1
|
Wang S, Yue Y, Wang X, Tan Y, Zhang Q. SCARF2 is a target for chronic obstructive pulmonary disease: Evidence from multi-omics research and cohort validation. Aging Cell 2024:e14266. [PMID: 38958042 DOI: 10.1111/acel.14266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
Age-related chronic inflammatory lung diseases impose a threat on public health, including idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). However, their etiology and potential targets have not been clarified. We performed genome-wide meta-analysis for IPF with the largest sample size (2883 cases and 741,929 controls) and leveraged the summary statistics of COPD (17,547 cases and 617,598 controls). Transcriptome-wide and proteome-wide Mendelian randomization (MR) designs, together with genetic colocalization, were implemented to find robust targets. The mediation effect was assessed using leukocyte telomere length (LTL). The single-cell transcriptome analysis was performed to link targets with cell types. Individual-level data from UK Biobank (UKB) were used to validate our findings. Sixteen genetically predicted plasma proteins were causally associated with the risk of IPF and 6 proteins were causally associated with COPD. Therein, genetically-elevated plasma level of SCARF2 protein should reduce the risk of both IPF (odds ratio, OR = 0.9974 [0.9970, 0.9978]) and COPD (OR = 0.7431 [0.6253, 0.8831]) and such effects were not mediated by LTL. Genetic colocalization further corroborated these MR results of SCARF2. The transcriptome-wide MR confirmed that higher expression level of SCARF2 was associated with a reduced risk of both. However, the single-cell RNA analysis indicated that SCARF2 expression level was only relatively lower in epithelial cells of COPD lung tissue compared to normal lung tissue. UKB data implicated an inverse association of serum SCARF2 protein with COPD (hazard ratio, HR = 1.215 [1.106, 1.335]). The SCARF2 gene should be a novel target for COP.
Collapse
Affiliation(s)
- Sai Wang
- Department of Otorhinolaryngology, The First Hospital of China Medical University, Shenyang, China
| | - Yuanyi Yue
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xueqing Wang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yue Tan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qiang Zhang
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| |
Collapse
|
2
|
Yuan H, Yang S, Han P, Sun M, Zhou C. Drug target genes and molecular mechanism investigation in isoflurane-induced anesthesia based on WGCNA and machine learning methods. Toxicol Mech Methods 2024; 34:319-333. [PMID: 38054380 DOI: 10.1080/15376516.2023.2286619] [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: 07/24/2023] [Accepted: 11/18/2023] [Indexed: 12/07/2023]
Abstract
PURPOSE This study sought to identify drug target genes and their associated molecular mechanisms during isoflurane-induced anesthesia in clinical applications. METHODS Microarray data (ID: GSE64617; isoflurane-treated vs. normal samples) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened and hub genes were investigated using weighted correlation network analysis (WGCNA). Protein-protein interactions (PPIs) were constructed among the co-DEGs (common genes between DEGs and hub genes), followed by functional enrichment analyses. Then, three machine learning methods were used to reveal drug targets, followed by validation, nomogram analysis, and gene set enrichment analysis. Finally, an miRNA-target network was constructed. RESULTS A total of 686 DEGs were identified between the two groups-of which, 183 DEGs integrated with genes revealed by WCGNA were identified as co-genes. These genes, including contactin-associated protein 1 (CNTNAP1), are mainly involved in functions such as action potentials. PPI network analysis revealed three models, with the machine learning analysis exploring four drug target genes: A2H, FAM155B, SCARF2, and SDR16C5. ROC and nomogram analyses demonstrated the ideal diagnostic value of these target genes. Finally, miRNA-mRNA pairs were constructed based on the four mRNAs and associated 174 miRNAs. CONCLUSION FA2H, FAM155B, SCARF2, and SDR16C5 may be novel drug target genes for isoflurane-induced anesthesia. CNTNAP1 may participate in the progression of isoflurane-induced anesthesia via its action potential function.
Collapse
Affiliation(s)
- Honglei Yuan
- Department of Anesthesiology, Taian City Central Hospital, Taian, Shandong, China
| | - Shengqiang Yang
- Department of Anesthesiology, Taian City Central Hospital, Taian, Shandong, China
| | - Peng Han
- Department of Anesthesiology, Taian City Central Hospital, Taian, Shandong, China
| | - Mingya Sun
- Taian City Taishan District Dai Temple Community Health Service Center, Taian, Shandong, China
| | - Chao Zhou
- Department of Anesthesiology, Taian City Central Hospital, Taian, Shandong, China
| |
Collapse
|
3
|
Vo TTT, Kong G, Kim C, Juang U, Gwon S, Jung W, Nguyen H, Kim SH, Park J. Exploring scavenger receptor class F member 2 and the importance of scavenger receptor family in prediagnostic diseases. Toxicol Res 2023; 39:341-353. [PMID: 37398563 PMCID: PMC10313632 DOI: 10.1007/s43188-023-00176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 07/04/2023] Open
Abstract
Scavenger Receptor Class F Member 2 (SCARF2), also known as the Type F Scavenger Receptor Family gene, encodes for Scavenger Receptor Expressed by Endothelial Cells 2 (SREC-II). This protein is a crucial component of the scavenger receptor family and is vital in protecting mammals from infectious diseases. Although research on SCARF2 is limited, mutations in this protein have been shown to cause skeletal abnormalities in both SCARF2-deficient mice and individuals with Van den Ende-Gupta syndrome (VDEGS), which is also associated with SCARF2 mutations. In contrast, other scavenger receptors have demonstrated versatile responses and have been found to aid in pathogen elimination, lipid transportation, intracellular cargo transportation, and work in tandem with various coreceptors. This review will concentrate on recent progress in comprehending SCARF2 and the functions played by members of the Scavenger Receptor Family in pre-diagnostic diseases.
Collapse
Affiliation(s)
- Thuy-Trang T. Vo
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Gyeyeong Kong
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Chaeyeong Kim
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Uijin Juang
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Suhwan Gwon
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Woohyeong Jung
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Huonggiang Nguyen
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Seon-Hwan Kim
- Department of Neurosurgery, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| | - Jongsun Park
- Department of Pharmacology, College of Medicine, Chungnam National University, 266 Munhwa-ro, Jung-gu, Daejeon, 35015 Republic of Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, 35015 Republic of Korea
| |
Collapse
|
4
|
Óskarsdóttir S, Boot E, Crowley TB, Loo JCY, Arganbright JM, Armando M, Baylis AL, Breetvelt EJ, Castelein RM, Chadehumbe M, Cielo CM, de Reuver S, Eliez S, Fiksinski AM, Forbes BJ, Gallagher E, Hopkins SE, Jackson OA, Levitz-Katz L, Klingberg G, Lambert MP, Marino B, Mascarenhas MR, Moldenhauer J, Moss EM, Nowakowska BA, Orchanian-Cheff A, Putotto C, Repetto GM, Schindewolf E, Schneider M, Solot CB, Sullivan KE, Swillen A, Unolt M, Van Batavia JP, Vingerhoets C, Vorstman J, Bassett AS, McDonald-McGinn DM. Updated clinical practice recommendations for managing children with 22q11.2 deletion syndrome. Genet Med 2023; 25:100338. [PMID: 36729053 DOI: 10.1016/j.gim.2022.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/03/2023] Open
Abstract
This review aimed to update the clinical practice guidelines for managing children and adolescents with 22q11.2 deletion syndrome (22q11.2DS). The 22q11.2 Society, the international scientific organization studying chromosome 22q11.2 differences and related conditions, recruited expert clinicians worldwide to revise the original 2011 pediatric clinical practice guidelines in a stepwise process: (1) a systematic literature search (1992-2021), (2) study selection and data extraction by clinical experts from 9 different countries, covering 24 subspecialties, and (3) creation of a draft consensus document based on the literature and expert opinion, which was further shaped by survey results from family support organizations regarding perceived needs. Of 2441 22q11.2DS-relevant publications initially identified, 2344 received full-text reviews, including 1545 meeting criteria for potential relevance to clinical care of children and adolescents. Informed by the available literature, recommendations were formulated. Given evidence base limitations, multidisciplinary recommendations represent consensus statements of good practice for this evolving field. These recommendations provide contemporary guidance for evaluation, surveillance, and management of the many 22q11.2DS-associated physical, cognitive, behavioral, and psychiatric morbidities while addressing important genetic counseling and psychosocial issues.
