun 2022; 13:4295. [PMID: 35879318 PMCID: PMC9314430 DOI: 10.1038/s41467-022-32057-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/13/2022] [Indexed: 11/08/2022] Open
Abstract
Parents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.
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Affiliation(s)
- Natalia Benetti
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Quentin Gouil
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andres Tapia Del Fierro
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Tamara Beck
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia
| | - Kelsey Breslin
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia
| | - Andrew Keniry
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.
| | - Marnie E Blewitt
- The Epigenetics and Development Division, WEHI, Parkville, VIC, Australia.
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
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15
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Epigenetic modifier SMCHD1 maintains a normal pool of long-term hematopoietic stem cells. iScience 2022; 25:104684. [PMID: 35856023 PMCID: PMC9287190 DOI: 10.1016/j.isci.2022.104684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/16/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
SMCHD1 (structural maintenance of chromosomes hinge domain containing 1) is a noncanonical SMC protein that mediates long-range repressive chromatin structures. SMCHD1 is required for X chromosome inactivation in female cells and repression of imprinted and clustered autosomal genes, with SMCHD1 mutations linked to human diseases facioscapulohumeral muscular dystrophy (FSHD) and bosma arhinia and micropthalmia syndrome (BAMS). We used a conditional mouse model to investigate SMCHD1 in hematopoiesis. Smchd1-deleted mice maintained steady-state hematopoiesis despite showing an impaired reconstitution capacity in competitive bone marrow transplantations and age-related hematopoietic stem cell (HSC) loss. This phenotype was more pronounced in Smchd1-deleted females, which showed a loss of quiescent HSCs and fewer B cells. Gene expression profiling of Smchd1-deficient HSCs and B cells revealed known and cell-type-specific SMCHD1-sensitive genes and significant disruption to X-linked gene expression in female cells. These data show SMCHD1 is a regulator of HSCs whose effects are more profound in females.
SMCHD1 is not required to maintain steady-state hematopoiesis Smchd1-deletion leads to loss of adult hematopoietic stem cells Smchd1-deleted female mice are more severely affected than males SMCHD1 maintains cellular quiescence in female hematopoietic stem cells
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16
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Xue S, Ly TTN, Vijayakar RS, Chen J, Ng J, Mathuru AS, Magdinier F, Reversade B. HOX epimutations driven by maternal SMCHD1/LRIF1 haploinsufficiency trigger homeotic transformations in genetically wildtype offspring. Nat Commun 2022; 13:3583. [PMID: 35739109 PMCID: PMC9226161 DOI: 10.1038/s41467-022-31185-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
The body plan of animals is laid out by an evolutionary-conserved HOX code which is colinearly transcribed after zygotic genome activation (ZGA). Here we report that SMCHD1, a chromatin-modifying enzyme needed for X-inactivation in mammals, is maternally required for timely HOX expression. Using zebrafish and mouse Smchd1 knockout animals, we demonstrate that Smchd1 haplo-insufficiency brings about precocious and ectopic HOX transcription during oogenesis and embryogenesis. Unexpectedly, wild-type offspring born to heterozygous knockout zebrafish smchd1 mothers exhibited patent vertebrate patterning defects. The loss of maternal Smchd1 was accompanied by HOX epi-mutations driven by aberrant DNA methylation. We further show that this regulation is mediated by Lrif1, a direct interacting partner of Smchd1, whose knockout in zebrafish phenocopies that of Smchd1. Rather than being a short-lived maternal effect, HOX mis-regulation is stably inherited through cell divisions and persists in cultured fibroblasts derived from FSHD2 patients haploinsufficient for SMCHD1. We conclude that maternal SMCHD1/LRIF1 sets up an epigenetic state in the HOX loci that can only be reset in the germline. Such an unusual inter-generational inheritance, whereby a phenotype can be one generation removed from its genotype, casts a new light on how unresolved Mendelian diseases may be interpreted.
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Affiliation(s)
- Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | | | - Jingyi Chen
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Joel Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ajay S Mathuru
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Yale-NUS College, Singapore, Singapore
- Department of Physiology, School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Paediatrics, School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Medical Genetics, KOÇ University, Istanbul, Turkey.
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17
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Zinc finger protein 280C contributes to colorectal tumorigenesis by maintaining epigenetic repression at H3K27me3-marked loci. Proc Natl Acad Sci U S A 2022; 119:e2120633119. [PMID: 35605119 PMCID: PMC9295756 DOI: 10.1073/pnas.2120633119] [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] [Indexed: 11/30/2022] Open
Abstract
This study uncovered the role of ZNF280C, a known DNA damage response protein, as a tumorigenic transcription regulator that contributes to colorectal tumorigenesis and metastasis through maintaining an epigenetic repression program at key cancer gene loci. These findings identified a contributor with potential prognostic value to colorectal pathogenesis and provide mechanistic insight to the essential function of transcription factor in fine-tuning the activity of chromatin regulators for proper transcription control. Dysregulated epigenetic and transcriptional programming due to abnormalities of transcription factors (TFs) contributes to and sustains the oncogenicity of cancer cells. Here, we unveiled the role of zinc finger protein 280C (ZNF280C), a known DNA damage response protein, as a tumorigenic TF in colorectal cancer (CRC), required for colitis-associated carcinogenesis and Apc deficiency–driven intestinal tumorigenesis in mice. Consistently, ZNF280C silencing in human CRC cells inhibited proliferation, clonogenicity, migration, xenograft growth, and liver metastasis. As a C2H2 (Cys2-His2) zinc finger-containing TF, ZNF280C occupied genomic intervals with both transcriptionally active and repressive states and coincided with CCCTC-binding factor (CTCF) and cohesin binding. Notably, ZNF280C was crucial for the repression program of trimethylation of histone H3 at lysine 27 (H3K27me3)-marked genes and the maintenance of both focal and broad H3K27me3 levels. Mechanistically, ZNF280C counteracted CTCF/cohesin activities and condensed the chromatin environment at the cis elements of certain tumor suppressor genes marked by H3K27me3, at least partially through recruiting the epigenetic repressor structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1). In clinical relevance, ZNF280C was highly expressed in primary CRCs and distant metastases, and a higher ZNF280C level independently predicted worse prognosis of CRC patients. Thus, our study uncovered a contributor with good prognostic value to CRC pathogenesis and also elucidated the essence of DNA-binding TFs in orchestrating the epigenetic programming of gene regulation.
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18
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Heher P, Ganassi M, Weidinger A, Engquist EN, Pruller J, Nguyen TH, Tassin A, Declèves AE, Mamchaoui K, Banerji CRS, Grillari J, Kozlov AV, Zammit PS. Interplay between mitochondrial reactive oxygen species, oxidative stress and hypoxic adaptation in facioscapulohumeral muscular dystrophy: Metabolic stress as potential therapeutic target. Redox Biol 2022; 51:102251. [PMID: 35248827 PMCID: PMC8899416 DOI: 10.1016/j.redox.2022.102251] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is characterised by descending skeletal muscle weakness and wasting. FSHD is caused by mis-expression of the transcription factor DUX4, which is linked to oxidative stress, a condition especially detrimental to skeletal muscle with its high metabolic activity and energy demands. Oxidative damage characterises FSHD and recent work suggests metabolic dysfunction and perturbed hypoxia signalling as novel pathomechanisms. However, redox biology of FSHD remains poorly understood, and integrating the complex dynamics of DUX4-induced metabolic changes is lacking. Here we pinpoint the kinetic involvement of altered mitochondrial ROS metabolism and impaired mitochondrial function in aetiology of oxidative stress in FSHD. Transcriptomic analysis in FSHD muscle biopsies reveals strong enrichment for pathways involved in mitochondrial complex I assembly, nitrogen metabolism, oxidative stress response and hypoxia signalling. We found elevated mitochondrial ROS (mitoROS) levels correlate with increases in steady-state mitochondrial membrane potential in FSHD myogenic cells. DUX4 triggers mitochondrial membrane polarisation prior to oxidative stress generation and apoptosis through mitoROS, and affects mitochondrial health through lipid peroxidation. We identify complex I as the primary target for DUX4-induced mitochondrial dysfunction, with strong correlation between complex I-linked respiration and cellular oxygenation/hypoxia signalling activity in environmental hypoxia. Thus, FSHD myogenesis is uniquely susceptible to hypoxia-induced oxidative stress as a consequence of metabolic mis-adaptation. Importantly, mitochondria-targeted antioxidants rescue FSHD pathology more effectively than conventional antioxidants, highlighting the central involvement of disturbed mitochondrial ROS metabolism. This work provides a pathomechanistic model by which DUX4-induced changes in oxidative metabolism impair muscle function in FSHD, amplified when metabolic adaptation to varying O2 tension is required.
