1
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Huang D, Ovcharenko I. The contribution of silencer variants to human diseases. Genome Biol 2024; 25:184. [PMID: 38978133 PMCID: PMC11232194 DOI: 10.1186/s13059-024-03328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/28/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Although disease-causal genetic variants have been found within silencer sequences, we still lack a comprehensive analysis of the association of silencers with diseases. Here, we profiled GWAS variants in 2.8 million candidate silencers across 97 human samples derived from a diverse panel of tissues and developmental time points, using deep learning models. RESULTS We show that candidate silencers exhibit strong enrichment in disease-associated variants, and several diseases display a much stronger association with silencer variants than enhancer variants. Close to 52% of candidate silencers cluster, forming silencer-rich loci, and, in the loci of Parkinson's-disease-hallmark genes TRIM31 and MAL, the associated SNPs densely populate clustered candidate silencers rather than enhancers displaying an overall twofold enrichment in silencers versus enhancers. The disruption of apoptosis in neuronal cells is associated with both schizophrenia and bipolar disorder and can largely be attributed to variants within candidate silencers. Our model permits a mechanistic explanation of causative SNP effects by identifying altered binding of tissue-specific repressors and activators, validated with a 70% of directional concordance using SNP-SELEX. Narrowing the focus of the analysis to individual silencer variants, experimental data confirms the role of the rs62055708 SNP in Parkinson's disease, rs2535629 in schizophrenia, and rs6207121 in type 1 diabetes. CONCLUSIONS In summary, our results indicate that advances in deep learning models for the discovery of disease-causal variants within candidate silencers effectively "double" the number of functionally characterized GWAS variants. This provides a basis for explaining mechanisms of action and designing novel diagnostics and therapeutics.
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Affiliation(s)
- Di Huang
- Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ivan Ovcharenko
- Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
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2
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Hu B, Zhang X, Fan H, Jin X, Qi Y, Liu R, Li X, Duan M, Zhang C, Li S, Yao W, Hao C. FOXF1 reverses lung fibroblasts transdifferentiation via inhibiting TGF-β/SMAD2/3 pathway in silica-induced pulmonary fibrosis. Int Immunopharmacol 2024; 133:112067. [PMID: 38608444 DOI: 10.1016/j.intimp.2024.112067] [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: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Silicosis is one of the most common and severe types of pneumoconiosis and is characterized by lung dysfunction, persistent lung inflammation, pulmonary nodule formation, and irreversible pulmonary fibrosis. The transdifferentiation of fibroblasts into myofibroblasts is one of the main reasons for the exacerbation of silicosis. However, the underlying mechanism of transcription factors regulating silicosis fibrosis has not been clarified. The aim of this study was to investigate the potential mechanism of transcription factor FOXF1 in fibroblast transdifferentiation in silica-induced pulmonary fibrosis. Therefore, a silicosis mouse model was established, and we found that FOXF1 expression level was significantly down-regulated in the silicosis group, and after overexpression of FOXF1 by adeno-associated virus (AAV), FOXF1 expression level was up-regulated, and silicosis fibrosis was alleviated. In order to further explore the specific regulatory mechanism of FOXF1 in silicosis, we established a fibroblasts transdifferentiation model induced by TGF-β in vitro. In the model, the expression levels of SMAD2/3 and P-SMAD2/3 were up-regulated, but the expression levels of SMAD2/3 and P-SMAD2/3 were down-regulated, inhibiting transdifferentiation and accumulation of extracellular matrix after the overexpressed FOXF1 plasmid was constructed. However, after silencing FOXF1, the expression levels of SMAD2/3 and P-SMAD2/3 were further up-regulated, aggravating transdifferentiation and accumulation of extracellular matrix. These results indicate that the activation of FOXF1 in fibroblasts can slow down the progression of silicosis fibrosis by inhibiting TGF-β/SMAD2/3 classical pathway, which provides a new idea for further exploration of silicosis treatment.
