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Lee SA, Hong JM, Lee JH, Choi YC, Park HJ. Transcriptome profiling of skeletal muscles from Korean patients with Bethlem myopathy. Medicine (Baltimore) 2023; 102:e33122. [PMID: 36862922 PMCID: PMC9981387 DOI: 10.1097/md.0000000000033122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Bethlem myopathy is one of the collagens VI-related muscular dystrophies caused by mutations in the collagen VI genes. The study was designed to analyze the gene expression profiles in the skeletal muscle of patients with Bethlem myopathy. Six skeletal muscle samples from 3 patients with Bethlem myopathy and 3 control subjects were analyzed by RNA-sequencing. 187 transcripts were significantly differentially expressed, with 157 upregulated and 30 downregulated transcripts in the Bethlem group. Particularly, 1 (microRNA-133b) was considerably upregulated, and 4 long intergenic non-protein coding RNAs, LINC01854, MBNL1-AS1, LINC02609, and LOC728975, were significantly downregulated. We categorized differentially expressed gene using Gene Ontology and showed that Bethlem myopathy is strongly associated with the organization of extracellular matrix (ECM). Kyoto Encyclopedia of Genes and Genomes pathway enrichment reflected themes with significant enrichment of the ECM-receptor interaction (hsa04512), complement and coagulation cascades (hsa04610), and focal adhesion (hsa04510). We confirmed that Bethlem myopathy is strongly associated with the organization of ECM and the wound healing process. Our results demonstrate transcriptome profiling of Bethlem myopathy, and provide new insights into the path mechanism of Bethlem myopathy associated with non-protein coding RNAs.
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Affiliation(s)
- Seung-Ah Lee
- Department of Neurology, Ewha Womans University Mokdong Hospital, Ewha Womans University College of Medicine, Yangcheon-gu, Seoul, Republic of Korea
| | - Ji-Man Hong
- Department of Neurology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Gyeonggi-do, Republic of Korea
| | - Jung Hwan Lee
- Department of Neurology, Seoul St. Mary’s Hospital, College of Medicine, Seocho-gu, Seoul, Republic of Korea
| | - Young-Chul Choi
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyung Jun Park
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- * Correspondence: Hyung Jun Park, Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul 06273, Korea (e-mail: )
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KWONG AKY, ZHANG Y, HO RSL, GAO Y, LING X, TSANG MHY, LUK HM, CHUNG BHY, BÖNNEMANN CG, JAVED A, CHAN SHS. COLLAGEN VI-RELATED MYOPATHIES: CLINICAL VARIABILITY, PHENOTYPE-GENOTYPE CORRELATION AND EXPLORATORY TRANSCRIPTOME STUDY. Neuromuscul Disord 2023; 33:371-381. [PMID: 37023487 DOI: 10.1016/j.nmd.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023]
Abstract
Collagen VI-related myopathies are a group of disorders that cause muscle weakness and joint contractures with significant variability in disease severity among patients. Here we report the clinical and genetic characteristics of 13 Chinese patients. Detailed histological, radiological and muscle transcriptomic evaluations were also conducted for selected representative patients. Across the cohort, fifteen putative disease causal variants were identified in three genes encoding collagen VI subunits, COL6A1 (n=6), COL6A2 (n=5), and COL6A3 (n=4). Most of these variants (12/15, 80%) were dominant negative and occurred at the triple helical domain. The rest (3/15, 20%) were located at the C-terminus. Two previously unreported variants, an in-frame mutation (COL6A1:c.1084_1092del) and a missense mutation (COL6A2:c.811G>C), were also noted. The transcriptome data from the muscle biopsies of two patients in the study with dominant negative mutations [COL6A2:c.811G>C and COL6A1:c.930+189C>T] supports the accepted aetiology of Collagen VI myopathy as dysfunction of the extracellular matrix. It also suggests there are perturbations to skeletal muscle differentiation and skeletal system development. It should be noted that although the phenotypes of patients can be mostly explained by the position and dominant-negative effect of the variants, exceptions and variability still exist and have to be reckoned with. This study provides valuable data explaining the varying severity of phenotypes among ethnically Chinese patients.