Collapse
Affiliation(s)
- Sólveig Óskarsdóttir
- Department of Pediatric Rheumatology and Immunology, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Erik Boot
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands.
| | - Terrence Blaine Crowley
- The 22q and You Center, Clinical Genetics Center, and Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Joanne C Y Loo
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
| | - Jill M Arganbright
- Department of Otorhinolaryngology, Children's Mercy Hospital and University of Missouri Kansas City School of Medicine, Kansas City, MO
| | - Marco Armando
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Adriane L Baylis
- Department of Plastic and Reconstructive Surgery, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH
| | - Elemi J Breetvelt
- Department of Psychiatry, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Genetics & Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - René M Castelein
- Department of Orthopedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Madeline Chadehumbe
- Division of Neurology, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Christopher M Cielo
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Pulmonary and Sleep Medicine, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Steven de Reuver
- Department of Orthopedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stephan Eliez
- Fondation Pôle Autisme, Department of Psychiatry, Geneva University School of Medecine, Geneva, Switzerland
| | - Ania M Fiksinski
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands; Department of Pediatric Psychology, University Medical Centre, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Brian J Forbes
- Division of Ophthalmology, The 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Emily Gallagher
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle Children's Hospital, Seattle, WA
| | - Sarah E Hopkins
- Division of Neurology, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Oksana A Jackson
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Cleft Lip and Palate Program, Division of Plastic, Reconstructive and Oral Surgery, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lorraine Levitz-Katz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Endocrinology and Diabetes, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Michele P Lambert
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Hematology, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bruno Marino
- Pediatric Cardiology Unit, Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Maria R Mascarenhas
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Gastroenterology, Hepatology and Nutrition, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Julie Moldenhauer
- Richard D. Wood Jr. Center for Fetal Diagnosis and Treatment, 22q and You Center, The Children's Hospital of Philadelphia, Philadelphia, PA; Departments of Obstetrics and Gynecology and Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | | | - Ani Orchanian-Cheff
- Library and Information Services and The Institute of Education Research (TIER), University Health Network, Toronto, Ontario, Canada
| | - Carolina Putotto
- Pediatric Cardiology Unit, Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Gabriela M Repetto
- Rare Diseases Program, Institute for Sciences and Innovation in Medicine, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Erica Schindewolf
- Richard D. Wood Jr. Center for Fetal Diagnosis and Treatment, 22q and You Center, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maude Schneider
- Clinical Psychology Unit for Intellectual and Developmental Disabilities, Faculty of Psychology and Educational Sciences, University of Geneva, Geneva, Switzerland
| | - Cynthia B Solot
- Department of Speech-Language Pathology and Center for Childhood Communication, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kathleen E Sullivan
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Allergy and Immunology, 22q and You Center, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ann Swillen
- Center for Human Genetics, University Hospital UZ Leuven, and Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marta Unolt
- Pediatric Cardiology Unit, Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy; Department of Pediatric Cardiology and Cardiac Surgery, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Jason P Van Batavia
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Urology, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Claudia Vingerhoets
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands; Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Jacob Vorstman
- Department of Psychiatry, Hospital for Sick Children, Toronto, Ontario, Canada; Genetics & Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anne S Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Genetics & Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.
| | - Donna M McDonald-McGinn
- The 22q and You Center, Clinical Genetics Center, and Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Department of Human Biology and Medical Genetics, Sapienza University, Rome, Italy.
| |
Collapse
|
5
|
Boot E, Óskarsdóttir S, Loo JCY, Crowley TB, Orchanian-Cheff A, Andrade DM, Arganbright JM, Castelein RM, Cserti-Gazdewich C, de Reuver S, Fiksinski AM, Klingberg G, Lang AE, Mascarenhas MR, Moss EM, Nowakowska BA, Oechslin E, Palmer L, Repetto GM, Reyes NGD, Schneider M, Silversides C, Sullivan KE, Swillen A, van Amelsvoort TAMJ, Van Batavia JP, Vingerhoets C, McDonald-McGinn DM, Bassett AS. Updated clinical practice recommendations for managing adults with 22q11.2 deletion syndrome. Genet Med 2023; 25:100344. [PMID: 36729052 DOI: 10.1016/j.gim.2022.11.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 02/03/2023] Open
Abstract
This review aimed to update the clinical practice guidelines for managing adults with 22q11.2 deletion syndrome (22q11.2DS). The 22q11.2 Society recruited expert clinicians worldwide to revise the original clinical practice guidelines for adults in a stepwise process according to best practices: (1) a systematic literature search (1992-2021), (2) study selection and synthesis by clinical experts from 8 countries, covering 24 subspecialties, and (3) formulation of consensus recommendations based on the literature and further shaped by patient advocate survey results. Of 2441 22q11.2DS-relevant publications initially identified, 2344 received full-text review, with 2318 meeting inclusion criteria (clinical care relevance to 22q11.2DS) including 894 with potential relevance to adults. The evidence base remains limited. Thus multidisciplinary recommendations represent statements of current best practice for this evolving field, informed by the available literature. These recommendations provide guidance for the recognition, evaluation, surveillance, and management of the many emerging and chronic 22q11.2DS-associated multisystem morbidities relevant to adults. The recommendations also address key genetic counseling and psychosocial considerations for the increasing numbers of adults with this complex condition.
Collapse
Affiliation(s)
- Erik Boot
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands; The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands.
| | - Sólveig Óskarsdóttir
- Department of Pediatric Rheumatology and Immunology, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Joanne C Y Loo
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Terrence Blaine Crowley
- 22q and You Center, Clinical Genetics Center, and Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ani Orchanian-Cheff
- Library and Information Services, and The Institute of Education Research (TIER), University Health Network, Toronto, Ontario, Canada
| | - Danielle M Andrade
- Adult Genetic Epilepsy Program, Toronto Western Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Jill M Arganbright
- Division of Otolaryngology, Children's Mercy Hospital and University of Missouri Kansas City School of Medicine, Kansas City, MO
| | - René M Castelein
- Department of Orthopedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Steven de Reuver
- Department of Orthopedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ania M Fiksinski
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands; Department of Pediatric Psychology, University Medical Centre, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | | | - Anthony E Lang
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Maria R Mascarenhas
- Division of Gastroenterology and 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA
| | | | | | - Erwin Oechslin
- Toronto Adult Congenital Heart Disease Program, Peter Munk Cardiac Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Lisa Palmer
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Gabriela M Repetto
- Rare Diseases Program, Institute for Sciences and Innovation in Medicine, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Nikolai Gil D Reyes
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Maude Schneider
- Clinical Psychology Unit for Intellectual and Developmental Disabilities, Faculty of Psychology and Educational Sciences, University of Geneva, Geneva, Switzerland
| | - Candice Silversides
- Toronto ACHD Program, Mount Sinai and Toronto General Hospitals, University of Toronto, Toronto, Ontario, Canada
| | - Kathleen E Sullivan
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA; Division of Allergy and Immunology and 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ann Swillen
- Center for Human Genetics, University Hospital UZ Leuven, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jason P Van Batavia
- Department of Surgery, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA; Division of Urology and 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Claudia Vingerhoets
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands; Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Donna M McDonald-McGinn
- 22q and You Center, Clinical Genetics Center, and Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA; Department of Human Biology and Medical Genetics, Sapienza University, Rome, Italy.
| | - Anne S Bassett
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Mental Health and Division of Cardiology, Department of Medicine, and Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.
| |
Collapse
|
6
|
Kaur B, Kaur J, Kashyap N, Arora JS, Mukhopadhyay CS. A comprehensive review of genomic perspectives of canine diseases as a model to study human disorders. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2023; 87:3-8. [PMID: 36606040 PMCID: PMC9808881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 01/07/2023]
Abstract
The domestic dog has been given considerable attention as a system for investigating the genetics of human diseases. Population diversity and breed structure are unique features that make dogs particularly amenable to genetic studies. Dogs show distinguished features of breed-specific homogeneity, which is associated with striking interbreed heterogeneity. This review discusses the significance of studying the genetic maps, genome-wide association studies (GWAS), and usefulness of this species as an animal model. Most canine genetic disorders are similar to those of humans, including inherited, psychiatric, and genetic disorders. In addition to revealing new candidate genes, canine models allow access to experimental resources, such as cells, tissues, and even live animals, for research and intervention purposes.