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Affiliation(s)
- Botao Hu
- School of Public Health, Zhengzhou University, Henan, China
| | - Xuesong Zhang
- School of Public Health, Zhengzhou University, Henan, China
| | - Hui Fan
- Department of Ultrasound, The Third Affiliated Hospital of Zhengzhou University, Henan, China
| | - Xiaofei Jin
- Department of Ultrasound, The Third Affiliated Hospital of Zhengzhou University, Henan, China
| | - Yuanmeng Qi
- School of Public Health, Zhengzhou University, Henan, China
| | - Ruimin Liu
- School of Public Health, Zhengzhou University, Henan, China
| | - Xiaoying Li
- School of Public Health, Zhengzhou University, Henan, China
| | - Meixiu Duan
- School of Public Health, Zhengzhou University, Henan, China
| | | | - Shiyu Li
- School of Public Health, Zhengzhou University, Henan, China
| | - Wu Yao
- School of Public Health, Zhengzhou University, Henan, China
| | - Changfu Hao
- School of Public Health, Zhengzhou University, Henan, China.
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3
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Narumi S, Nagasaki K, Kiriya M, Uehara E, Akiba K, Tanase-Nakao K, Shimura K, Abe K, Sugisawa C, Ishii T, Miyako K, Hasegawa Y, Maruo Y, Muroya K, Watanabe N, Nishihara E, Ito Y, Kogai T, Kameyama K, Nakabayashi K, Hata K, Fukami M, Shima H, Kikuchi A, Takayama J, Tamiya G, Hasegawa T. Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities. Nat Genet 2024; 56:869-876. [PMID: 38714868 PMCID: PMC11096107 DOI: 10.1038/s41588-024-01735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024]
Abstract
Insufficient thyroid hormone production in newborns is referred to as congenital hypothyroidism. Multinodular goiter (MNG), characterized by an enlarged thyroid gland with multiple nodules, is usually seen in adults and is recognized as a separate disorder from congenital hypothyroidism. Here we performed a linkage analysis of a family with both nongoitrous congenital hypothyroidism and MNG and identified a signal at 15q26.1. Follow-up analyses with whole-genome sequencing and genetic screening in congenital hypothyroidism and MNG cohorts showed that changes in a noncoding TTTG microsatellite on 15q26.1 were frequently observed in congenital hypothyroidism (137 in 989) and MNG (3 in 33) compared with controls (3 in 38,722). Characterization of the noncoding variants with epigenomic data and in vitro experiments suggested that the microsatellite is located in a thyroid-specific transcriptional repressor, and its activity is disrupted by the variants. Collectively, we presented genetic evidence linking nongoitrous congenital hypothyroidism and MNG, providing unique insights into thyroid abnormalities.
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Affiliation(s)
- Satoshi Narumi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Keisuke Nagasaki
- Division of Pediatrics, Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Erika Uehara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhisa Akiba
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Kanako Tanase-Nakao
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiro Shimura
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kiyomi Abe
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Chiho Sugisawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Internal Medicine, Ito Hospital, Tokyo, Japan
| | - Tomohiro Ishii
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenichi Miyako
- Department of Endocrinology and Metabolism, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Yukihiro Hasegawa
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yoshihiro Maruo
- Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | | | - Eijun Nishihara
- Center for Excellence in Thyroid Care, Kuma Hospital, Kobe, Japan
| | - Yuka Ito
- Department of Genetic Diagnosis and Laboratory Medicine, Dokkyo Medical University, Mibu, Japan
| | - Takahiko Kogai
- Department of Genetic Diagnosis and Laboratory Medicine, Dokkyo Medical University, Mibu, Japan
| | - Kaori Kameyama
- Department of Pathology, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirohito Shima
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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4
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Jurgens JA, Barry BJ, Chan WM, MacKinnon S, Whitman MC, Matos Ruiz PM, Pratt BM, England EM, Pais L, Lemire G, Groopman E, Glaze C, Russell KA, Singer-Berk M, Di Gioia SA, Lee AS, Andrews C, Shaaban S, Wirth MM, Bekele S, Toffoloni M, Bradford VR, Foster EE, Berube L, Rivera-Quiles C, Mensching FM, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Wilson MW, Weisburd B, Lek M, Brand H, Talkowski ME, MacArthur DG, O’Donnell-Luria A, Robson CD, Hunter DG, Engle EC. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304594. [PMID: 38585811 PMCID: PMC10996726 DOI: 10.1101/2024.03.22.24304594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Purpose To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs). Methods We coupled phenotyping with exome or genome sequencing of 467 pedigrees with genetically unsolved oCCDDs, integrating analyses of pedigrees, human and animal model phenotypes, and de novo variants to identify rare candidate single nucleotide variants, insertion/deletions, and structural variants disrupting protein-coding regions. Prioritized variants were classified for pathogenicity and evaluated for genotype/phenotype correlations. Results Analyses elucidated phenotypic subgroups, identified pathogenic/likely pathogenic variant(s) in 43/467 probands (9.2%), and prioritized variants of uncertain significance in 70/467 additional probands (15.0%). These included known and novel variants in established oCCDD genes, genes associated with syndromes that sometimes include oCCDDs (e.g., MYH10, KIF21B, TGFBR2, TUBB6), genes that fit the syndromic component of the phenotype but had no prior oCCDD association (e.g., CDK13, TGFB2), genes with no reported association with oCCDDs or the syndromic phenotypes (e.g., TUBA4A, KIF5C, CTNNA1, KLB, FGF21), and genes associated with oCCDD phenocopies that had resulted in misdiagnoses. Conclusion This study suggests that unsolved oCCDDs are clinically and genetically heterogeneous disorders often overlapping other Mendelian conditions and nominates many candidates for future replication and functional studies.