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Lee PC, Klaeger S, Le PM, Korthauer K, Cheng J, Ananthapadmanabhan V, Frost TC, Stevens JD, Wong AY, Iorgulescu JB, Tarren AY, Chea VA, Carulli IP, Lemvigh CK, Pedersen CB, Gartin AK, Sarkizova S, Wright KT, Li LW, Nomburg J, Li S, Huang T, Liu X, Pomerance L, Doherty LM, Apffel AM, Wallace LJ, Rachimi S, Felt KD, Wolff JO, Witten E, Zhang W, Neuberg D, Lane WJ, Zhang G, Olsen LR, Thakuria M, Rodig SJ, Clauser KR, Starrett GJ, Doench JG, Buhrlage SJ, Carr SA, DeCaprio JA, Wu CJ, Keskin DB. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma. J Clin Invest 2022; 132:e151666. [PMID: 35775490 PMCID: PMC9246387 DOI: 10.1172/jci151666] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
Cancers avoid immune surveillance through an array of mechanisms, including perturbation of HLA class I antigen presentation. Merkel cell carcinoma (MCC) is an aggressive, HLA-I-low, neuroendocrine carcinoma of the skin often caused by the Merkel cell polyomavirus (MCPyV). Through the characterization of 11 newly generated MCC patient-derived cell lines, we identified transcriptional suppression of several class I antigen presentation genes. To systematically identify regulators of HLA-I loss in MCC, we performed parallel, genome-scale, gain- and loss-of-function screens in a patient-derived MCPyV-positive cell line and identified MYCL and the non-canonical Polycomb repressive complex 1.1 (PRC1.1) as HLA-I repressors. We observed physical interaction of MYCL with the MCPyV small T viral antigen, supporting a mechanism of virally mediated HLA-I suppression. We further identify the PRC1.1 component USP7 as a pharmacologic target to restore HLA-I expression in MCC.
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Affiliation(s)
- Patrick C. Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Phuong M. Le
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jingwei Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Varsha Ananthapadmanabhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas C. Frost
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jonathan D. Stevens
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Alan Y.L. Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - J. Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Anna Y. Tarren
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Vipheaviny A. Chea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Isabel P. Carulli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Camilla K. Lemvigh
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Christina B. Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ashley K. Gartin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kyle T. Wright
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Letitia W. Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jason Nomburg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Teddy Huang
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology
| | - Lucas Pomerance
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, and
| | - Laura M. Doherty
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Annie M. Apffel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Luke J. Wallace
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Suzanna Rachimi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - William J. Lane
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Guanglan Zhang
- Department of Computer Science, Metropolitan College, Boston University, Boston, Massachusetts, USA
| | - Lars R. Olsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Manisha Thakuria
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Merkel Cell Carcinoma Center of Excellence, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts, USA
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Center for Immuno-Oncology and
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gabriel J. Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sara J. Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - James A. DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
- Merkel Cell Carcinoma Center of Excellence, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Computer Science, Metropolitan College, Boston University, Boston, Massachusetts, USA
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4
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Jiménez‐Mallebrera C. The importance of verifying the novelty of a finding and the value of combining results. Ann Clin Transl Neurol 2022; 9:893-894. [PMID: 35655399 PMCID: PMC9186143 DOI: 10.1002/acn3.51572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Affiliation(s)
- Cecilia Jiménez‐Mallebrera
- Neuromuscular Unit, Institut de Recerca Sant Joan dee DéuHospital Sant Joan de Déu BarcelonaBarcelonaSpain
- Department of GeneticsUniversity of BarcelonaBarcelonaSpain
- CIBERERSpanish Biomedical Research NetworkMonforte de Lemos, MadridSpain
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5
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Bateman JF, Shoulders MD, Lamandé SR. Collagen misfolding mutations: the contribution of the unfolded protein response to the molecular pathology. Connect Tissue Res 2022; 63:210-227. [PMID: 35225118 PMCID: PMC8977234 DOI: 10.1080/03008207.2022.2036735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mutations in collagen genes cause a broad range of connective tissue pathologies. Structural mutations that impact procollagen assembly or triple helix formation and stability are a common and important mutation class. How misfolded procollagens engage with the cellular proteostasis machinery and whether they can elicit a cytotoxic unfolded protein response (UPR) is a topic of considerable research interest. Such interest is well justified since modulating the UPR could offer a new approach to treat collagenopathies for which there are no current disease mechanism-targeting therapies. This review scrutinizes the evidence underpinning the view that endoplasmic reticulum stress and chronic UPR activation contributes significantly to the pathophysiology of the collagenopathies. While there is strong evidence that the UPR contributes to the pathology for collagen X misfolding mutations, the evidence that misfolding mutations in other collagen types induce a canonical, cytotoxic UPR is incomplete. To gain a more comprehensive understanding about how the UPR amplifies to pathology, and thus what types of manipulations of the UPR might have therapeutic relevance, much more information is needed about how specific misfolding mutation types engage differentially with the UPR and downstream signaling responses. Most importantly, since the capacity of the proteostasis machinery to respond to collagen misfolding is likely to vary between cell types, reflecting their functional roles in collagen and extracellular matrix biosynthesis, detailed studies on the UPR should focus as much as possible on the actual target cells involved in the collagen pathologies.