Collapse
|
7
|
Odeh O, Barqawi T, Rashid H, Almashhdi S, Shboul M. Identification of a novel variant of SCARF2 in a Jordanian family with a van den Ende-Gupta Syndrome and literature review. Clin Dysmorphol 2022; 31:157-161. [PMID: 35256560 DOI: 10.1097/mcd.0000000000000415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Osama Odeh
- Department of Medicine, Faculty of Medicine, The University of Jordan, Amman
| | - Tawfiq Barqawi
- Department of Medicine, Faculty of Medicine, The University of Jordan, Amman
| | - Hussein Rashid
- Department of Medicine, Faculty of Medicine, The University of Jordan, Amman
| | - Safa Almashhdi
- Department of Medicine, Faculty of Medicine, The University of Jordan, Amman
| | - Mohammad Shboul
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| |
Collapse
|
8
|
Construction of Copy Number Variation Map Identifies Small Regions of Overlap and Candidate Genes for Atypical Female Genitalia Development. REPRODUCTIVE MEDICINE 2022. [DOI: 10.3390/reprodmed3020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs) have been implicated in various conditions of differences of sexual development (DSD). Generally, larger genomic aberrations are more often considered disease-causing or clinically relevant, but over time, smaller CNVs have been associated with various forms of DSD. The main objective of this study is to identify small CNVs and the smallest regions of overlap (SROs) in patients with atypical female genitalia (AFG) and build a CNV map of AFG. We queried the DECIPHER database for recurrent duplications and/or deletions detected across the genome of AFG individuals. From these data, we constructed a chromosome map consisting of SROs and investigated such regions for genes that may be associated with the development of atypical female genitalia. Our study identified 180 unique SROs (7.95 kb to 45.34 Mb) distributed among 22 chromosomes. The most SROs were found in chromosomes X, 17, 11, and 22. None were found in chromosome 3. From these SROs, we identified 22 genes as potential candidates. Although none of these genes are currently associated with AFG, a literature review indicated that almost half were potentially involved in the development and/or function of the reproductive system, and only one gene was associated with a disorder that reported an individual patient with ambiguous genitalia. Our data regarding novel SROs requires further functional investigation to determine the role of the identified candidate genes in the development of atypical female genitalia, and this paper should serve as a catalyst for downstream molecular studies that may eventually affect the genetic counseling, diagnosis, and management of these DSD patients.
Collapse
|
9
|
Kim S, Mun S, Shin W, Han K, Kim MY. Identification of Potentially Pathogenic Variants Associated with Recurrence in Medication-Related Osteonecrosis of the Jaw (MRONJ) Patients Using Whole-Exome Sequencing. J Clin Med 2022; 11:jcm11082145. [PMID: 35456240 PMCID: PMC9030961 DOI: 10.3390/jcm11082145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Bisphosphonates are antiresorptive and antiangiogenic drugs that prevent and treat bone loss and mineralization in women with postmenopausal osteoporosis and cancer patients. Medication-related osteonecrosis of the jaw (MRONJ) is commonly caused by tooth extraction and dental trauma. Although genetic and pathological studies about MRONJ have been conducted, the pathogenesis of MRONJ still remains unclear. Methods: We aimed to identify genetic variants associated with MRONJ, using whole-exome sequencing (WES). Ten MRONJ patients prescribed bisphosphonates were recruited for WES, and jawbone tissue and blood samples were collected from the patients. Results: The analysis of the WES data found a total of 1866 SNP and 40 InDel variants which are specific to MRONJ. The functional classification assay using Gene Ontology and pathway analysis discovered that genes bearing the MRONJ variants are significantly enriched for keratinization and calcium ion transport. Some of the variants are potential pathogenic variants (24 missense mutations and seven frameshift mutations) with MAF < 0.01. Conclusions: The variants are located in eight different genes (KRT18, MUC5AC, NBPF9, PABPC3, MST1L, ASPN, ATN1, and SLAIN1). Nine deleterious SNPs significantly associated with MRONJ were found in the KRT18 and PABPC3 genes. It suggests that KRT18 and PABPC3 could be MRONJ-related key genes.
Collapse
Affiliation(s)
- Songmi Kim
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea (S.M.)
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
| | - Seyoung Mun
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea (S.M.)
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan 31116, Korea;
| | - Kyudong Han
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea (S.M.)
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
- Correspondence: (K.H.); (M.-Y.K.); Tel.: +82-41-550-1240 (K.H.); +82-41-550-1912 (M.-Y.K.)
| | - Moon-Young Kim
- Department of Oral and Maxillofacial Surgery, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Correspondence: (K.H.); (M.-Y.K.); Tel.: +82-41-550-1240 (K.H.); +82-41-550-1912 (M.-Y.K.)
| |
Collapse
|
10
|
Karaer D, Karaer K. Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome. Am J Med Genet A 2022; 188:1881-1884. [PMID: 35224863 DOI: 10.1002/ajmg.a.62707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2022]
Abstract
Van den Ende-Gupta syndrome (VDEGS) (MIM#600920) is characterized by skeletal and craniofacial abnormalities that include prominent ears, downslanting palpebral fissures, blepharophimosis, hypoplastic maxilla with or without a cleft palate, a narrow and convex nasal bridge and an everted lower lip, camptodactyly and arachnodactyly. Intelligence is normal. Recent studies have reported that patients with VDEGS have pathogenic variants in the SCARF2 gene on chromosome 22q11.21. Here, we report two Turkish patients with two novel variants [c.2291_2292insC (p.Ser765LeufsTer6) and c.488G>A (p.Cys63Tyr)] in the SCARF2 gene. In silico analysis predicted that both of these novel variants were pathogenic. To the best of our knowledge, this is the first case report of this syndrome in Turkey.
Collapse
Affiliation(s)
- Derya Karaer
- Faculty of Medicine, Department of Medical Genetic, Pamukkale University, Denizli, Turkey
| | - Kadri Karaer
- Faculty of Medicine, Department of Medical Genetic, Pamukkale University, Denizli, Turkey
| |
Collapse
|
11
|
Scavenger receptor class F member 2 (SCARF2) as a novel therapeutic target in glioblastoma. Toxicol Res 2022; 38:249-256. [PMID: 35419275 PMCID: PMC8960497 DOI: 10.1007/s43188-022-00125-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 10/19/2022] Open
Abstract
Scavenger receptor class F member 2 (SCARF2) is expressed by endothelial cells with very large cytoplasmic domains and is the second isotype, also known as scavenger receptor expressed by endothelial cells 2 (SREC-2). SREC-1 plays an important role in the binding and endocytosis of various endogenous and exogenous ligands. Many studies have been carried out on modified low-density lipoprotein internalization activity, but there have been few studies on SCARF2. Higher expression of SCARF2 has been found in glioblastoma (GBM) than normal brain tissue. Through analysis of The Cancer Genome Atlas database, it was confirmed that SCARF2 is widely expressed in GBM, and increased SCARF2 expression correlated with a poor prognosis in patients with glioma. The results of this study showed that the expression of SCARF2 is increased in GBM cell lines and patients, suggesting that SCARF2 may be a potential diagnostic marker and therapeutic molecule for cancers including glioma.
Collapse
|
12
|
Wicker-Planquart C, Tacnet-Delorme P, Preisser L, Dufour S, Delneste Y, Housset D, Frachet P, Thielens NM. Insights into the ligand binding specificity of SREC-II (scavenger receptor expressed by endothelial cells). FEBS Open Bio 2021; 11:2693-2704. [PMID: 34328698 PMCID: PMC8487046 DOI: 10.1002/2211-5463.13260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/24/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022] Open
Abstract
SREC-II (scavenger receptor expressed by endothelial cells-II) is a membrane protein encoded by the SCARF2 gene, with high homology to class F scavenger receptor SR-F1, but no known scavenging function. We produced the extracellular domain of SREC-II in a recombinant form and investigated its capacity to interact with common scavenger receptor ligands, including acetylated low density lipoprotein (AcLDL) and maleylated or acetylated BSA (MalBSA or AcBSA). Whereas no binding was observed for AcLDL, SREC-II ectodomain interacted strongly with MalBSA and bound with high affinity to AcBSA, a property shared with the SR-F1 ectodomain. SREC-II ectodomain also interacted with two SR-F1 specific ligands, complement C1q and calreticulin, with affinities in the 100 nM range. We proceeded to generate a stable CHO cell line overexpressing full-length SREC-II; binding of MalBSA to these cells was significantly increased compared to non-transfected CHO cells. In contrast, no increase in binding could be detected for C1q and calreticulin. We show for the first time that SREC-II has the capacity to interact with the common scavenger receptor ligand MalBSA. In addition, our data highlight similarities and differences in the ligand binding properties of SREC-II in soluble form and at the cell surface, and show that endogenous protein ligands of the ectodomain of SREC-II, such as C1q and calreticulin, are shared with the corresponding domain of SR-F1.