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Affiliation(s)
- Philipp Heher
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK.
| | - Massimo Ganassi
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Adelheid Weidinger
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Elise N Engquist
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Johanna Pruller
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Thuy Hang Nguyen
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000, Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000, Mons, Belgium
| | - Anne-Emilie Declèves
- Department of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 7000, Mons, Belgium
| | - Kamel Mamchaoui
- Institut de Myologie, Sorbonne University, INSERM UMRS974, Paris, France
| | - Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Johannes Grillari
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria; Institute for Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andrey V Kozlov
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK.
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19
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SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization. Biochem J 2021; 478:2555-2569. [PMID: 34109974 PMCID: PMC8286825 DOI: 10.1042/bcj20210278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an epigenetic regulator that mediates gene expression silencing at targeted sites across the genome. Our current understanding of SMCHD1's molecular mechanism, and how substitutions within SMCHD1 lead to the diseases, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS), are only emerging. Recent structural studies of its two component domains - the N-terminal ATPase and C-terminal SMC hinge - suggest that dimerization of each domain plays a central role in SMCHD1 function. Here, using biophysical techniques, we demonstrate that the SMCHD1 ATPase undergoes dimerization in a process that is dependent on both the N-terminal UBL (Ubiquitin-like) domain and ATP binding. We show that neither the dimerization event, nor the presence of a C-terminal extension past the transducer domain, affect SMCHD1's in vitro catalytic activity as the rate of ATP turnover remains comparable to the monomeric protein. We further examined the functional importance of the N-terminal UBL domain in cells, revealing that its targeted deletion disrupts the localization of full-length SMCHD1 to chromatin. These findings implicate UBL-mediated SMCHD1 dimerization as a crucial step for chromatin interaction, and thereby for promoting SMCHD1-mediated gene silencing.
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20
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Laberthonnière C, Novoa-del-Toro EM, Chevalier R, Broucqsault N, Rao VV, Trani JP, Nguyen K, Xue S, Reversade B, Robin JD, Baudot A, Magdinier F. AKT Signaling Modifies the Balance between Cell Proliferation and Migration in Neural Crest Cells from Patients Affected with Bosma Arhinia and Microphthalmia Syndrome. Biomedicines 2021; 9:751. [PMID: 34209568 PMCID: PMC8301469 DOI: 10.3390/biomedicines9070751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022] Open
Abstract
Over the recent years, the SMCHD1 (Structural Maintenance of Chromosome flexible Hinge Domain Containing 1) chromatin-associated factor has triggered increasing interest after the identification of variants in three rare and unrelated diseases, type 2 Facio Scapulo Humeral Dystrophy (FSHD2), Bosma Arhinia and Microphthalmia Syndrome (BAMS), and the more recently isolated hypogonadotrophic hypogonadism (IHH) combined pituitary hormone deficiency (CPHD) and septo-optic dysplasia (SOD). However, it remains unclear why certain mutations lead to a specific muscle defect in FSHD while other are associated with severe congenital anomalies. To gain further insights into the specificity of SMCHD1 variants and identify pathways associated with the BAMS phenotype and related neural crest defects, we derived induced pluripotent stem cells from patients carrying a mutation in this gene. We differentiated these cells in neural crest stem cells and analyzed their transcriptome by RNA-Seq. Besides classical differential expression analyses, we analyzed our data using MOGAMUN, an algorithm allowing the extraction of active modules by integrating differential expression data with biological networks. We found that in BAMS neural crest cells, all subnetworks that are associated with differentially expressed genes converge toward a predominant role for AKT signaling in the control of the cell proliferation-migration balance. Our findings provide further insights into the distinct mechanism by which defects in neural crest migration might contribute to the craniofacial anomalies in BAMS.
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Affiliation(s)
- Camille Laberthonnière
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Elva Maria Novoa-del-Toro
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Raphaël Chevalier
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Natacha Broucqsault
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Vanitha Venkoba Rao
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; (V.V.R.); (S.X.)
| | - Jean Philippe Trani
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Karine Nguyen
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
- Département de Génétique Médicale, Hôpital Timone Enfants, 13005 Marseille, France
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; (V.V.R.); (S.X.)
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138632, Singapore;
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138632, Singapore;
- Department of Paediatrics, National University of Singapore, Singapore 138632, Singapore
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul 34010, Turkey
- Academic Medical Center (AMC), Reproductive Biology Laboratory, 1012 Amsterdam-Zuidoost, The Netherlands
| | - Jérôme D. Robin
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Anais Baudot
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
| | - Frédérique Magdinier
- Aix-Marseille Univ-INSERM, MMG, 13005 Marseille, France; (C.L.); (E.M.N.-d.-T.); (R.C.); (N.B.); (J.P.T.); (K.N.); (J.D.R.); (A.B.)
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21
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Relating SMCHD1 structure to its function in epigenetic silencing. Biochem Soc Trans 2021; 48:1751-1763. [PMID: 32779700 PMCID: PMC7458401 DOI: 10.1042/bst20200242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023]
Abstract
The structural maintenance of chromosomes hinge domain containing protein 1 (SMCHD1) is a large multidomain protein involved in epigenetic gene silencing. Variations in the SMCHD1 gene are associated with two debilitating human disorders, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS). Failure of SMCHD1 to silence the D4Z4 macro-repeat array causes FSHD, yet the consequences on gene silencing of SMCHD1 variations associated with BAMS are currently unknown. Despite the interest due to these roles, our understanding of the SMCHD1 protein is in its infancy. Most knowledge of SMCHD1 function is based on its similarity to the structural maintenance of chromosomes (SMC) proteins, such as cohesin and condensin. SMC proteins and SMCHD1 share similar domain organisation and affect chromatin conformation. However, there are important differences between the domain architectures of SMC proteins and SMCHD1, which distinguish SMCHD1 as a non-canonical member of the family. In the last year, the crystal structures of the two key domains crucial to SMCHD1 function, the ATPase and hinge domains, have emerged. These structures reveal new insights into how SMCHD1 may bind and regulate chromatin structure, and address how amino acid variations in SMCHD1 may contribute to BAMS and FSHD. Here, we contrast SMCHD1 with canonical SMC proteins, and relate the ATPase and hinge domain structures to their roles in SMCHD1-mediated epigenetic silencing and disease.
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22
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Huang Z, Yu J, Cui W, Johnson BK, Kim K, Pfeifer GP. The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins. SCIENCE ADVANCES 2021; 7:7/4/eabb9149. [PMID: 33523915 PMCID: PMC7817097 DOI: 10.1126/sciadv.abb9149] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/24/2020] [Indexed: 05/15/2023]
Abstract
5-Methylcytosine (5mC) oxidases, the ten-eleven translocation (TET) proteins, initiate DNA demethylation, but it is unclear how 5mC oxidation is regulated. We show that the protein SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) is found in complexes with TET proteins and negatively regulates TET activities. Removal of SMCHD1 from mouse embryonic stem (ES) cells induces DNA hypomethylation, preferentially at SMCHD1 target sites and accumulation of 5-hydroxymethylcytosine (5hmC), along with promoter demethylation and activation of the Dux double-homeobox gene. In the absence of SMCHD1, ES cells acquire a two-cell (2c) embryo-like state characterized by activation of an early embryonic transcriptome that is substantially imposed by Dux Using Smchd1/Tet1/Tet2/Tet3 quadruple-knockout cells, we show that DNA demethylation, activation of Dux, and other genes upon SMCHD1 loss depend on TET proteins. These data identify SMCHD1 as an antagonist of the 2c-like state of ES cells and of TET-mediated DNA demethylation.