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Affiliation(s)
- John F. Bateman
- Murdoch Children’s Research Institute, Australia,Department of Paediatrics, University of Melbourne, Australia
| | | | - Shireen R. Lamandé
- Murdoch Children’s Research Institute, Australia,Department of Paediatrics, University of Melbourne, Australia
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6
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Ramesova A, Vesela B, Svandova E, Lesot H, Matalova E. Caspase-9 inhibition decreases expression of Mmp9 during chondrogenesis. Histochem Cell Biol 2022; 157:403-413. [PMID: 34999953 DOI: 10.1007/s00418-021-02067-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 01/03/2023]
Abstract
Besides cell death, caspase-9 participates in non-apoptotic events, including cell differentiation. To evaluate a possible impact on the expression of chondrogenic/osteogenic factors, a caspase-9 inhibitor was tested in vitro. For this purpose, mouse forelimb-derived micromass cultures, the most common chondrogenic in vitro model, were used. The following analyses were performed based on polymerase chain reaction (PCR) arrays and real-time PCR. The expression of several chondrogenesis-related genes was shown to be altered, some of which may impact chondrogenic differentiation (Bmp4, Bmp7, Sp7, Gli1), mineral deposition (Alp, Itgam) or the remodelling of the extracellular matrix (Col1a2, Mmp9) related to endochondral ossification. From the cluster of genes with altered expression, Mmp9 showed the most significant decrease in expression, of more than 50-fold. Additionally, we determined the possible impact of caspase-9 downregulation on the expression of other Mmp genes. A mild increase in Mmp14 was observed, but there was no change in the expression of other studied Mmp genes (-2, -3, -8, -10, -12, -13). Interestingly, inhibition of Mmp9 in micromasses led to decreased expression of some chondrogenic markers related to caspase-9. These samples also showed a decreased expression of caspase-9 itself, suggesting a bidirectional regulation of these two enzymes. These results indicate a specific impact of caspase-9 inhibition on the expression of Mmp9. The localisation of these two enzymes overlaps in resting, proliferative and pre-hypertrophic chondrocytes during in vivo development, which supports their multiple functions, either apoptotic or non-apoptotic. Notably, a coincidental expression pattern was identified in Pik3cg, a possible candidate for Mmp9 regulation.
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Affiliation(s)
- A Ramesova
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic.,Department of Physiology, Faculty of Veterinary Medicine, Veterinary University, Brno, Czech Republic
| | - B Vesela
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic.,Department of Physiology, Faculty of Veterinary Medicine, Veterinary University, Brno, Czech Republic
| | - E Svandova
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic. .,Department of Physiology, Faculty of Veterinary Medicine, Veterinary University, Brno, Czech Republic.