Collapse
Affiliation(s)
| | | | - Laurence Preisser
- Univ Angers, Université de Nantes, CHU Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France
| | - Samy Dufour
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Yves Delneste
- Univ Angers, Université de Nantes, CHU Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France
| | | | | | | |
Collapse
|
13
|
Hildebrandt CC, Patel N, Graham JM, Bamshad M, Nickerson DA, White JJ, Marvin CT, Miller DE, Grand KL, Sanchez-Lara PA, Schweitzer D, Al-Zaidan HI, Al Masseri Z, Alkuraya FS, Lin AE. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. Am J Med Genet A 2021; 185:2136-2149. [PMID: 33783941 DOI: 10.1002/ajmg.a.62194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/18/2021] [Accepted: 02/27/2021] [Indexed: 12/29/2022]
Abstract
Van den Ende-Gupta syndrome (VDEGS) is a rare autosomal recessive condition characterized by distinctive facial and skeletal features, and in most affected persons, by biallelic pathogenic variants in SCARF2. We review the type and frequency of the clinical features in 36 reported individuals with features of VDEGS, 15 (42%) of whom had known pathogenic variants in SCARF2, 6 (16%) with negative SCARF2 testing, and 15 (42%) not tested. We also report three new individuals with pathogenic variants in SCARF2 and clinical features of VDEGS. Of the six persons without known pathogenic variants in SCARF2, three remain unsolved despite extensive genetic testing. Three were found to have pathogenic ABL1 variants using whole exome sequencing (WES) or whole genome sequencing (WGS). Their phenotype was consistent with the congenital heart disease and skeletal malformations syndrome (CHDSKM), which has been associated with ABL1 variants. Of the three unsolved cases, two were brothers who underwent WGS and targeted long-range sequencing of both SCARF2 and ABL1, and the third person who underwent WES and RNA sequencing for SCARF2. Because these affected individuals with classical features of VDEGS lacked a detectable pathogenic SCARF2 variant, genetic heterogeneity is likely. Our study shows the importance of performing genetic testing on individuals with the VDEGS "phenotype," either as a targeted gene analysis (SCARF2, ABL1) or WES/WGS. Additionally, individuals with the combination of arachnodactyly and blepharophimosis should undergo echocardiography while awaiting results of molecular testing due to the overlapping physical features of VDEGS and CHDSKM.
Collapse
Affiliation(s)
- Clara C Hildebrandt
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA.,Boston Children's Hospital Medical Biochemical Fellowship, Boston, Massachusetts, USA
| | - Nisha Patel
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - John M Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | | | - Colby T Marvin
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Katheryn L Grand
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Daniela Schweitzer
- Division of Pediatric Genetics, Department of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Hamad I Al-Zaidan
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Zainab Al Masseri
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Angela E Lin
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA
| |
Collapse
|
14
|
Motahari Z, Moody SA, Maynard TM, LaMantia AS. In the line-up: deleted genes associated with DiGeorge/22q11.2 deletion syndrome: are they all suspects? J Neurodev Disord 2019; 11:7. [PMID: 31174463 PMCID: PMC6554986 DOI: 10.1186/s11689-019-9267-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND 22q11.2 deletion syndrome (22q11DS), a copy number variation (CNV) disorder, occurs in approximately 1:4000 live births due to a heterozygous microdeletion at position 11.2 (proximal) on the q arm of human chromosome 22 (hChr22) (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011). This disorder was known as DiGeorge syndrome, Velo-cardio-facial syndrome (VCFS) or conotruncal anomaly face syndrome (CTAF) based upon diagnostic cardiovascular, pharyngeal, and craniofacial anomalies (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011; Burn et al., J Med Genet 30:822-4, 1993) before this phenotypic spectrum was associated with 22q11.2 CNVs. Subsequently, 22q11.2 deletion emerged as a major genomic lesion associated with vulnerability for several clinically defined behavioral deficits common to a number of neurodevelopmental disorders (Fernandez et al., Principles of Developmental Genetics, 2015; Robin and Shprintzen, J Pediatr 147:90-6, 2005; Schneider et al., Am J Psychiatry 171:627-39, 2014). RESULTS The mechanistic relationships between heterozygously deleted 22q11.2 genes and 22q11DS phenotypes are still unknown. We assembled a comprehensive "line-up" of the 36 protein coding loci in the 1.5 Mb minimal critical deleted region on hChr22q11.2, plus 20 protein coding loci in the distal 1.5 Mb that defines the 3 Mb typical 22q11DS deletion. We categorized candidates based upon apparent primary cell biological functions. We analyzed 41 of these genes that encode known proteins to determine whether haploinsufficiency of any single 22q11.2 gene-a one gene to one phenotype correspondence due to heterozygous deletion restricted to that locus-versus complex multigenic interactions can account for single or multiple 22q11DS phenotypes. CONCLUSIONS Our 22q11.2 functional genomic assessment does not support current theories of single gene haploinsufficiency for one or all 22q11DS phenotypes. Shared molecular functions, convergence on fundamental cell biological processes, and related consequences of individual 22q11.2 genes point to a matrix of multigenic interactions due to diminished 22q11.2 gene dosage. These interactions target fundamental cellular mechanisms essential for development, maturation, or homeostasis at subsets of 22q11DS phenotypic sites.
Collapse
Affiliation(s)
- Zahra Motahari
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Sally Ann Moody
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Thomas Michael Maynard
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Anthony-Samuel LaMantia
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| |
Collapse
|
15
|
Al‐Dewik N, Al‐Mureikhi M, Shahbeck N, Ali R, Al‐Mesaifri F, Mahmoud L, Othman A, AlMulla M, Sulaiman RA, Musa S, Abdoh G, El‐Akouri K, Solomon BD, Ben‐Omran T. Clinical genetics and genomic medicine in Qatar. Mol Genet Genomic Med 2018; 6:702-712. [PMID: 30264509 PMCID: PMC6160705 DOI: 10.1002/mgg3.474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 01/16/2023] Open
Abstract
Clinical genetics and genomic medicine in Qatar.
Collapse
Affiliation(s)
- Nader Al‐Dewik
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Mariam Al‐Mureikhi
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Noora Shahbeck
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Rehab Ali
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Fatma Al‐Mesaifri
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Laila Mahmoud
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Amna Othman
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Mariam AlMulla
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Reem Al Sulaiman
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Sara Musa
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | - Ghassan Abdoh
- Department of PediatricsNewborn Screening UnitHamad Medical CorporationDohaQatar
| | - Karen El‐Akouri
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
| | | | - Tawfeg Ben‐Omran
- Section of Clinical and Metabolic GeneticsDepartment of PediatricsHamad Medical CorporationDohaQatar
- Weill Cornell Medical CollegeDohaQatar
- Sidra MedicineDohaQatar
| |
Collapse
|
16
|
Samsonraj RM, Paradise CR, Dudakovic A, Sen B, Nair AA, Dietz AB, Deyle DR, Cool SM, Rubin J, van Wijnen AJ. Validation of Osteogenic Properties of Cytochalasin D by High-Resolution RNA-Sequencing in Mesenchymal Stem Cells Derived from Bone Marrow and Adipose Tissues. Stem Cells Dev 2018; 27:1136-1145. [PMID: 29882479 DOI: 10.1089/scd.2018.0037] [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: 12/12/2022] Open
Abstract
Differentiation of mesenchymal stromal/stem cells (MSCs) involves a series of molecular signals and gene transcription events required for attaining cell lineage commitment. Modulation of the actin cytoskeleton using cytochalasin D (CytoD) drives osteogenesis at early timepoints in bone marrow-derived MSCs and also initiates a robust osteogenic differentiation program in adipose tissue-derived MSCs. To understand the molecular basis for these pronounced effects on osteogenic differentiation, we investigated global changes in gene expression in CytoD-treated murine and human MSCs by high-resolution RNA-sequencing (RNA-seq) analysis. A three-way bioinformatic comparison between human adipose tissue-derived MSCs (hAMSCs), human bone marrow-derived MSCs (hBMSCs), and mouse bone marrow-derived MSCs (mBMSCs) revealed significant upregulation of genes linked to extracellular matrix organization, cell adhesion and bone metabolism. As anticipated, the activation of these differentiation-related genes is accompanied by a downregulation of nuclear and cell cycle-related genes presumably reflecting cytostatic effects of CytoD. We also identified eight novel CytoD activated genes-VGLL4, ARHGAP24, KLHL24, RCBTB2, BDH2, SCARF2, ACAD10, HEPH-which are commonly upregulated across the two species and tissue sources of our MSC samples. We selected the Hippo pathway-related VGLL4 gene, which encodes the transcriptional co-factor Vestigial-like 4, for further study because this pathway is linked to osteogenesis. VGLL4 small interfering RNA depletion reduces mineralization of hAMSCs during CytoD-induced osteogenic differentiation. Together, our RNA-seq analyses suggest that while the stimulatory effects of CytoD on osteogenesis are pleiotropic and depend on the biological state of the cell type, a small group of genes including VGLL4 may contribute to MSC commitment toward the bone lineage.