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Affiliation(s)
- Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jiyoung Yu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Asan Medical Center, University of Ulsan, College of Medicine, Songpa, Seoul, South Korea
| | - Wei Cui
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Benjamin K Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kyunggon Kim
- Asan Medical Center, University of Ulsan, College of Medicine, Songpa, Seoul, South Korea
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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23
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Wanigasuriya I, Gouil Q, Kinkel SA, Tapia Del Fierro A, Beck T, Roper EA, Breslin K, Stringer J, Hutt K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME. Smchd1 is a maternal effect gene required for genomic imprinting. eLife 2020; 9:55529. [PMID: 33186096 PMCID: PMC7665889 DOI: 10.7554/elife.55529] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic imprinting establishes parental allele-biased expression of a suite of mammalian genes based on parent-of-origin specific epigenetic marks. These marks are under the control of maternal effect proteins supplied in the oocyte. Here we report epigenetic repressor Smchd1 as a novel maternal effect gene that regulates the imprinted expression of ten genes in mice. We also found zygotic SMCHD1 had a dose-dependent effect on the imprinted expression of seven genes. Together, zygotic and maternal SMCHD1 regulate three classic imprinted clusters and eight other genes, including non-canonical imprinted genes. Interestingly, the loss of maternal SMCHD1 does not alter germline DNA methylation imprints pre-implantation or later in gestation. Instead, what appears to unite most imprinted genes sensitive to SMCHD1 is their reliance on polycomb-mediated methylation as germline or secondary imprints, therefore we propose that SMCHD1 acts downstream of polycomb imprints to mediate its function.
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Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andrés Tapia Del Fierro
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ellise A Roper
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jessica Stringer
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Karla Hutt
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Heather J Lee
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
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24
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Stromiedel H, Van Quekelberghe C, Yigit G, Naimi AA, Bahlmann F, Sader R, Guchlerner M, Lüchtenberg M, Latta K, Cho CH, Wollnik B, Kunzmann S. [A Newborn Suffering from Arhinia: Neonatologic Challenges During Primary Care of the Newborn With Bosma Arhinia Microphthalmia Syndrome (BAMS)]. Z Geburtshilfe Neonatol 2020; 224:377-380. [PMID: 32882744 DOI: 10.1055/a-1224-4465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
ZusammenfassungAnhand eines weiblichen Neugeborenen soll das seltene Krankheitsbild der
konnatalen Nasenagenesie vorgestellt werden. In der Schwangerschaft fielen
eine intrauterine Wachstumsrestriktion mit Polyhydramnion und eine
Mittelgesichtshypoplasie auf. Das Atemwegsmanagement nach primärer
Sectio in der 38+4 SSW gelang mittels Schienung durch einen
Güdel- bzw. im Verlauf Rachentubus ohne Zeichen einer
respiratorischen Insuffizienz. Neben der vollständigen Nasenagenesie
zeigten sich bei unauffälligen zerebralen Strukturen ein
Hypertelorismus, ein gotischer Gaumen, ein beidseitiger Mikrophthalmus und
Iriskolobom. Die Nahrungsaufnahme wurde mit einer orogastralen Sonde
sichergestellt, durch Trinktraining und einen speziellen Schnuller konnten
eine bessere Koordination und Trinkleistung erzielt werden. Der sich bei
assoziierten Fehlbildungen ergebende Verdacht auf ein
Bosma-Arhinie-Mikrophthalmie-Syndrom (BAMS) wurde humangenetisch durch den
Nachweis einer heterozygoten de novo Mutation im SMCHD1-Gen, welches eine
Schlüsselfunktion in der Embryogenese der menschlichen Nase spielt,
bestätigt (c.1043A>G; pHis348Arg). Aus neonatologischer
Sicht ist oftmals die initiale Kreißsaal-Versorgung eine
Herausforderung: Patienten mit Nasenagenesie werden häufig
postpartal intubiert und elektiv tracheotomiert. Bei fehlender
respiratorischer Problematik und Nahrungsaufnahme mit perzentilengerechtem
Wachstum besteht jedoch keine dringliche Indikation zur frühzeitigen
plastisch-chirurgischen Versorgung, insbesondere da diese mit Gefahren wie
Sepsis und Wachstumsstörungen im Mittelgesicht behaftet ist.
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Affiliation(s)
- Helen Stromiedel
- Klinik für Neonatologie und pädiatrische Intensivmedizin, Bürgerhospital Frankfurt, Frankfurt am Main
| | - Chantal Van Quekelberghe
- Klinik für Kinder- und Jugendmedizin, Bürgerhospital und Clementine Kinderhospital gemeinnützige GmbH, Frankfurt am Main
| | - Gökhan Yigit
- Institut für Humangenetik, Georg-August-Universität Göttingen Universitätsmedizin, Göttingen
| | - Ammar Al Naimi
- Klinik für Geburtshilfe, Bürgerhospital Frankfurt, Frankfurt am Main
| | - Franz Bahlmann
- Klinik für Geburtshilfe, Bürgerhospital Frankfurt, Frankfurt am Main
| | - Robert Sader
- Klinik für Mund-, Kiefer-, Plastische Gesichtschirurgie, Universitätsklinikum Frankfurt, Frankfurt am Main
| | - Marina Guchlerner
- Klinik für Kinderaugenheilkunde, Schielbehandlung und plastisch-rekonstruktive Lidchirurgie, Bürgerhospital Frankfurt, Frankfurt am Main
| | - Marc Lüchtenberg
- Klinik für Kinderaugenheilkunde, Schielbehandlung und plastisch-rekonstruktive Lidchirurgie, Bürgerhospital Frankfurt, Frankfurt am Main
| | - Kay Latta
- Klinik für Kinder- und Jugendmedizin, Bürgerhospital und Clementine Kinderhospital gemeinnützige GmbH, Frankfurt am Main
| | - Chie Hee Cho
- Institut für diagnostische Radiologie, Charité Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin
| | - Bernd Wollnik
- Institut für Humangenetik, Georg-August-Universität Göttingen Universitätsmedizin, Göttingen
| | - Steffen Kunzmann
- Klinik für Neonatologie und pädiatrische Intensivmedizin, Bürgerhospital Frankfurt, Frankfurt am Main
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25
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Rojas LA, Valentine E, Accorsi A, Maglio J, Shen N, Robertson A, Kazmirski S, Rahl P, Tawil R, Cadavid D, Thompson LA, Ronco L, Chang AN, Cacace AM, Wallace O. p38 α Regulates Expression of DUX4 in a Model of Facioscapulohumeral Muscular Dystrophy. J Pharmacol Exp Ther 2020; 374:489-498. [PMID: 32576599 DOI: 10.1124/jpet.119.264689] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/26/2020] [Indexed: 03/08/2025] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the loss of repression at the D4Z4 locus leading to aberrant double homeobox 4 (DUX4) expression in skeletal muscle. Activation of this early embryonic transcription factor results in the expression of its target genes causing muscle fiber death. Although progress toward understanding the signals driving DUX4 expression has been made, the factors and pathways involved in the transcriptional activation of this gene remain largely unknown. Here, we describe the identification and characterization of p38α as a novel regulator of DUX4 expression in FSHD myotubes. By using multiple highly characterized, potent, and specific inhibitors of p38α/β, we show a robust reduction of DUX4 expression, activity, and cell death across patient-derived FSHD1 and FSHD2 lines. RNA-seq profiling reveals that a small number of genes are differentially expressed upon p38α/β inhibition, the vast majority of which are DUX4 target genes. Our results reveal a novel and apparently critical role for p38α in the aberrant activation of DUX4 in FSHD and support the potential of p38α/β inhibitors as effective therapeutics to treat FSHD at its root cause. SIGNIFICANCE STATEMENT: Using patient-derived facioscapulohumeral muscular dystrophy (FSHD) myotubes, we characterize the pharmacological relationships between p38α/β inhibition, double homeobox 4 (DUX4) expression, its downstream transcriptional program, and muscle cell death. p38α/β inhibition results in potent and specific DUX4 downregulation across multiple genotypes without significant effects in the process of myogenesis in vitro. These findings highlight the potential of p38α/β inhibitors for the treatment of FSHD, a condition that today has no approved therapies.
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Affiliation(s)
- L Alejandro Rojas
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Erin Valentine
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Anthony Accorsi
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Joseph Maglio
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Ning Shen
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Alan Robertson
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Steven Kazmirski
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Peter Rahl
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Rabi Tawil
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Diego Cadavid
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Lorin A Thompson
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Lucienne Ronco
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Aaron N Chang
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Angela M Cacace
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
| | - Owen Wallace
- Fulcrum Therapeutics, Cambridge, Massachusetts (L.A.R., E.V., A.A., J.M., N.S., A.R., S.K., P.R., D.C., L.A.T., L.R., A.N.C., A.M.C., O.W.) and University of Rochester Medical Center, Department of Neurology, Rochester, New York (R.T.)