| | - H Lesot
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - E Matalova
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic.,Department of Physiology, Faculty of Veterinary Medicine, Veterinary University, Brno, Czech Republic
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7
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Guadagnin E, Mohassel P, Johnson KR, Yang L, Santi M, Uapinyoying P, Dastgir J, Hu Y, Dillmann A, Cookson MR, Foley AR, Bönnemann CG. Transcriptome analysis of collagen VI-related muscular dystrophy muscle biopsies. Ann Clin Transl Neurol 2021; 8:2184-2198. [PMID: 34729958 PMCID: PMC8607456 DOI: 10.1002/acn3.51450] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/04/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
Objective To define the transcriptomic changes responsible for the histologic alterations in skeletal muscle and their progression in collagen VI‐related muscular dystrophy (COL6‐RD). Methods COL6‐RD patient muscle biopsies were stratified into three groups based on the overall level of pathologic severity considering degrees of fibrosis, muscle fiber atrophy, and fatty replacement of muscle tissue. Using microarray and RNA‐Seq, we then performed global gene expression profiling on the same muscle biopsies and compared their transcriptome with age‐ and sex‐matched controls. Results COL6‐RD muscle biopsy transcriptomes as a group revealed prominent upregulation of muscle extracellular matrix component genes and the downregulation of skeletal muscle and mitochondrion‐specific genes. Upregulation of the TGFβ pathway was the most conspicuous change across all biopsies and was fully evident even in the mildest/earliest histological group. There was no difference in the overall transcriptional signature between the different histologic groups but polyserial analysis identified relative changes along with COL6‐RD histological severity. Interpretation Overall, our study establishes the prominent dysregulation of extracellular matrix genes, TGFβ signaling, and its downstream cellular pathways at the transcriptomic level in COL6‐RD muscle.
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Affiliation(s)
- Eleonora Guadagnin
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA
| | - Kory R Johnson
- Bioinformatics Section, Intramural Information Technology & Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Drive, BG 10 RM 5S223, Bethesda, Maryland, 20892, USA
| | - Lin Yang
- Division of Biomedical Informatics, Department of Biomedical Engineering, University of Florida, 1064 Center Drive, NEB 364, Gainsville, Florida, 32611, USA
| | - Mariarita Santi
- Department of Pathology, Children's Hospital of Philadelphia, 324 South 34th Street, Philadelphia, Pennsylvania, 19104, USA
| | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA.,Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, DC, 20010, USA
| | - Jahannaz Dastgir
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA.,Atlantic Health System, Goryeb Children's Hospital, Morristown, New Jersey, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA
| | - Allissa Dillmann
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, 35 Convent Drive, BG 35 RM 1A116, Bethesda, Maryland, 20892, USA
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, 35 Convent Drive, BG 35 RM 1A116, Bethesda, Maryland, 20892, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, BLDG 35 RM 2A116, Bethesda, Maryland, 20892, USA
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8
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Wang P, Teng Z, Liu X, Liu X, Kong C, Lu S. A new single nucleotide polymorphism affects the predisposition to thoracic ossification of the posterior longitudinal ligament. J Orthop Surg Res 2019; 14:438. [PMID: 31831033 PMCID: PMC6909598 DOI: 10.1186/s13018-019-1481-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/20/2019] [Indexed: 01/13/2023] Open
Abstract
Background Thoracic ossification of the posterior longitudinal ligament (T-OPLL) is one of the common factors that cause thoracic spinal stenosis, which results in intractable myelopathy and radiculopathy. Our previous study first reported rs201153092A site mutation in the collagen 6A1 (COL6A1) gene as a potentially pathogenic locus for T-OPLL. We aimed to determine whether the rs201153092A site mutation causes abnormal expression of the COL6A1 in Han Chinese patients with T-OPLL and whether this locus is also associated with cervical-OPLL. Methods Peripheral blood was collected from a total of 60 patients with T-OPLL disease (30 patients carrying the rs201153092A site mutation in COL6A1 and 30 wild-type patients) and 400 northern Chinese individuals (200 cervical-OPLL patients and 200 control subjects) using the Sequenom system. The expression of COL6A1 was analyzed by enzyme-linked immunosorbent assay, reverse transcription-quantitative polymerase chain reaction, and Western blotting. Results rs201153092A mutation resulted in markedly increased COL6A1 gene expression levels in peripheral blood samples. The allele frequency and genotype frequency results showed that this locus is no difference between cervical-OPLL patients and controls. Conclusions The rs201153092A site mutation of COL6A1 can significantly increase the expression of COL6A1. The COL6A1 gene rs201153092A site polymorphism is a potential pathogenic mutation in T-OPLL disease, which may be only associated with the occurrence of T-OPLL.