Collapse
Affiliation(s)
| | - Christopher R Paradise
- 2 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences , Mayo Clinic, Rochester, Minnesota.,3 Center for Regenerative Medicine, Mayo Clinic , Rochester, Minnesota
| | - Amel Dudakovic
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota
| | - Buer Sen
- 4 Department of Medicine, University of North Carolina , Chapel Hill, North Carolina
| | - Asha A Nair
- 5 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
| | - Allan B Dietz
- 6 Laboratory Medicine and Pathology, Mayo Clinic , Rochester, Minnesota
| | - David R Deyle
- 7 Department of Medical Genetics, Mayo Clinic , Rochester, Minnesota
| | - Simon M Cool
- 8 Glycotherapeutics Group, Institute of Medical Biology , Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Janet Rubin
- 3 Center for Regenerative Medicine, Mayo Clinic , Rochester, Minnesota
| | - Andre J van Wijnen
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota.,3 Center for Regenerative Medicine, Mayo Clinic , Rochester, Minnesota
| |
Collapse
|
17
|
Schneider M, Al-Shareffi E, Haltiwanger RS. Biological functions of fucose in mammals. Glycobiology 2018; 27:601-618. [PMID: 28430973 DOI: 10.1093/glycob/cwx034] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022] Open
Abstract
Fucose is a 6-deoxy hexose in the l-configuration found in a large variety of different organisms. In mammals, fucose is incorporated into N-glycans, O-glycans and glycolipids by 13 fucosyltransferases, all of which utilize the nucleotide-charged form, GDP-fucose, to modify targets. Three of the fucosyltransferases, FUT8, FUT12/POFUT1 and FUT13/POFUT2, are essential for proper development in mice. Fucose modifications have also been implicated in many other biological functions including immunity and cancer. Congenital mutations of a Golgi apparatus localized GDP-fucose transporter causes leukocyte adhesion deficiency type II, which results in severe developmental and immune deficiencies, highlighting the important role fucose plays in these processes. Additionally, changes in levels of fucosylated proteins have proven as useful tools for determining cancer diagnosis and prognosis. Chemically modified fucose analogs can be used to alter many of these fucose dependent processes or as tools to better understand them. In this review, we summarize the known roles of fucose in mammalian physiology and pathophysiology. Additionally, we discuss recent therapeutic advances for cancer and other diseases that are a direct result of our improved understanding of the role that fucose plays in these systems.
Collapse
Affiliation(s)
- Michael Schneider
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Esam Al-Shareffi
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA.,Department of Psychiatry, Georgetown University Hospital, Washington, DC 20007, USA
| | - Robert S Haltiwanger
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
18
|
Al-Qattan MM, Andejani DF, Sakati NA, Ramzan K, Imtiaz F. Inclusion of joint laxity, recurrent patellar dislocation, and short distal ulnae as a feature of Van Den Ende-Gupta syndrome: a case report. BMC MEDICAL GENETICS 2018; 19:18. [PMID: 29378527 PMCID: PMC5789735 DOI: 10.1186/s12881-018-0531-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/24/2018] [Indexed: 11/24/2022]
Abstract
Background Van Den Ende-Gupta Syndrome (VDEGS) is an extremely rare autosomal recessive syndrome with less than 20 reported families (approximately 40 patients) in the worldwide literature. Case presentation We have assessed one consanguineous Saudi family with typical features of VDEGS. Two siblings were affected with almost identical features; including blepharophimosis, arachnodactyly, flexion contractures of the elbows, camptodactyly, slender ribs, hooked lateral clavicular ends, and bilateral radial head dislocations. Both patients had several unusual features; including joint laxity, flat feet, recurrent patellar dislocations, and bilateral short distal ulnae. Full sequencing of SCARF2 revealed a homozygous mutation c.773G > A (p. Cys258Tyr) in both affected children. The parents (both with no abnormalities) were heterozygous for the same mutation. Conclusion Joint laxity, recurrent patellar dislocations, and short distal ulnae should be included as part of the clinical spectrum of VDEGS.
Collapse
Affiliation(s)
- Mohammad M Al-Qattan
- Department of Surgery, King Saud University, PO Box 18097, Riyadh, 11415, Saudi Arabia. .,King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. .,National Hospital, Riyadh, Saudi Arabia.
| | - Doaa F Andejani
- The Saudi Plastic Surgery program, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Nadia A Sakati
- Department of Pediatrics, King Faisal Specialist Hospital& Research Center, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| |
Collapse
|
19
|
Maisenbacher MK, Merrion K, Pettersen B, Young M, Paik K, Iyengar S, Kareht S, Sigurjonsson S, Demko ZP, Martin KA. Incidence of the 22q11.2 deletion in a large cohort of miscarriage samples. Mol Cytogenet 2017; 10:6. [PMID: 28293297 PMCID: PMC5345148 DOI: 10.1186/s13039-017-0308-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/22/2017] [Indexed: 03/16/2023] Open
Abstract
Background The 22q11.2 deletion syndrome is the most common microdeletion syndrome in livebirths, but data regarding its incidence in other populations is limited and also include ascertainment bias. This study was designed to determine the incidence of the 22q11.2 deletion in miscarriage samples sent for clinical molecular cytogenetic testing. Results Twenty-six thousand one hundred one fresh product of conception (POC) samples were sent to a CLIA- certified, CAP-accredited laboratory from April 2010–-May 2016 for molecular cytogenetic miscarriage testing using a single-nucleotide polymorphism (SNP)-based microarray platform. A retrospective review determined the incidence of the 22q11.2 deletion in this sample set. Fetal results were obtained in 22,451 (86%) cases, of which, 15 (0.07%) had a microdeletion in the 22q11.2 region (incidence, 1/1497). Of those, 12 (80%) cases were found in samples that were normal at the resolution of traditional karyotyping (i.e., had no chromosome abnormalities above 10 Mb in size) and three (20%) cases had additional findings (Trisomy 15, Trisomy 16, XXY). Ten (67%) cases with a 22q11.2 deletion had the common ~3 Mb deletion; the remaining 5 cases had deletions ranging in size from 0.65 to 1.5 Mb. A majority (12/15) of cases had a deletion on the maternally inherited chromosome. No significant relationship between maternal age and presence of a fetal 22q11.2 deletion was observed. Conclusions The observed incidence of 1/1497 for the 22q11.2 deletion in miscarriage samples is higher than the reported general population prevalence (1/4000–1/6000). Further research is needed to determine whether the 22q11.2 deletion is a causal factor for miscarriage.
Collapse
Affiliation(s)
| | | | | | - Michael Young
- Natera, Inc., 201 Industrial Road, San Carlos, 94070 CA USA
| | - Kiyoung Paik
- Natera, Inc., 201 Industrial Road, San Carlos, 94070 CA USA
| | - Sushma Iyengar
- Natera, Inc., 201 Industrial Road, San Carlos, 94070 CA USA
| | | | | | | | | |
Collapse
|
20
|
Hytönen MK, Lohi H. Canine models of human rare disorders. Rare Dis 2016; 4:e1241362. [PMID: 27803843 PMCID: PMC5070630 DOI: 10.1080/21675511.2016.1241362] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/10/2016] [Accepted: 09/21/2016] [Indexed: 12/21/2022] Open
Abstract
Millions of children worldwide are born with rare and debilitating developmental disorders each year. Although an increasing number of these conditions are being recognized at the molecular level, the characterization of the underlying pathophysiology remains a grand challenge. This is often due to the lack of appropriate patient material or relevant animal models. Dogs are coming to the rescue as physiologically relevant large animal models. Hundreds of spontaneous genetic conditions have been described in dogs, most with close counterparts to human rare disorders. Our recent examples include the canine models of human Caffey (SLC37A2), van den Ende-Gupta (SCARF2) and Raine (FAM20C) syndromes. These studies demonstrate the pathophysiological similarity of human and canine syndromes, and suggest that joint efforts to characterize both human and canine rare diseases could provide additional benefits to the advancement of the field of rare diseases. Besides revealing new candidate genes, canine models allow access to experimental resources such as cells, tissues and even live animals for research and intervention purposes.
Collapse
Affiliation(s)
- Marjo K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland; The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland; The Folkhälsan Institute of Genetics, Helsinki, Finland
| |
Collapse
|
21
|
Exome sequencing a review of new strategies for rare genomic disease research. Genomics 2016; 108:109-114. [PMID: 27387609 DOI: 10.1016/j.ygeno.2016.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/07/2016] [Accepted: 06/18/2016] [Indexed: 11/23/2022]
Abstract
The journey related to genomic information access and utilization by researchers and clinicians has barely begun to be travelled. There remains a broad horizon in the research and clinical arenas for fulfillment of that journey. Exciting is the potential depth and breadth of research, clinical applications, and more personalized medicine, that remain on the horizon. Exome sequencing has clarified the responsibilities of over 130 genes, greatly expanding the medical genetics database and enabling the development of orphan disease-based pharmaceuticals. Our research focus was to review >50 literature sources that related to rare genomic disease research and exome sequencing, as well as the new research and diagnostic strategies that were utilized. Using a systems approach, under discussion are ciliopathy, dermatology, otorhinolaryngology, immunology, gastroenterology, hematopoiesis, metabolic diseases, and the cardiovascular system. Also discussed are genetic, syndromic, and mitochondrial exome research. Recommendations for future research will also be discussed.