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26
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Interferon Alpha Induces Multiple Cellular Proteins That Coordinately Suppress Hepadnaviral Covalently Closed Circular DNA Transcription. J Virol 2020; 94:JVI.00442-20. [PMID: 32581092 DOI: 10.1128/jvi.00442-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022] Open
Abstract
Covalently closed circular DNA (cccDNA) of hepadnaviruses exists as an episomal minichromosome in the nucleus of an infected hepatocyte and serves as the template for the transcription of viral mRNAs. It had been demonstrated by others and us that interferon alpha (IFN-α) treatment of hepatocytes induced a prolonged suppression of human and duck hepatitis B virus cccDNA transcription, which is associated with the reduction of cccDNA-associated histone modifications specifying active transcription (H3K9ac or H3K27ac), but not the histone modifications marking constitutive (H3K9me3) or facultative (H3K27me3) heterochromatin formation. In our efforts to identify IFN-induced cellular proteins that mediate the suppression of cccDNA transcription by the cytokine, we found that downregulating the expression of signal transducer and activator of transcription 1 (STAT1), structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1), or promyelocytic leukemia (PML) protein increased basal level of cccDNA transcription activity and partially attenuated IFN-α suppression of cccDNA transcription. In contrast, ectopic expression of STAT1, SMCHD1, or PML significantly reduced cccDNA transcription activity. SMCHD1 is a noncanonical SMC family protein and implicated in epigenetic silencing of gene expression. PML is a component of nuclear domain 10 (ND10) and is involved in suppressing the replication of many DNA viruses. Mechanistic analyses demonstrated that STAT1, SMCHD1, and PML were recruited to cccDNA minichromosomes and phenocopied the IFN-α-induced posttranslational modifications of cccDNA-associated histones. We thus conclude that STAT1, SMCHD1, and PML may partly mediate the suppressive effect of IFN-α on hepadnaviral cccDNA transcription.IMPORTANCE Pegylated IFN-α is the only therapeutic regimen that can induce a functional cure of chronic hepatitis B in a small, but significant, fraction of treated patients. Understanding the mechanisms underlying the antiviral functions of IFN-α in hepadnaviral infection may reveal molecular targets for development of novel antiviral agents to improve the therapeutic efficacy of IFN-α. By a loss-of-function genetic screening of individual IFN-stimulated genes (ISGs) on hepadnaviral mRNAs transcribed from cccDNA, we found that downregulating the expression of STAT1, SMCHD1, or PML significantly increased the level of viral RNAs without altering the level of cccDNA. Mechanistic analyses indicated that those cellular proteins are recruited to cccDNA minichromosomes and induce the posttranslational modifications of cccDNA-associated histones similar to those induced by IFN-α treatment. We have thus identified three IFN-α-induced cellular proteins that suppress cccDNA transcription and may partly mediate IFN-α silencing of hepadnaviral cccDNA transcription.
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Zhang K, Wu DY, Zheng H, Wang Y, Sun QR, Liu X, Wang LY, Xiong WJ, Wang Q, Rhodes JDP, Xu K, Li L, Lin Z, Yu G, Xia W, Huang B, Du Z, Yao Y, Nasmyth KA, Klose RJ, Miao YL, Xie W. Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA. Mol Cell 2020; 79:234-250.e9. [PMID: 32579944 DOI: 10.1016/j.molcel.2020.06.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022]
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of 3D chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that, during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger topologically associating domains (TADs) at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell-specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.
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Affiliation(s)
- Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Dan-Ya Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Hui Zheng
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Yao Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Qiao-Ran Sun
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Li-Yan Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Wen-Jing Xiong
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | | | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Guang Yu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Bo Huang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Yao Yao
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China.
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28
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Rare variant of the epigenetic regulator SMCHD1 in a patient with pituitary hormone deficiency. Sci Rep 2020; 10:10985. [PMID: 32620854 PMCID: PMC7335161 DOI: 10.1038/s41598-020-67715-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/12/2020] [Indexed: 11/17/2022] Open
Abstract
Isolated hypogonadotropic hypogonadism (IHH), combined pituitary hormone deficiency (CPHD), and septo-optic dysplasia (SOD) constitute a disease spectrum whose etiology remains largely unknown. This study aimed to clarify whether mutations in SMCHD1, an epigenetic regulator gene, might underlie this disease spectrum. SMCHD1 is a causative gene for Bosma arhinia microphthalmia syndrome characterized by arhinia, microphthalmia and IHH. We performed mutation screening of SMCHD1 in patients with etiology-unknown IHH (n = 31) or CPHD (n = 43, 19 of whom also satisfied the SOD diagnostic criteria). Rare variants were subjected to in silico analyses and classified according to the American College of Medical Genetics and Genomics guidelines. Consequently, a rare likely pathogenic variant, p.Asp398Asn, was identified in one patient. The patient with p.Asp398Asn exhibited CPHD, optic nerve hypoplasia, and a thin retinal nerve fiber layer, and therefore satisfied the criteria of SOD. This patient showed a relatively low DNA methylation level of the 52 SMCHD1-target CpG sites at the D4Z4 locus. Exome sequencing for the patient excluded additional variants in other IHH/CPHD-causative genes. In vitro assays suggested functional impairment of the p.Asp398Asn variant. These results provide the first indication that SMCHD1 mutations represent a rare genetic cause of the HH-related disease spectrum.
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29
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Chen K, Birkinshaw RW, Gurzau AD, Wanigasuriya I, Wang R, Iminitoff M, Sandow JJ, Young SN, Hennessy PJ, Willson TA, Heckmann DA, Webb AI, Blewitt ME, Czabotar PE, Murphy JM. Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues. Sci Signal 2020; 13:13/636/eaaz5599. [PMID: 32546545 DOI: 10.1126/scisignal.aaz5599] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) is an epigenetic regulator in which polymorphisms cause the human developmental disorder, Bosma arhinia micropthalmia syndrome, and the degenerative disease, facioscapulohumeral muscular dystrophy. SMCHD1 is considered a noncanonical SMC family member because its hinge domain is C-terminal, because it homodimerizes rather than heterodimerizes, and because SMCHD1 contains a GHKL-type, rather than an ABC-type ATPase domain at its N terminus. The hinge domain has been previously implicated in chromatin association; however, the underlying mechanism involved and the basis for SMCHD1 homodimerization are unclear. Here, we used x-ray crystallography to solve the three-dimensional structure of the Smchd1 hinge domain. Together with structure-guided mutagenesis, we defined structural features of the hinge domain that participated in homodimerization and nucleic acid binding, and we identified a functional hotspot required for chromatin localization in cells. This structure provides a template for interpreting the mechanism by which patient polymorphisms within the SMCHD1 hinge domain could compromise function and lead to facioscapulohumeral muscular dystrophy.