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Affiliation(s)
- Peng Wang
- Department of Orthopedics, Xuanwu Hospital of Capital Medical University, 45 Changchun Street, Xicheng, Beijing, 100053, People's Republic of China
| | - Ze Teng
- Department of Radiology, Cancer Hospital Chinese Academy of Medical Sciences, Beijing, 100021, People's Republic of China
| | - Xiaoguang Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Xiao Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Chao Kong
- Department of Orthopedics, Xuanwu Hospital of Capital Medical University, 45 Changchun Street, Xicheng, Beijing, 100053, People's Republic of China
| | - Shibao Lu
- Department of Orthopedics, Xuanwu Hospital of Capital Medical University, 45 Changchun Street, Xicheng, Beijing, 100053, People's Republic of China.
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9
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Dupont JB, Guo J, Renaud-Gabardos E, Poulard K, Latournerie V, Lawlor MW, Grange RW, Gray JT, Buj-Bello A, Childers MK, Mack DL. AAV-Mediated Gene Transfer Restores a Normal Muscle Transcriptome in a Canine Model of X-Linked Myotubular Myopathy. Mol Ther 2019; 28:382-393. [PMID: 31784415 DOI: 10.1016/j.ymthe.2019.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 09/13/2019] [Accepted: 10/31/2019] [Indexed: 12/27/2022] Open
Abstract
Multiple clinical trials employing recombinant adeno-associated viral (rAAV) vectors have been initiated for neuromuscular disorders, including Duchenne and limb-girdle muscular dystrophies, spinal muscular atrophy, and recently X-linked myotubular myopathy (XLMTM). Our previous work on a canine model of XLMTM showed that a single rAAV8-cMTM1 systemic infusion corrected structural abnormalities within the muscle and restored contractile function, with affected dogs surviving more than 4 years post injection. This remarkable therapeutic efficacy presents a unique opportunity to identify the downstream molecular drivers of XLMTM pathology and to what extent the whole muscle transcriptome is restored to normal after gene transfer. Herein, RNA-sequencing was used to examine the transcriptomes of the Biceps femoris and Vastus lateralis in a previously described canine cohort that showed dose-dependent clinical improvements after rAAV8-cMTM1 gene transfer. Our analysis confirmed several dysregulated genes previously observed in XLMTM mice but also identified transcripts linked to XLMTM pathology. We demonstrated XLMTM transcriptome remodeling and dose-dependent normalization of gene expression after gene transfer and created metrics to pinpoint potential biomarkers of disease progression and correction.
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Affiliation(s)
- Jean-Baptiste Dupont
- Department of Rehabilitation Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jianjun Guo
- Audentes Therapeutics, San Francisco, CA 94108, USA
| | - Edith Renaud-Gabardos
- Genethon, INSERM UMR S951, Université Evry Val-d'Essone, Université Paris-Saclay, 91000 Evry, France
| | - Karine Poulard
- Genethon, INSERM UMR S951, Université Evry Val-d'Essone, Université Paris-Saclay, 91000 Evry, France
| | - Virginie Latournerie
- Genethon, INSERM UMR S951, Université Evry Val-d'Essone, Université Paris-Saclay, 91000 Evry, France
| | - Michael W Lawlor
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Robert W Grange
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - John T Gray
- Audentes Therapeutics, San Francisco, CA 94108, USA
| | - Ana Buj-Bello
- Genethon, INSERM UMR S951, Université Evry Val-d'Essone, Université Paris-Saclay, 91000 Evry, France
| | - Martin K Childers
- Department of Rehabilitation Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - David L Mack
- Department of Rehabilitation Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98109, USA.
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10
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Camilleri M, Sandler RS, Peery AF. Etiopathogenetic Mechanisms in Diverticular Disease of the Colon. Cell Mol Gastroenterol Hepatol 2019; 9:15-32. [PMID: 31351939 PMCID: PMC6881605 DOI: 10.1016/j.jcmgh.2019.07.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 02/08/2023]
Abstract
This article reviews epidemiological evidence of heritability and putative mechanisms in diverticular disease, with greatest attention to 3 recent studies of genetic associations with diverticular disease based on genome-wide or whole-genome sequencing studies in large patient cohorts. We provide an analysis of the biological plausibility of the significant associations with gene variants reported and highlight the relevance of ANO1, CPI-17 (aka PPP1R14A), COLQ6, COL6A1, CALCB or CALCA, COL6A1, ARHGAP15, and S100A10 to colonic neuromuscular function and tissue properties that may result in altered compliance and predispose to the development of diverticular disease. Such studies also identify candidate genes for future studies.