Collapse
|
22
|
Niederhoffer KY, Fahiminiya S, Eydoux P, Mawson J, Nishimura G, Jerome-Majewska LA, Patel MS. Diagnosis of Van den Ende-Gupta syndrome: Approach to the Marden-Walker-like spectrum of disorders. Am J Med Genet A 2016; 170:2310-21. [DOI: 10.1002/ajmg.a.37831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/16/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Karen Y. Niederhoffer
- Department of Medical Genetics; University of British Columbia; Vancouver British Columbia Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics; Pediatrics, McGill University; Montreal Quebec Canada
| | - Patrice Eydoux
- Department of Pathology Laboratory Medicine; University of British Columbia; Vancouver British Columbia Canada
| | - John Mawson
- Department of Radiology; University of British Columbia; Vancouver British Columbia Canada
| | - Gen Nishimura
- Department of Orthopaedic Surgery; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Loydie A. Jerome-Majewska
- Department of Human Genetics; Pediatrics, McGill University; Montreal Quebec Canada
- Pediatrics, McGill University; Montreal Quebec Canada
| | - Millan S. Patel
- Department of Medical Genetics; University of British Columbia; Vancouver British Columbia Canada
| |
Collapse
|
23
|
Hytönen MK, Arumilli M, Lappalainen AK, Owczarek-Lipska M, Jagannathan V, Hundi S, Salmela E, Venta P, Sarkiala E, Jokinen T, Gorgas D, Kere J, Nieminen P, Drögemüller C, Lohi H. Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes. PLoS Genet 2016; 12:e1006037. [PMID: 27187611 PMCID: PMC4871343 DOI: 10.1371/journal.pgen.1006037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/18/2016] [Indexed: 12/03/2022] Open
Abstract
One to two percent of all children are born with a developmental disorder requiring pediatric hospital admissions. For many such syndromes, the molecular pathogenesis remains poorly characterized. Parallel developmental disorders in other species could provide complementary models for human rare diseases by uncovering new candidate genes, improving the understanding of the molecular mechanisms and opening possibilities for therapeutic trials. We performed various experiments, e.g. combined genome-wide association and next generation sequencing, to investigate the clinico-pathological features and genetic causes of three developmental syndromes in dogs, including craniomandibular osteopathy (CMO), a previously undescribed skeletal syndrome, and dental hypomineralization, for which we identified pathogenic variants in the canine SLC37A2 (truncating splicing enhancer variant), SCARF2 (truncating 2-bp deletion) and FAM20C (missense variant) genes, respectively. CMO is a clinical equivalent to an infantile cortical hyperostosis (Caffey disease), for which SLC37A2 is a new candidate gene. SLC37A2 is a poorly characterized member of a glucose-phosphate transporter family without previous disease associations. It is expressed in many tissues, including cells of the macrophage lineage, e.g. osteoclasts, and suggests a disease mechanism, in which an impaired glucose homeostasis in osteoclasts compromises their function in the developing bone, leading to hyperostosis. Mutations in SCARF2 and FAM20C have been associated with the human van den Ende-Gupta and Raine syndromes that include numerous features similar to the affected dogs. Given the growing interest in the molecular characterization and treatment of human rare diseases, our study presents three novel physiologically relevant models for further research and therapy approaches, while providing the molecular identity for the canine conditions. Rare developmental disorders make a major contribution to pediatric hospital admissions and mortality. There is a growing interest in the development of therapeutics for these conditions, but that requires understanding of the genetic cause and pathology. Research can be facilitated by physiologically relevant models, such as dogs with corresponding disorders. We have characterized the clinical features and genetic causes of three developmental syndromes in dogs, including craniomandibular osteopathy (CMO), a previously undescribed skeletal syndrome, and dental hypomineralization, for which we identified mutations in the canine SLC37A2, SCARF2 and FAM20C genes, respectively. CMO is a clinical equivalent to an infantile cortical hyperostosis (Caffey disease) for which SLC37A2 is a new candidate gene. SLC37A2 is a glucose-phosphate transporter in osteoclasts, and its defect suggests an impaired glucose homeostasis in developing bone, leading to hyperostosis. Mutations in the SCARF2 and FAM20C genes have been associated with the human van den Ende-Gupta and Raine syndromes. Our study provides molecular identity for the canine conditions and presents three novel physiologically relevant models of human rare diseases.
Collapse
Affiliation(s)
- Marjo K. Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Meharji Arumilli
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Anu K. Lappalainen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | | | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sruthi Hundi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Elina Salmela
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Patrick Venta
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Eva Sarkiala
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Jokinen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Daniela Gorgas
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Juha Kere
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Pekka Nieminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
- * E-mail:
| |
Collapse
|
24
|
Diehl A, Mu W, Batista D, Gunay-Aygun M. An atypical 0.73 MB microduplication of 22q11.21 and a novel SALL4 missense mutation associated with thumb agenesis and radioulnar synostosis. Am J Med Genet A 2015; 167:1644-9. [PMID: 25823593 DOI: 10.1002/ajmg.a.37066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/06/2015] [Indexed: 01/14/2023]
Abstract
We describe a 0.73 Mb duplication of chromosome 22q11.21 between LCR-B and LCR-D and a missense mutation in a conserved C2H2 zinc finger domain of SALL4 in a cognitively normal patient with multiple skeletal anomalies including radioulnar synostosis, thumb aplasia, butterfly vertebrae, rib abnormalities, and hypoplasia of the humeral and femoral epiphyses. 22q11.21 is a common site for microdeletions and their reciprocal microduplications as a result of non-allelic homologous recombination between its multiple low copy repeat regions (LCR). DiGeorge /Velocardiofacial syndrome (DG/VCFS) is classically caused by a 3 Mb deletion between LCR-A and LCR-D or a 1.5 Mb deletion between LCR-A and LCR-B. The reciprocal syndrome to DG/VCFS is the recently described 22q11.2 microduplication, which usually presents with the typical 3 Mb or 1.5 Mb duplication. Numerous atypical deletions and duplications have been reported between other LCRs. Typically, SALL4-related Duane-radial ray syndrome is caused by deletions or nonsense mutations; the only missense SALL4 mutation described prior was thought to result in gain of function and produced cranial midline defects. The skeletal anomalies presented in this report have not been previously described in association with 22q11.2 microduplication nor SALL4 mutations.
Collapse
Affiliation(s)
- Adam Diehl
- School of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Weiyi Mu
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Denise Batista
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cytogenetics and Microarray Laboratory, Kennedy Krieger Institute, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Meral Gunay-Aygun
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
25
|
Racedo S, McDonald-McGinn D, Chung J, Goldmuntz E, Zackai E, Emanuel B, Zhou B, Funke B, Morrow B. Mouse and human CRKL is dosage sensitive for cardiac outflow tract formation. Am J Hum Genet 2015; 96:235-44. [PMID: 25658046 DOI: 10.1016/j.ajhg.2014.12.025] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/29/2014] [Indexed: 01/18/2023] Open
Abstract
The human chromosome 22q11.2 region is susceptible to rearrangements during meiosis leading to velo-cardio-facial/DiGeorge/22q11.2 deletion syndrome (22q11DS) characterized by conotruncal heart defects (CTDs) and other congenital anomalies. The majority of individuals have a 3 Mb deletion whose proximal region contains the presumed disease-associated gene TBX1 (T-box 1). Although a small subset have proximal nested deletions including TBX1, individuals with distal deletions that exclude TBX1 have also been identified. The deletions are flanked by low-copy repeats (LCR22A, B, C, D). We describe cardiac phenotypes in 25 individuals with atypical distal nested deletions within the 3 Mb region that do not include TBX1 including 20 with LCR22B to LCR22D deletions and 5 with nested LCR22C to LCR22D deletions. Together with previous reports, 12 of 37 (32%) with LCR22B-D deletions and 5 of 34 (15%) individuals with LCR22C-D deletions had CTDs including tetralogy of Fallot. In the absence of TBX1, we hypothesized that CRKL (Crk-like), mapping to the LCR22C-D region, might contribute to the cardiac phenotype in these individuals. We created an allelic series in mice of Crkl, including a hypomorphic allele, to test for gene expression effects on phenotype. We found that the spectrum of heart defects depends on Crkl expression, occurring with analogous malformations to that in human individuals, suggesting that haploinsufficiency of CRKL could be responsible for the etiology of CTDs in individuals with nested distal deletions and might act as a genetic modifier of individuals with the typical 3 Mb deletion.