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Affiliation(s)
- Kelan Chen
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alexandra D Gurzau
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ruoyun Wang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Megan Iminitoff
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Patrick J Hennessy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Tracy A Willson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Denise A Heckmann
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia.,School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
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30
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Strafella C, Caputo V, Galota RM, Campoli G, Bax C, Colantoni L, Minozzi G, Orsini C, Politano L, Tasca G, Novelli G, Ricci E, Giardina E, Cascella R. The variability of SMCHD1 gene in FSHD patients: evidence of new mutations. Hum Mol Genet 2020; 28:3912-3920. [PMID: 31600781 PMCID: PMC6969370 DOI: 10.1093/hmg/ddz239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 12/31/2022] Open
Abstract
In this study, we investigated the sequence of (Structural Maintenance of Chromosomes flexible Hinge Domain containing 1) SMCHD1 gene in a cohort of clinically defined FSHD (facioscapulohumeral muscular dystrophy) patients in order to assess the distribution of SMCHD1 variants, considering the D4Z4 fragment size in terms of repeated units (RUs; short fragment: 1–7 RU, borderline: 8-10RU and normal fragment: >11RU). The analysis of SMCHD1 revealed the presence of 82 variants scattered throughout the introns, exons and 3’untranslated region (3′UTR) of the gene. Among them, 64 were classified as benign polymorphisms and 6 as VUS (variants of uncertain significance). Interestingly, seven pathogenic/likely pathogenic variants were identified in patients carrying a borderline or normal D4Z4 fragment size, namely c.182_183dupGT (p.Q62Vfs*48), c.2129dupC (p.A711Cfs*11), c.3469G>T (p.G1157*), c.5150_5151delAA (p.K1717Rfs*16) and c.1131+2_1131+5delTAAG, c.3010A>T (p.K1004*), c.853G>C (p.G285R). All of them were predicted to disrupt the structure and conformation of SMCHD1, resulting in the loss of GHKL-ATPase and SMC hinge essential domains. These results are consistent with the FSHD symptomatology and the Clinical Severity Score (CSS) of patients. In addition, five variants (c.*1376A>C, rs7238459; c.*1579G>A, rs559994; c.*1397A>G, rs150573037; c.*1631C>T, rs193227855; c.*1889G>C, rs149259359) were identified in the 3′UTR region of SMCHD1, suggesting a possible miRNA-dependent regulatory effect on FSHD-related pathways. The present study highlights the clinical utility of next-generation sequencing (NGS) platforms for the molecular diagnosis of FSHD and the importance of integrating molecular findings and clinical data in order to improve the accuracy of genotype–phenotype correlations.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, Rome, 00142, Italy.,Department of Biomedicine and Prevention, Tor Vergata University, Rome, 00133, Italy
| | - Valerio Caputo
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, 00133, Italy
| | | | - Giulia Campoli
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, Rome, 00142, Italy
| | - Cristina Bax
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, Rome, 00142, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, Rome, 00142, Italy
| | - Giulietta Minozzi
- Department of Veterinary Medicine (DIMEVET), University of Milan, Milan, 20100, Italy
| | - Chiara Orsini
- vCardiomyology and Medical Genetics, Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, 80131, Italy
| | - Luisa Politano
- vCardiomyology and Medical Genetics, Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, 80131, Italy
| | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, 00168, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, 00133, Italy.,Neuromed Institute IRCCS, Pozzilli, 86077, Italy
| | - Enzo Ricci
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, 00168, Italy.,Istituto di Neurologia, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, Rome, 00142, Italy.,Department of Biomedicine and Prevention, Tor Vergata University, Rome, 00133, Italy
| | - Raffaella Cascella
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, 00133, Italy.,Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, 1000, Albania
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31
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Jiang S, Williams K, Kong X, Zeng W, Nguyen NV, Ma X, Tawil R, Yokomori K, Mortazavi A. Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PLoS Genet 2020; 16:e1008754. [PMID: 32365093 PMCID: PMC7224571 DOI: 10.1371/journal.pgen.1008754] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/14/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022] Open
Abstract
FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we performed bulk RNA-seq on a 6-day differentiation time-course in primary FSHD2 patient myoblasts. We identify a set of 54 genes upregulated in FSHD2 cells, termed FSHD-induced genes. Using single-cell and single-nucleus RNA-seq on myoblasts and differentiated myotubes, respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes ("FSHD-Lo" and "FSHD Hi", respectively). FSHD-Hi myotube nuclei coexpress multiple DUX4 target genes including DUXA, LEUTX and ZSCAN4, and also upregulate cell cycle-related genes with significant enrichment of E2F target genes and p53 signaling activation. We found more FSHD-Hi nuclei than DUX4-positive nuclei, and confirmed with in situ RNA/protein detection that DUX4 transcribed in only one or two nuclei is sufficient for DUX4 protein to activate target genes across multiple nuclei within the same myotube. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results suggest that the DUXA can take over the role of DUX4 to maintain target gene expression. These results provide a possible explanation as to why it is easier to detect DUX4 target genes than DUX4 itself in patient cells and raise the possibility of a self-sustaining network of gene dysregulation triggered by the limited DUX4 expression.
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Affiliation(s)
- Shan Jiang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Katherine Williams
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Weihua Zeng
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Nam Viet Nguyen
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Xinyi Ma
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
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32
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Salort-Campana E, Fatehi F, Beloribi-Djefaflia S, Roche S, Nguyen K, Bernard R, Cintas P, Solé G, Bouhour F, Ollagnon E, Sacconi S, Echaniz-Laguna A, Kuntzer T, Levy N, Magdinier F, Attarian S. Type 1 FSHD with 6-10 Repeated Units: Factors Underlying Severity in Index Cases and Disease Penetrance in Their Relatives Attention. Int J Mol Sci 2020; 21:E2221. [PMID: 32210100 PMCID: PMC7139460 DOI: 10.3390/ijms21062221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular defects in type 1 facioscapulohumeral muscular dystrophy (FSHD) are caused by a heterozygous contraction of the D4Z4 repeat array from 1 to 10 repeat units (RUs) on 4q35. This study compared (1) the phenotype and severity of FSHD1 between patients carrying 6-8 vs. 9-10 RUs, (2) the amount of methylation in different D4Z4 regions between patients with FSHD1 with different clinical severity scores (CSS). This cross-sectional multicenter study was conducted to measure functional scales and for genetic analysis. Patients were classified into two categories according to RUs: Group 1, 6-8; Group 2, 9-10. Methylation analysis was performed in 27 patients. A total of 99 carriers of a contracted D4Z4 array were examined. No significant correlations between RUs and CSS (r = 0.04, p = 0.73) and any of the clinical outcome scales were observed between the two groups. Hypomethylation was significantly more pronounced in patients with high CSS (>3.5) than those with low CSS (<1.5) (in DR1 and 5P), indicating that the extent of hypomethylation might modulate disease severity. In Group 1, the disease severity is not strongly correlated with the allele size and is mostly correlated with the methylation of D4Z4 regions.
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Affiliation(s)
- Emmanuelle Salort-Campana
- Reference Center of Neuromuscular disorders and ALS, Timone University Hospital, AP-HM, 264 rue Saint-Pierre, Cedex 05 13385 Marseille, France; (E.S.-C.); (F.F.); (S.B.-D.)
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
| | - Farzad Fatehi
- Reference Center of Neuromuscular disorders and ALS, Timone University Hospital, AP-HM, 264 rue Saint-Pierre, Cedex 05 13385 Marseille, France; (E.S.-C.); (F.F.); (S.B.-D.)
| | - Sadia Beloribi-Djefaflia
- Reference Center of Neuromuscular disorders and ALS, Timone University Hospital, AP-HM, 264 rue Saint-Pierre, Cedex 05 13385 Marseille, France; (E.S.-C.); (F.F.); (S.B.-D.)
| | - Stéphane Roche
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
| | - Karine Nguyen
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
| | - Rafaelle Bernard
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
| | - Pascal Cintas
- Service de Neurologie et d’explorations fonctionnelles, Centre Hospitalier Universitaire de Toulouse, 31000 Toulouse, France;
| | - Guilhem Solé
- Reference Center of Neuromuscular Disorders AOC, Bordeaux University Hospitals, 33000 Bordeaux, France;
| | - Françoise Bouhour
- Electroneuromyography and Neuromuscular Department, GHE Neurologic Hospital, Cedex 69677 Lyon-Bron, France;
| | | | - Sabrina Sacconi
- Neuromuscular Disease Specialized Center, Nice University Hospital, 06000 Nice, France;
| | - Andoni Echaniz-Laguna
- Neurology Department, APHP, CHU de Bicêtre, 78 rue du Général Leclerc, Cedex 94276 Le Kremlin-Bicêtre, France;
| | - Thierry Kuntzer
- Nerve-Muscle Unit, Department of Clinical Neurosciences, Lausanne University, Hospital (CHUV), Lausanne 1002, Switzerland;
| | - Nicolas Levy
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
| | - Frédérique Magdinier
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
| | - Shahram Attarian
- Reference Center of Neuromuscular disorders and ALS, Timone University Hospital, AP-HM, 264 rue Saint-Pierre, Cedex 05 13385 Marseille, France; (E.S.-C.); (F.F.); (S.B.-D.)
- Medical Genetics, Aix Marseille Université—Inserm UMR_1251, 13005 Marseille, France; (S.R.); (K.N.); (R.B.); (N.L.); (F.M.)
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Fuller AK, McCrary HC, Graham ME, Skirko JR. The Case of the Missing Nose: Congenital Arhinia Case Presentation and Management Recommendations. Ann Otol Rhinol Laryngol 2020; 129:645-648. [PMID: 32100546 DOI: 10.1177/0003489420909415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To discuss the presentation and management of infants with arhinia or congenital absence of the nose. METHODS This case report describes an infant with arhinia that was diagnosed prenatally. In addition to a discussion of the case, a review of the literature was completed to define appropriate postnatal work-up and management. RESULTS The patient is a term male infant, diagnosed with arhinia on ultrasound and magnetic resonance imaging (MRI) performed at 21-weeks gestational age. Upon birth, the patient was subsequently intubated, followed by tracheostomy due to complete nasal obstruction. Through a genetics evaluation, the patient was found to be heterozygous for the SMCHD1 gene, with hypomethylation at the D4Z4 locus. Plans for reconstruction will be based on future imaging and the development of any nasal patency, however, the patient's family plans to utilize a prosthetic nose until the patient is older. CONCLUSION Arhinia is a rare condition causing respiratory distress in the neonatal period. While stabilization of the airway is the first priority, further management is not clearly defined given the rarity of the malformation. This case discusses stabilization of the airway with a review of treatment and reconstructive options.