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Affiliation(s)
- Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Anne F Peery
- Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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11
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Lim PJ, Lindert U, Opitz L, Hausser I, Rohrbach M, Giunta C. Transcriptome Profiling of Primary Skin Fibroblasts Reveal Distinct Molecular Features Between PLOD1- and FKBP14-Kyphoscoliotic Ehlers-Danlos Syndrome. Genes (Basel) 2019; 10:E517. [PMID: 31288483 PMCID: PMC6678841 DOI: 10.3390/genes10070517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/03/2022] Open
Abstract
Kyphoscoliotic Ehlers-Danlos Syndrome (kEDS) is a rare genetic heterogeneous disease clinically characterized by congenital muscle hypotonia, kyphoscoliosis, and joint hypermobility. kEDS is caused by biallelic pathogenic variants in either PLOD1 or FKBP14. PLOD1 encodes the lysyl hydroxylase 1 enzyme responsible for hydroxylating lysyl residues in the collagen helix, which undergo glycosylation and form crosslinks in the extracellular matrix thus contributing to collagen fibril strength. FKBP14 encodes a peptidyl-prolyl cis-trans isomerase that catalyzes collagen folding and acts as a chaperone for types III, VI, and X collagen. Despite genetic heterogeneity, affected patients with mutations in either PLOD1 or FKBP14 are clinically indistinguishable. We aim to better understand the pathomechanism of kEDS to characterize distinguishing and overlapping molecular features underlying PLOD1-kEDS and FKBP14-kEDS, and to identify novel molecular targets that may expand treatment strategies. Transcriptome profiling by RNA sequencing of patient-derived skin fibroblasts revealed differential expression of genes encoding extracellular matrix components that are unique between PLOD1-kEDS and FKBP14-kEDS. Furthermore, we identified genes involved in inner ear development, vascular remodeling, endoplasmic reticulum (ER) stress, and protein trafficking that were differentially expressed in patient fibroblasts compared to controls. Overall, our study presents the first transcriptomics data in kEDS revealing distinct molecular features between PLOD1-kEDS and FKBP14-kEDS, and serves as a tool to better understand the disease.
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Affiliation(s)
- Pei Jin Lim
- Connective Tissue Unit, Division of Metabolism and Children's Research Centre, University Children's Hospital, 8032 Zürich, Switzerland
| | - Uschi Lindert
- Connective Tissue Unit, Division of Metabolism and Children's Research Centre, University Children's Hospital, 8032 Zürich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ingrid Hausser
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marianne Rohrbach
- Connective Tissue Unit, Division of Metabolism and Children's Research Centre, University Children's Hospital, 8032 Zürich, Switzerland.
| | - Cecilia Giunta
- Connective Tissue Unit, Division of Metabolism and Children's Research Centre, University Children's Hospital, 8032 Zürich, Switzerland.
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12
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Delbaere S, Dhooge T, Syx D, Petit F, Goemans N, Destrée A, Vanakker O, De Rycke R, Symoens S, Malfait F. Novel defects in collagen XII and VI expand the mixed myopathy/Ehlers-Danlos syndrome spectrum and lead to variant-specific alterations in the extracellular matrix. Genet Med 2019; 22:112-123. [PMID: 31273343 DOI: 10.1038/s41436-019-0599-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/19/2019] [Indexed: 12/26/2022] Open
Abstract
PURPOSE To date, heterozygous or homozygous COL12A1 variants have been reported in 13 patients presenting with a clinical phenotype overlapping with collagen VI-related myopathies and Ehlers-Danlos syndrome (EDS). The small number of reported patients limits thorough investigation of this newly identified syndrome, currently coined as myopathic EDS. METHODS DNA from 78 genetically unresolved patients fulfilling the clinical criteria for myopathic EDS was sequenced using a next-generation panel of COL12A1, COL6A1, COL6A2, and COL6A3. RESULTS Among this cohort, we identified four pathogenic heterozygous in-frame exon skipping (∆) defects in COL12A1, clustering to the thrombospondin N-terminal region and the adjacent collagenous domain (Δ52, Δ53, Δ54, and Δ56 respectively), one heterozygous COL12A1 arginine-to-cysteine substitution of unclear significance (p.(Arg1863Cys)), and compound heterozygous pathogenic COL6A1 variants (c.[98-6G>A];[301C>T]) in one proband. Variant-specific intracellular accumulation of collagen XII chains, extracellular overmodification of the long isoform and near-absence of the short isoform of collagen XII, and extracellular decrease of decorin and tenascin-X were observed for the COL12A1 variants. In contrast, the COL6A1 variants abolished collagen VI and V deposition and increased tenascin-X levels. CONCLUSION Our data further support the significant clinical overlap between myopathic EDS and collagen VI-related myopathies, and emphasize the variant-specific consequences of collagen XII defects.