Collapse
|
26
|
Chen B, Brinkmann K, Chen Z, Pak CW, Liao Y, Shi S, Henry L, Grishin NV, Bogdan S, Rosen MK. The WAVE regulatory complex links diverse receptors to the actin cytoskeleton. Cell 2014; 156:195-207. [PMID: 24439376 DOI: 10.1016/j.cell.2013.11.048] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 09/06/2013] [Accepted: 11/25/2013] [Indexed: 02/02/2023]
Abstract
The WAVE regulatory complex (WRC) controls actin cytoskeletal dynamics throughout the cell by stimulating the actin-nucleating activity of the Arp2/3 complex at distinct membrane sites. However, the factors that recruit the WRC to specific locations remain poorly understood. Here, we have identified a large family of potential WRC ligands, consisting of ∼120 diverse membrane proteins, including protocadherins, ROBOs, netrin receptors, neuroligins, GPCRs, and channels. Structural, biochemical, and cellular studies reveal that a sequence motif that defines these ligands binds to a highly conserved interaction surface of the WRC formed by the Sra and Abi subunits. Mutating this binding surface in flies resulted in defects in actin cytoskeletal organization and egg morphology during oogenesis, leading to female sterility. Our findings directly link diverse membrane proteins to the WRC and actin cytoskeleton and have broad physiological and pathological ramifications in metazoans.
Collapse
Affiliation(s)
- Baoyu Chen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Klaus Brinkmann
- Institut für Neurobiologie, Universität Münster, 48149 Münster, Germany
| | - Zhucheng Chen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Chi W Pak
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yuxing Liao
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Shuoyong Shi
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Lisa Henry
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Nick V Grishin
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Sven Bogdan
- Institut für Neurobiologie, Universität Münster, 48149 Münster, Germany.
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| |
Collapse
|
27
|
Migliavacca MP, Sobreira NLM, Antonialli GPM, Oliveira MM, Melaragno MISA, Casteels I, de Ravel T, Brunoni D, Valle D, Perez ABA. Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion. Am J Med Genet A 2014; 164A:1170-4. [PMID: 24478002 DOI: 10.1002/ajmg.a.36425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 11/30/2013] [Indexed: 11/11/2022]
Abstract
Van den Ende-Gupta Syndrome (VDEGS) is an autosomal recessive disorder characterized by blepharophimosis, distinctive nose, hypoplastic maxilla, and skeletal abnormalities. Using homozygosity mapping in four VDEGS patients from three consanguineous families, Anastacio et al. [Anastacio et al. (2010); Am J Hum Genet 87:553-559] identified homozygous mutations in SCARF2, located at 22q11.2. Bedeschi et al. [2010] described a VDEGS patient with sclerocornea and cataracts with compound heterozygosity for the common 22q11.2 microdeletion and a hemizygous SCARF2 mutation. Because sclerocornea had been described in DiGeorge-velo-cardio-facial syndrome but not in VDEGS, they suggested that the ocular abnormalities were caused by the 22q11.2 microdeletion. We report on a 23-year-old male who presented with bilateral sclerocornea and the VDGEGS phenotype who was subsequently found to be homozygous for a 17 bp deletion in exon 4 of SCARF2. The occurrence of bilateral sclerocornea in our patient together with that of Bedeschi et al., suggests that the full VDEGS phenotype may include sclerocornea resulting from homozygosity or compound heterozygosity for loss of function variants in SCARF2.
Collapse
Affiliation(s)
- Michele P Migliavacca
- Clinical Genetics, Department of Morphology and Genetics, UNIFESP, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med 2014; 8:42-57. [PMID: 24384736 DOI: 10.1007/s11684-014-0303-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/30/2013] [Indexed: 12/23/2022]
Abstract
The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.
Collapse
|
29
|
The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. Hum Genet 2013; 132:1197-211. [PMID: 23907654 DOI: 10.1007/s00439-013-1344-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/20/2013] [Indexed: 02/08/2023]
Abstract
Autozygosity, or the inheritance of two copies of an ancestral allele, has the potential to not only reveal phenotypes caused by biallelic mutations in autosomal recessive genes, but to also facilitate the mapping of such mutations by flagging the surrounding haplotypes as tractable runs of homozygosity (ROH), a process known as autozygosity mapping. Since SNPs replaced microsatellites as markers for the purpose of genomewide identification of ROH, autozygosity mapping of Mendelian genes has witnessed a significant acceleration. Historically, successful mapping traditionally required favorable family structure that permits the identification of an autozygous interval that is amenable to candidate gene selection and confirmation by Sanger sequencing. This requirement presented a major bottleneck that hindered the utilization of simplex cases and many multiplex families with autosomal recessive phenotypes. However, the advent of next-generation sequencing that enables massively parallel sequencing of DNA has largely bypassed this bottleneck and thus ushered in an era of unprecedented pace of Mendelian disease gene discovery. The ability to identify a single causal mutation among a massive number of variants that are uncovered by next-generation sequencing can be challenging, but applying autozygosity as a filter can greatly enhance the enrichment process and its throughput. This review will discuss the power of combining the best of both techniques in the mapping of recessive disease genes and offer some tips to troubleshoot potential limitations.
Collapse
|
30
|
Patel N, Salih MA, Alshammari MJ, Abdulwahhab F, Adly N, Alzahrani F, Elgamal EA, Elkhashab HY, Al-Qattan M, Alkuraya FS. Expanding the clinical spectrum and allelic heterogeneity in van den Ende-Gupta syndrome. Clin Genet 2013; 85:492-4. [PMID: 23808541 DOI: 10.1111/cge.12205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 05/22/2013] [Accepted: 05/23/2013] [Indexed: 11/30/2022]
Affiliation(s)
- N Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Watkins D, Rosenblatt DS. Lessons in biology from patients with inborn errors of vitamin B12 metabolism. Biochimie 2013; 95:1019-22. [PMID: 23402785 DOI: 10.1016/j.biochi.2013.01.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 01/28/2013] [Indexed: 01/14/2023]
Abstract
BACKGROUND Since 1975 cells lines from patients with suspected inborn errors of vitamin B12 metabolism have been referred to our laboratory because of elevations of homocysteine, methylmalonic acid, or both. DESIGN Cultured fibroblasts from patients were subjected to a battery of tests: incorporation of labelled propionate and methyltetrahydrofolate into cellular macromolecules, to test the functional integrity of methylmalonyl-CoA mutase and methionine synthase, respectively; uptake of labelled cyanocobalamin and synthesis of adenosylcobalamin and methylcobalamin; and, where applicable, complementation analysis. RESULTS This approach has allowed for the discovery of novel steps in the cellular transport and metabolism of vitamin B12, including those involving cellular uptake, the efflux of vitamin B12 from lysosomes, and the synthesis of adenosylcobalamin and methylcobalamin. For all of these disorders, the responsible genes have been discovered. CONCLUSION The study of highly selected patients with suspected inborn errors of metabolism has consistently resulted in the discovery of previously unknown metabolic steps and has provided new lessons in biology.
Collapse
Affiliation(s)
- David Watkins
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | |
Collapse
|
32
|
McDonald-McGinn DM, Fahiminiya S, Revil T, Nowakowska BA, Suhl J, Bailey A, Mlynarski E, Lynch DR, Yan AC, Bilaniuk LT, Sullivan KE, Warren ST, Emanuel BS, Vermeesch JR, Zackai EH, Jerome-Majewska LA. Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS. J Med Genet 2012; 50:80-90. [PMID: 23231787 PMCID: PMC3585484 DOI: 10.1136/jmedgenet-2012-101320] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder, affecting an estimated 1 : 2000–4000 live births. Patients with 22q11.2DS have a broad spectrum of phenotypic abnormalities which generally includes congenital cardiac abnormalities, palatal anomalies, and immunodeficiency. Additional findings, such as skeletal anomalies and autoimmune disorders, can confer significant morbidity in a subset of patients. 22q11.2DS is a contiguous gene DS and over 40 genes are deleted in patients; thus deletion of several genes within this region contributes to the clinical features. Mutations outside or on the remaining 22q11.2 allele are also known to modify the phenotype. Methods We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals. Results and conclusions In four unrelated patients, we identified three novel mutations in SNAP29, the gene implicated in the autosomal recessive condition cerebral dysgenesis, neuropathy, ichthyosis and keratoderma (CEDNIK). SNAP29 maps to 22q11.2 and encodes a soluble SNARE protein that is predicted to mediate vesicle fusion at the endoplasmic reticulum or Golgi membranes. This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome. Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.