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Affiliation(s)
- Andrew K Fuller
- School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Hilary C McCrary
- Division of Otolaryngology, University of Utah, Salt Lake City, UT, USA
| | - M Elise Graham
- Department of Otolaryngology, Western University, London, ON, Canada
| | - Jonathan R Skirko
- Division of Otolaryngology, University of Utah, Salt Lake City, UT, USA
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Vančevska A, Ahmed W, Pfeiffer V, Feretzaki M, Boulton SJ, Lingner J. SMCHD1 promotes ATM-dependent DNA damage signaling and repair of uncapped telomeres. EMBO J 2020; 39:e102668. [PMID: 32080884 DOI: 10.15252/embj.2019102668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMCHD1) has been implicated in X-chromosome inactivation, imprinting, and DNA damage repair, and mutations in SMCHD1 can cause facioscapulohumeral muscular dystrophy. More recently, SMCHD1 has also been identified as a component of telomeric chromatin. Here, we report that SMCHD1 is required for DNA damage signaling and non-homologous end joining (NHEJ) at unprotected telomeres. Co-depletion of SMCHD1 and the shelterin subunit TRF2 reduced telomeric 3'-overhang removal in time-course experiments, as well as the number of chromosome end fusions. SMCHD1-deficient cells displayed reduced ATM S1981 phosphorylation and diminished formation of γH2AX foci and of 53BP1-containing telomere dysfunction-induced foci (TIFs), indicating defects in DNA damage checkpoint signaling. Removal of TPP1 and subsequent activation of ATR signaling rescued telomere fusion events in TRF2-depleted SMCHD1 knockout cells. Together, these data indicate that SMCHD1 depletion reduces telomere fusions in TRF2-depleted cells due to defects in ATM-dependent checkpoint signaling and that SMCHD1 mediates DNA damage response activation upstream of ATM phosphorylation at uncapped telomeres.
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Affiliation(s)
- Aleksandra Vančevska
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,The Francis Crick Institute, London, UK
| | - Wareed Ahmed
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Verena Pfeiffer
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marianna Feretzaki
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Bansal P, Kondaveeti Y, Pinter SF. Forged by DXZ4, FIRRE, and ICCE: How Tandem Repeats Shape the Active and Inactive X Chromosome. Front Cell Dev Biol 2020; 7:328. [PMID: 32076600 PMCID: PMC6985041 DOI: 10.3389/fcell.2019.00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Recent efforts in mapping spatial genome organization have revealed three evocative and conserved structural features of the inactive X in female mammals. First, the chromosomal conformation of the inactive X reveals a loss of topologically associated domains (TADs) present on the active X. Second, the macrosatellite DXZ4 emerges as a singular boundary that suppresses physical interactions between two large TAD-depleted "megadomains." Third, DXZ4 reaches across several megabases to form "superloops" with two other X-linked tandem repeats, FIRRE and ICCE, which also loop to each other. Although all three structural features are conserved across rodents and primates, deletion of mouse and human orthologs of DXZ4 and FIRRE from the inactive X have revealed limited impact on X chromosome inactivation (XCI) and escape in vitro. In contrast, loss of Xist or SMCHD1 have been shown to impair TAD erasure and gene silencing on the inactive X. In this perspective, we summarize these results in the context of new research describing disruption of X-linked tandem repeats in vivo, and discuss their possible molecular roles through the lens of evolutionary conservation and clinical genetics. As a null hypothesis, we consider whether the conservation of some structural features on the inactive X may reflect selection for X-linked tandem repeats on account of necessary cis- and trans-regulatory roles they may play on the active X, rather than the inactive X. Additional hypotheses invoking a role for X-linked tandem repeats on X reactivation, for example in the germline or totipotency, remain to be assessed in multiple developmental models spanning mammalian evolution.
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Affiliation(s)
- Prakhar Bansal
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Stefan F. Pinter
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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36
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Schall PZ, Ruebel ML, Latham KE. A New Role for SMCHD1 in Life's Master Switch and Beyond. Trends Genet 2019; 35:948-955. [PMID: 31668908 DOI: 10.1016/j.tig.2019.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 12/29/2022]
Abstract
Structural maintenance of chromosomes flexible hinge-domain containing protein 1 (SMCHD1) has emerged as a key regulator of embryonic genome function. Its functions have now extended well beyond the initial findings of effects on X chromosome inactivation associated with lethality in female embryos homozygous for a null allele. Autosomal dominant effects impact stem cell properties as well as postnatal health. Recent studies have revealed that SMCHD1 plays an important role as a maternal effect gene that regulates the master switch of life, namely embryonic genome activation, as well as subsequent preimplantation development and term viability. These discoveries mark SMCHD1 as a major regulator linking developmental processes to adult disorders including a form of muscular dystrophy.
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Affiliation(s)
- Peter Z Schall
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA; Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Meghan L Ruebel
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA; Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA; Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI 48824, USA.
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37
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Wang CY, Brand H, Shaw ND, Talkowski ME, Lee JT. Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans. Genetics 2019; 213:685-703. [PMID: 31420322 PMCID: PMC6781896 DOI: 10.1534/genetics.119.302600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.
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Affiliation(s)
- Chen-Yu Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Natalie D Shaw
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael E Talkowski
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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38
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Midic U, Vincent KA, Wang K, Lokken A, Severance AL, Ralston A, Knott JG, Latham KE. Novel key roles for structural maintenance of chromosome flexible domain containing 1 (Smchd1) during preimplantation mouse development. Mol Reprod Dev 2019; 85:635-648. [PMID: 29900695 DOI: 10.1002/mrd.23001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/08/2018] [Indexed: 12/16/2022]
Abstract
Structural maintenance of chromosome flexible domain containing 1 (Smchd1) is a chromatin regulatory gene for which mutations are associated with facioscapulohumeral muscular dystrophy and arhinia. The contribution of oocyte- and zygote-expressed SMCHD1 to early development was examined in mice ( Mus musculus) using a small interfering RNA knockdown approach. Smchd1 knockdown compromised long-term embryo viability, with reduced embryo nuclear volumes at the morula stage, reduced blastocyst cell number, formation and hatching, and reduced viability to term. RNA sequencing analysis of Smchd1 knockdown morulae revealed aberrant increases in expression of a small number of trophectoderm (TE)-related genes and reduced expression of cell proliferation genes, including S-phase kinase-associated protein 2 ( Skp2). Smchd1 expression was elevated in embryos deficient for Caudal-type homeobox transcription factor 2 ( Cdx2, a key regulator of TE specification), indicating that Smchd1 is normally repressed by CDX2. These results indicate that Smchd1 plays an important role in the preimplantation embryo, regulating early gene expression and contributing to long-term embryo viability. These results extend the known functions of SMCHD1 to the preimplantation period and highlight important function for maternally expressed Smchd1 messenger RNA and protein.
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Affiliation(s)
- Uros Midic
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Kailey A Vincent
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Kai Wang
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Alyson Lokken
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Ashley L Severance
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Amy Ralston
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Jason G Knott
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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40
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Ruebel ML, Vincent KA, Schall PZ, Wang K, Latham KE. SMCHD1 terminates the first embryonic genome activation event in mouse two-cell embryos and contributes to a transcriptionally repressive state. Am J Physiol Cell Physiol 2019; 317:C655-C664. [PMID: 31365290 DOI: 10.1152/ajpcell.00116.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Embryonic genome activation (EGA) in mammals begins with transient expression of a large group of genes (EGA1). Importantly, entry into and exit from the 2C/EGA state is essential for viability. Dux family member genes play an integral role in EGA1 by activating other EGA marker genes such as Zscan4 family members. We previously reported that structural maintenance of chromosomes flexible hinge domain-containing protein 1 (Smchd1) is expressed at the mRNA and protein levels in mouse oocytes and early embryos and that elimination of Smchd1 expression inhibits inner cell mass formation, blastocyst formation and hatching, and term development. We extend these observations here by showing that siRNA knockdown of Smchd1 in zygotes results in overexpression of Dux and Zscan4 in two-cell embryos, with continued overexpression of Dux at least through the eight-cell stage as well as prolonged expression of Zscan4. These results are consistent with a role for SMCHD1 in promoting exit from the EGA1 state and establishing SMCHD1 as a maternal effect gene and the first chromatin regulatory factor identified with this role. Additionally, bioinformatics analysis reveals that SMCHD1 also contributes to the creation of a transcriptionally repressive state to allow correct gene regulation.