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Affiliation(s)
- Sarah Delbaere
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Tibbe Dhooge
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Delfien Syx
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Florence Petit
- Department of Clinical Genetics, CHU Lille, Université Lille, Lille, France
| | - Nathalie Goemans
- Department of Child Neurology, University Hospital Leuven, Leuven, Belgium.,Department of Development and Regeneration, University of Leuven, Leuven, Belgium
| | - Anne Destrée
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Olivier Vanakker
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology and Expertise Centre for Transmission Electron Microscopy, Ghent University, Ghent, Belgium.,Center for Inflammation Research and BioImaging Core, VIB, Ghent, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Fransiska Malfait
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.
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13
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Gonorazky HD, Naumenko S, Ramani AK, Nelakuditi V, Mashouri P, Wang P, Kao D, Ohri K, Viththiyapaskaran S, Tarnopolsky MA, Mathews KD, Moore SA, Osorio AN, Villanova D, Kemaladewi DU, Cohn RD, Brudno M, Dowling JJ. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. Am J Hum Genet 2019; 104:466-483. [PMID: 30827497 PMCID: PMC6407525 DOI: 10.1016/j.ajhg.2019.01.012] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Gene-panel and whole-exome analyses are now standard methodologies for mutation detection in Mendelian disease. However, the diagnostic yield achieved is at best 50%, leaving the genetic basis for disease unsolved in many individuals. New approaches are thus needed to narrow the diagnostic gap. Whole-genome sequencing is one potential strategy, but it currently has variant-interpretation challenges, particularly for non-coding changes. In this study we focus on transcriptome analysis, specifically total RNA sequencing (RNA-seq), by using monogenetic neuromuscular disorders as proof of principle. We examined a cohort of 25 exome and/or panel "negative" cases and provided genetic resolution in 36% (9/25). Causative mutations were identified in coding and non-coding exons, as well as in intronic regions, and the mutational pathomechanisms included transcriptional repression, exon skipping, and intron inclusion. We address a key barrier of transcriptome-based diagnostics: the need for source material with disease-representative expression patterns. We establish that blood-based RNA-seq is not adequate for neuromuscular diagnostics, whereas myotubes generated by transdifferentiation from an individual's fibroblasts accurately reflect the muscle transcriptome and faithfully reveal disease-causing mutations. Our work confirms that RNA-seq can greatly improve diagnostic yield in genetically unresolved cases of Mendelian disease, defines strengths and challenges of the technology, and demonstrates the suitability of cell models for RNA-based diagnostics. Our data set the stage for development of RNA-seq as a powerful clinical diagnostic tool that can be applied to the large population of individuals with undiagnosed, rare diseases and provide a framework for establishing minimally invasive strategies for doing so.
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Affiliation(s)
- Hernan D Gonorazky
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergey Naumenko
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Viswateja Nelakuditi
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Pouria Mashouri
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peiqui Wang
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dennis Kao
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Krish Ohri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Katherine D Mathews
- Departments of Pediatrics and Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Andres N Osorio
- Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Hospital Universitari Sant Joan de Deu, Barcelona 08950, Spain; Center for the Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona 08950, Spain
| | - David Villanova
- GenomicTales Parc de la Mola, 10, AD700 Escaldes-Engordany, Andorra
| | - Dwi U Kemaladewi
- Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Michael Brudno
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G 0A4, Canada.
| | - James J Dowling
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
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