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Affiliation(s)
- Julie A. Jurgens
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brenda J. Barry
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Mary C. Whitman
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | | | - Brandon M. Pratt
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Eleina M. England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynn Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Carmen Glaze
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn A. Russell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvio Alessandro Di Gioia
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, 10591, USA
| | - Arthur S. Lee
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline Andrews
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Sherin Shaaban
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Megan M. Wirth
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Sarah Bekele
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Melissa Toffoloni
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | | | - Emma E. Foster
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Lindsay Berube
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | | | | | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack M. Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E. Talkowski
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline D. Robson
- Division of Neuroradiology, Department of Radiology, Boston Children’s Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - David G. Hunter
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth C. Engle
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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5
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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [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: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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6
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Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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7
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Novis LE, Raskin S, Teive HA. New Horizons on the Diagnosis of Hereditary Ataxia. Mov Disord Clin Pract 2023; 10:1597-1598. [PMID: 37982113 PMCID: PMC10654831 DOI: 10.1002/mdc3.13877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 11/21/2023] Open
Affiliation(s)
- Luiz Eduardo Novis
- Neurodegenerative Diseases Group, Post‐Graduate Program in Internal Medicine, Internal Medicine Department, Hospital de ClínicasFederal University of ParanáCuritibaBrazil
| | - Salmo Raskin
- Postgraduate Program in Child and Adolescent, Department of PediatricsFederal University of ParanáCuritibaBrazil
| | - Helio A.G. Teive
- Movement Disorders Unit, Neurology Service, Internal Medicine Department, Hospital de ClínicasFederal University of ParanáCuritibaBrazil
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8
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Martin-Geary AC, Blakes AJM, Dawes R, Findlay SD, Lord J, Walker S, Talbot-Martin J, Wieder N, D’Souza EN, Fernandes M, Hilton S, Lahiri N, Campbell C, Jenkinson S, DeGoede CGEL, Anderson ER, Burge CB, Sanders SJ, Ellingford J, Baralle D, Banka S, Whiffin N. Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295416. [PMID: 37745552 PMCID: PMC10516070 DOI: 10.1101/2023.09.12.23295416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown. Methods We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8,040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7,862 unrelated probands against matched unaffected controls. Results We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations. Conclusions Overall, we demonstrate the value of screening promoters and UTRs to uncover additional diagnoses for previously undiagnosed individuals with rare disease and provide a framework for doing so without dramatically increasing interpretation burden.
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Affiliation(s)
- Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Alexander J M Blakes
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | | | | | | | - Nechama Wieder
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Maria Fernandes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nayana Lahiri
- St George’s, University of London & St George’s University Hospitals NHS Foundation Trust, Institute of Molecular and Clinical Sciences, London, SW17 0QT, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Christian G E L DeGoede
- Department of Paediatric Neurology, Clinical research Facility, Lancashire Teaching Hospitals NHS Trust
- Manchester Metropolitan University
| | - Emily R Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | | | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- New York Genome Center, New York, NY, USA
| | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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