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Affiliation(s)
- Meghan L Ruebel
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Kailey A Vincent
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Peter Z Schall
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Kai Wang
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan.,Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, Michigan
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41
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Pedersen LC, Inoue K, Kim S, Perera L, Shaw ND. A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1. Commun Biol 2019; 2:255. [PMID: 31312724 PMCID: PMC6620310 DOI: 10.1038/s42003-019-0499-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/08/2019] [Indexed: 12/16/2022] Open
Abstract
Variants in the gene SMCHD1, which encodes an epigenetic repressor, have been linked to both congenital arhinia and a late-onset form of muscular dystrophy called facioscapulohumeral muscular dystrophy type 2 (FSHD2). This suggests that SMCHD1 has a diversity of functions in both developmental time and space. The C-terminal end of SMCHD1 contains an SMC-hinge domain which mediates homodimerization and chromatin association, whereas the molecular architecture of the N-terminal region, which harbors the GHKL-ATPase domain, is not well understood. We present the crystal structure of the human SMCHD1 N-terminal ATPase module bound to ATP as a functional dimer. The dimer is stabilized by a novel N-terminal ubiquitin-like fold and by a downstream transducer domain. While disease variants map to what appear to be critical interdomain/intermolecular interfaces, only the FSHD2-specific mutant constructs we tested consistently abolish ATPase activity and/or dimerization. These data suggest that the full functional profile of SMCHD1 has yet to be determined.
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Affiliation(s)
- Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Kaoru Inoue
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Susan Kim
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Natalie D. Shaw
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
- Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114 USA
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42
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Dion C, Roche S, Laberthonnière C, Broucqsault N, Mariot V, Xue S, Gurzau AD, Nowak A, Gordon CT, Gaillard MC, El-Yazidi C, Thomas M, Schlupp-Robaglia A, Missirian C, Malan V, Ratbi L, Sefiani A, Wollnik B, Binetruy B, Salort Campana E, Attarian S, Bernard R, Nguyen K, Amiel J, Dumonceaux J, Murphy JM, Déjardin J, Blewitt ME, Reversade B, Robin JD, Magdinier F. SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite. Nucleic Acids Res 2019; 47:2822-2839. [PMID: 30698748 PMCID: PMC6451109 DOI: 10.1093/nar/gkz005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022] Open
Abstract
The DNA methylation epigenetic signature is a key determinant during development. Rules governing its establishment and maintenance remain elusive especially at repetitive sequences, which account for the majority of methylated CGs. DNA methylation is altered in a number of diseases including those linked to mutations in factors that modify chromatin. Among them, SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain Containing 1) has been of major interest following identification of germline mutations in Facio-Scapulo-Humeral Dystrophy (FSHD) and in an unrelated developmental disorder, Bosma Arhinia Microphthalmia Syndrome (BAMS). By investigating why germline SMCHD1 mutations lead to these two different diseases, we uncovered a role for this factor in de novo methylation at the pluripotent stage. SMCHD1 is required for the dynamic methylation of the D4Z4 macrosatellite upon reprogramming but seems dispensable for methylation maintenance. We find that FSHD and BAMS patient's cells carrying SMCHD1 mutations are both permissive for DUX4 expression, a transcription factor whose regulation has been proposed as the main trigger for FSHD. These findings open new questions as to what is the true aetiology for FSHD, the epigenetic events associated with the disease thus calling the current model into question and opening new perspectives for understanding repetitive DNA sequences regulation.
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Affiliation(s)
- Camille Dion
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | | | - Natacha Broucqsault
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Virginie Mariot
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Agnieszka Nowak
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Claire El-Yazidi
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Morgane Thomas
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Andrée Schlupp-Robaglia
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
- Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
- Centre de ressources biologiques, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Chantal Missirian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
- Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Valérie Malan
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Liham Ratbi
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Campus Göttingen, 37073 Göttingen, Germany
| | - Bernard Binetruy
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Emmanuelle Salort Campana
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
- Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
- Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Rafaelle Bernard
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
- Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
- Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Jérôme Déjardin
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore
- Department of Paediatrics, National University of Singapore, Singapore, Singapore
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey
- Reproductive Biology Laboratory, Academic Medical Center (AMC), Amsterdam-Zuidoost, The Netherlands
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
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Facioscapulohumeral muscular dystrophy (FSHD) molecular diagnosis: from traditional technology to the NGS era. Neurogenetics 2019; 20:57-64. [PMID: 30911870 DOI: 10.1007/s10048-019-00575-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/17/2019] [Indexed: 02/08/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a genetic neuromuscular disorder which mainly affects the muscles of the face, shoulder, and upper arms. FSHD is generally associated with the contraction of D4Z4 macrosatellite repeats on 4q35 chromosome or mutations in SMCHD1, which are responsible of the toxic expression of DUX4 in muscle tissue. Despite the recent application of NGS techniques in the clinical practice, the molecular diagnosis of FSHD is still performed with dated techniques such as Southern blotting. The diagnosis of FSHD requires therefore specific skills on both modern and less modern analytical protocols. Considering that clinical and molecular diagnosis of FSHD is challenging, it is not surprising that only few laboratories offer a comprehensive characterization of FSHD, which requires the education of professionals on traditional techniques even in the era of NGS. In conclusion, the study of FSHD provides an excellent example of using classical and modern molecular technologies which are equally necessary for the analysis of DNA repetitive traits associated with specific disorders.
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Tong Y, Song Y, Deng S. Combined analysis and validation for DNA methylation and gene expression profiles associated with prostate cancer. Cancer Cell Int 2019; 19:50. [PMID: 30867653 PMCID: PMC6399908 DOI: 10.1186/s12935-019-0753-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/08/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is a malignancy cause of cancer deaths and frequently diagnosed in male. This study aimed to identify tumor suppressor genes, hub genes and their pathways by combined bioinformatics analysis. METHODS A combined analysis method was used for two types of microarray datasets (DNA methylation and gene expression profiles) from the Gene Expression Omnibus (GEO). Differentially methylated genes (DMGs) were identified by the R package minfi and differentially expressed genes (DEGs) were screened out via the R package limma. A total of 4451 DMGs and 1509 DEGs, identified with nine overlaps between DMGs, DEGs and tumor suppressor genes, were screened for candidate tumor suppressor genes. All these nine candidate tumor suppressor genes were validated by TCGA (The Cancer Genome Atlas) database and Oncomine database. And then, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed by DAVID (Database for Annotation, Visualization and Integrated Discovery) database. Protein-protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. At last, Kaplan-Meier analysis was performed to validate these genes. RESULTS The candidate tumor suppressor genes were IKZF1, PPM1A, FBP1, SMCHD1, ALPL, CASP5, PYHIN1, DAPK1 and CASP8. By validation in TCGA database, PPM1A, DAPK1, FBP1, PYHIN1, ALPL and SMCHD1 were significant. The hub genes were FGFR1, FGF13 and CCND1. These hub genes were identified from the PPI network, and sub-networks revealed by these genes were involved in significant pathways. CONCLUSION In summary, the study indicated that the combined analysis for identifying target genes with PCa by bioinformatics tools promote our understanding of the molecular mechanisms and underlying the development of PCa. And the hub genes might serve as molecular targets and diagnostic biomarkers for precise diagnosis and treatment of PCa.
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Affiliation(s)
- Yanqiu Tong
- Laboratory of Forensic Medicine and Biomedical Informatics, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
- School of Humanity, Chongqing Jiaotong University, Chongqing, 400074 People’s Republic of China
| | - Yang Song
- Department of Device, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Shixiong Deng
- Laboratory of Forensic Medicine and Biomedical Informatics, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
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Cascella R, Strafella C, Caputo V, Galota RM, Errichiello V, Scutifero M, Petillo R, Marella GL, Arcangeli M, Colantoni L, Zampatti S, Ricci E, Deidda G, Politano L, Giardina E. Digenic Inheritance of Shortened Repeat Units of the D4Z4 Region and a Loss-of-Function Variant in SMCHD1 in a Family With FSHD. Front Neurol 2018; 9:1027. [PMID: 30546343 PMCID: PMC6279899 DOI: 10.3389/fneur.2018.01027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a neuromuscular disorder which is typically transmitted by an autosomal dominant pattern, although reduced penetrance and sporadic cases caused by de novo mutations, are often observed. FSHD may be caused by a contraction of a repetitive element, located on chromosome 4 (4q35). This locus is named D4Z4 and consists of 11 to more than 100 repeated units (RU). The D4Z4 is normally hypermethylated and the genes located on this locus are silenced. In case of FSHD, the D4Z4 region is characterized by 1–10 repeats and results in the region being hypomethylated. However, 5% of FSHD cases do not carry the short allele of D4Z4 region. To date, two forms of FSHD (FSHD1 and FSHD2) are known. FSHD2 is usually observed in patients without the D4Z4 fragment contraction and carrying variants in SMCHD1 (18p11.32) gene. We report the case of a young adult patient who shows severe symptoms of FSHD. Preliminary genetic analysis did not clarify the phenotype, therefore we decided to study the family members by genetic and epigenetic approaches. The analysis of D4Z4 fragment resulted to be 8 RU in the affected proband and in his father; 26 RU in the mother and 25 RU in the maternal uncle. SMCHD1 analysis revealed a heterozygous variation within the exon 41. The variant was detected in the proband, her mother and the uncle. Furthermore, epigenetic analysis of CpG6 methylation regions showed significant hypomethylation in the affected patient (54%) and in the mother (56%), in contrast to the father (88%) and the uncle (81%) carrying higher methylation levels. The analysis of DR1 methylation levels reported hypomethylation for the proband (19%), the mother (11%), and the uncle (16%). The father showed normal DR1 methylation levels (>30%). Given these results, the combined inheritance of SMCHD1 variant and the short fragment might explain the severe FSHD phenotype displayed by the proband. On this subject, SMCHD1 analysis should be promoted in a larger number of patients, even in presence of D4Z4 contractions, to facilitate the genotype-phenotype correlation as well as, to enable a more precise diagnosis and prognosis of the disease.
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Affiliation(s)
- Raffaella Cascella
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Claudia Strafella
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy.,Emotest Laboratory, Pozzuoli, Italy
| | - Valerio Caputo
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | | | - Valeria Errichiello
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | - Marianna Scutifero
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Roberta Petillo
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Gian Luca Marella
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Mauro Arcangeli
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | - Luca Colantoni
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Stefania Zampatti
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Enzo Ricci
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Giancarlo Deidda
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo, Rome, Italy
| | - Luisa Politano
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
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46
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Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters. Nat Struct Mol Biol 2018; 25:766-777. [PMID: 30127357 DOI: 10.1038/s41594-018-0111-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022]
Abstract
The regulation of higher-order chromatin structure is complex and dynamic, and a full understanding of the suite of mechanisms governing this architecture is lacking. Here, we reveal the noncanonical SMC protein Smchd1 to be a novel regulator of long-range chromatin interactions in mice, and we add Smchd1 to the canon of epigenetic proteins required for Hox-gene regulation. The effect of losing Smchd1-dependent chromatin interactions has varying outcomes that depend on chromatin context. At autosomal targets transcriptionally sensitive to Smchd1 deletion, we found increased short-range interactions and ectopic enhancer activation. In contrast, the inactive X chromosome was transcriptionally refractive to Smchd1 ablation, despite chromosome-wide increases in short-range interactions. In the inactive X, we observed spreading of trimethylated histone H3 K27 (H3K27me3) domains into regions not normally decorated by this mark. Together, these data suggest that Smchd1 is able to insulate chromatin, thereby limiting access to other chromatin-modifying proteins.
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47
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Hiramuki Y, Tapscott SJ. Identification of SMCHD1 domains for nuclear localization, homo-dimerization, and protein cleavage. Skelet Muscle 2018; 8:24. [PMID: 30071896 PMCID: PMC6090946 DOI: 10.1186/s13395-018-0172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/24/2018] [Indexed: 12/04/2022] Open
Abstract
Background SMCHD1 is a disease modifier and a causative gene for facioscapulohumeral muscular dystrophy (FSHD) type 1 and type 2, respectively. A large variety of different mutations in SMCHD1 have been identified as causing FSHD2. In many cases, it is unclear how these mutations disrupt the normal function of SMCHD1. Methods We made and analyzed lenti-viral vectors that express Flag-tagged full-length or different mutant SMCHD1 proteins to better understand the functional domains of SMCHD1 in muscle cells. Results We identified regions necessary for nuclear localization, dimerization, and cleavage sites. Moreover, we confirmed that some mutants increased DUX4 expression in FSHD1 myoblasts. Conclusions These findings provide an additional basis for understanding the molecular consequences of SMCHD1 mutations. Electronic supplementary material The online version of this article (10.1186/s13395-018-0172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yosuke Hiramuki
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
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Gurzau AD, Chen K, Xue S, Dai W, Lucet IS, Ly TTN, Reversade B, Blewitt ME, Murphy JM. FSHD2- and BAMS-associated mutations confer opposing effects on SMCHD1 function. J Biol Chem 2018; 293:9841-9853. [PMID: 29748383 DOI: 10.1074/jbc.ra118.003104] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/03/2018] [Indexed: 01/01/2023] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (Smchd1) plays important roles in epigenetic silencing and normal mammalian development. Recently, heterozygous mutations in SMCHD1 have been reported in two disparate disorders: facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS). FSHD2-associated mutations lead to loss of function; however, whether BAMS is associated with loss- or gain-of-function mutations in SMCHD1 is unclear. Here, we have assessed the effect of SMCHD1 missense mutations from FSHD2 and BAMS patients on ATP hydrolysis activity and protein conformation and the effect of BAMS mutations on craniofacial development in a Xenopus model. These data demonstrated that FSHD2 mutations only result in decreased ATP hydrolysis, whereas many BAMS mutations can result in elevated ATPase activity and decreased eye size in Xenopus Interestingly, a mutation reported in both an FSHD2 patient and a BAMS patient results in increased ATPase activity and a smaller Xenopus eye size. Mutations in the extended ATPase domain increased catalytic activity, suggesting critical regulatory intramolecular interactions and the possibility of targeting this region therapeutically to boost SMCHD1's activity to counter FSHD.
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Affiliation(s)
- Alexandra D Gurzau
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,the Departments of Medical Biology and
| | - Kelan Chen
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,the Departments of Medical Biology and
| | - Shifeng Xue
- the Institute of Molecular and Cell Biology and.,Human Genetics and Embryology Laboratory, Institute of Medical Biology, A*STAR, Singapore
| | - Weiwen Dai
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Isabelle S Lucet
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,the Departments of Medical Biology and
| | - Thanh Thao Nguyen Ly
- the Institute of Molecular and Cell Biology and.,Human Genetics and Embryology Laboratory, Institute of Medical Biology, A*STAR, Singapore
| | - Bruno Reversade
- the Institute of Molecular and Cell Biology and.,Human Genetics and Embryology Laboratory, Institute of Medical Biology, A*STAR, Singapore.,the Department of Medical Genetics, Koç University School of Medicine (KUSoM), 34450 Sarıyer/Istanbul, Turkey.,the Department of Paediatrics, School of Medicine, National University of Singapore, Singapore, and.,Amsterdam Reproduction and Development, Academic Medical Centre and VU University Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Marnie E Blewitt
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, .,the Departments of Medical Biology and.,Genetics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - James M Murphy
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, .,the Departments of Medical Biology and
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Ryan TM, Trewhella J, Murphy JM, Keown JR, Casey L, Pearce FG, Goldstone DC, Chen K, Luo Z, Kobe B, McDevitt CA, Watkin SA, Hawley AM, Mudie ST, Samardzic Boban V, Kirby N. An optimized SEC-SAXS system enabling high X-ray dose for rapid SAXS assessment with correlated UV measurements for biomolecular structure analysis. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576717017101] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new optimized size exclusion chromatography small-angle X-ray scattering (SEC-SAXS) system for biomolecular SAXS at the Australian Synchrotron SAXS/WAXS beamline has been developed. The compact configuration reduces sample dilution to maximize sensitivity. Coflow sample presentation allows an 11-fold increase in flux on sample without capillary fouling, improving throughput and data quality, which are now primarily limited by the full flux available on the beamline. Multi-wavelength fibre optic UV analysis in close proximity to the X-ray beam allows for accurate concentration determination for samples with known UV extinction coefficients and thus estimation of the molecular weight of the scattering particle from the forward X-ray scattering intensity. Fast-flow low-volume SEC columns provide sample throughput competitive with batch concentration series measurements, albeit with a concomitant reduction of potential resolution relative to lower flow rates and larger SEC columns. The performance of the system is demonstrated using a set of model proteins, and its utility to solve various challenges is illustrated with a diverse suite of protein samples. These developments increase the quality and rigor of SEC-SAXS analysis and open new avenues for biomolecular solution SEC-SAXS studies that have been challenged by low sample yields, temporal instability, radiation sensitivity and complex mixtures.
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