Collapse
Affiliation(s)
- Donna M McDonald-McGinn
- Division of Human Genetics, The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Casals F, Idaghdour Y, Hussin J, Awadalla P. Next-generation sequencing approaches for genetic mapping of complex diseases. J Neuroimmunol 2012; 248:10-22. [PMID: 22285396 DOI: 10.1016/j.jneuroim.2011.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/30/2011] [Accepted: 12/15/2011] [Indexed: 01/12/2023]
Abstract
The advent of next generation sequencing technologies has opened new possibilities in the analysis of human disease. In this review we present the main next-generation sequencing technologies, with their major contributions and possible applications to the study of the genetic etiology of complex diseases.
Collapse
Affiliation(s)
- Ferran Casals
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.
| | | | | | | |
Collapse
|
34
|
Puffenberger EG, Jinks RN, Sougnez C, Cibulskis K, Willert RA, Achilly NP, Cassidy RP, Fiorentini CJ, Heiken KF, Lawrence JJ, Mahoney MH, Miller CJ, Nair DT, Politi KA, Worcester KN, Setton RA, Dipiazza R, Sherman EA, Eastman JT, Francklyn C, Robey-Bond S, Rider NL, Gabriel S, Morton DH, Strauss KA. Genetic mapping and exome sequencing identify variants associated with five novel diseases. PLoS One 2012; 7:e28936. [PMID: 22279524 PMCID: PMC3260153 DOI: 10.1371/journal.pone.0028936] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 11/17/2011] [Indexed: 01/12/2023] Open
Abstract
The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.
Collapse
Affiliation(s)
- Erik G Puffenberger
- Clinic for Special Children, Strasburg, Pennsylvania, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Lin X, Tang W, Ahmad S, Lu J, Colby CC, Zhu J, Yu Q. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res 2012; 288:67-76. [PMID: 22269275 DOI: 10.1016/j.heares.2012.01.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 01/04/2012] [Accepted: 01/06/2012] [Indexed: 01/25/2023]
Abstract
The goal of sequencing the entire human genome for $1000 is almost in sight. However, the total costs including DNA sequencing, data management, and analysis to yield a clear data interpretation are unlikely to be lowered significantly any time soon to make studies on a population scale and daily clinical uses feasible. Alternatively, the targeted enrichment of specific groups of disease and biological pathway-focused genes and the capture of up to an entire human exome (~1% of the genome) allowing an unbiased investigation of the complete protein-coding regions in the genome are now routine. Targeted gene capture followed by sequencing with massively parallel next-generation sequencing (NGS) has the advantages of 1) significant cost saving, 2) higher sequencing accuracy because of deeper achievable coverage, 3) a significantly shorter turnaround time, and 4) a more feasible data set for a bioinformatic analysis outcome that is functionally interpretable. Gene capture combined with NGS has allowed a much greater number of samples to be examined than is currently practical with whole-genome sequencing. Such an approach promises to bring a paradigm shift to biomedical research of Mendelian disorders and their clinical diagnoses, ultimately enabling personalized medicine based on one's genetic profile. In this review, we describe major methodologies currently used for gene capture and detection of genetic variations by NGS. We will highlight applications of this technology in studies of genetic disorders and discuss issues pertaining to applications of this powerful technology in genetic screening and the discovery of genes implicated in syndromic and non-syndromic hearing loss.
Collapse
Affiliation(s)
- Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA.
| | | | | | | | | | | | | |
Collapse
|
36
|
Lai-Cheong JE, McGrath JA. Next-Generation Diagnostics for Inherited Skin Disorders. J Invest Dermatol 2011; 131:1971-3. [DOI: 10.1038/jid.2011.253] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
37
|
Londin ER, Keller MA, D'Andrea MR, Delgrosso K, Ertel A, Surrey S, Fortina P. Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. BMC Genomics 2011; 12:464. [PMID: 21943378 PMCID: PMC3203102 DOI: 10.1186/1471-2164-12-464] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 09/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background The creation of lymphoblastoid cell lines (LCLs) through Epstein-Barr virus (EBV) transformation of B-lymphocytes can result in a valuable biomaterial for cell biology research and a renewable source of DNA. While LCLs have been used extensively in cellular and genetic studies, the process of cell transformation and expansion during culturing may introduce genomic changes that may impact their use and the interpretation of subsequent genetic findings. Results We performed whole exome sequencing on a tetrad family using DNA derived from peripheral blood mononuclear cells (PBMCs) and LCLs from each individual. We generated over 4.7 GB of mappable sequence to a 125X read coverage per sample. An average of 19,354 genetic variants were identified. Comparison of the two DNA sources from each individual showed an average concordance rate of 95.69%. By lowering the variant calling parameters, the concordance rate between the paired samples increased to 99.82%. Sanger sequencing of a subset of the remaining discordant variants did confirm the presence of de novo mutations arising in LCLs. Conclusions By varying software stringency parameters, we identified 99% concordance between DNA sequences derived from the two different sources from the same donors. These results suggest that LCLs are an appropriate representation of the genetic material of the donor and suggest that EBV transformation can result in low-level generation of de novo mutations. Therefore, use of PBMC or early passage EBV-transformed cells is recommended. These findings have broad-reaching implications, as there are thousands of LCLs in public biorepositories and individual laboratories.
Collapse
|
38
|
Smith KR, Bromhead CJ, Hildebrand MS, Shearer AE, Lockhart PJ, Najmabadi H, Leventer RJ, McGillivray G, Amor DJ, Smith RJ, Bahlo M. Reducing the exome search space for mendelian diseases using genetic linkage analysis of exome genotypes. Genome Biol 2011; 12:R85. [PMID: 21917141 PMCID: PMC3308048 DOI: 10.1186/gb-2011-12-9-r85] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 07/28/2011] [Accepted: 09/13/2011] [Indexed: 11/29/2022] Open
Abstract
Many exome sequencing studies of Mendelian disorders fail to optimally exploit family information. Classical genetic linkage analysis is an effective method for eliminating a large fraction of the candidate causal variants discovered, even in small families that lack a unique linkage peak. We demonstrate that accurate genetic linkage mapping can be performed using SNP genotypes extracted from exome data, removing the need for separate array-based genotyping. We provide software to facilitate such analyses.
Collapse
Affiliation(s)
- Katherine R Smith
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
In recent years, researchers have identified a large number of complex diseases/traits-associated genetic variants by performing genome-wide association studies (GWAS), which may provide important clues on understanding the mechanisms of related diseases. However, GWAS has its own limitations in terms of being false positive, false negative results, very few SNPs located in the functional areas and insensitive to detect rare and structural variations, which results in the application limitation of this method. With the development of the next-generation sequencing technology, whole genome and exome sequencing developed rapidly and provide an opportunity for us to deal with the problem caused by GWAS. This high-throughput sequencing technology is applied for sequencing the exome (1% of genome) to discover most of the diseases-related variations in exons. Furthermore, it is highly effective to detect common and rare variations. Due to these advantages, exome sequencing has become a powerful and efficient strategy for identifying the genes responsible for mendelian disorders and complex diseases, which will be very helpful for the diseases clinical diagnosis.
Collapse
|
40
|
Shi Y, Li Y, Zhang D, Zhang H, Li Y, Lu F, Liu X, He F, Gong B, Cai L, Li R, Liao S, Ma S, Lin H, Cheng J, Zheng H, Shan Y, Chen B, Hu J, Jin X, Zhao P, Chen Y, Zhang Y, Lin Y, Li X, Fan Y, Yang H, Wang J, Yang Z. Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet 2011; 7:e1002084. [PMID: 21695231 PMCID: PMC3111487 DOI: 10.1371/journal.pgen.1002084] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 03/31/2011] [Indexed: 12/21/2022] Open
Abstract
Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3′UTR+12 C>G, and 3′UTR+592 G>A) in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE). Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form. People with myopia see near objects more clearly than objects far away. Myopia is the most common ocular disorder worldwide, with a high prevalence in Asian (40%–70%) and Caucasian (20%–30%) populations. Although the etiologies of myopia have not yet been established, previous studies have indicated the involvement of genetic and environmental factors (such as close working habits, higher education levels, and higher socioeconomic class). Genetic factors play a critical role in the development of myopia, especially high myopia. In this study, we use exome sequencing, a powerful tool for a disease gene identification, to identify a gene involved in high myopia in a monogenic form among Han Chinese. Mutations in zinc finger protein 644 isoform 1 (ZNF644) were identified as potentially responsible for the phenotype of high myopia. The main feature of high myopia is axial elongation of the eye globe. Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, a mutant ZNF644 protein may impact the normal eye development and therefore may underlie the axial elongation of the eye globe in high myopia patients. Further study of the biological function of ZNF644 will provide insight into the pathogenesis of myopia.
Collapse
Affiliation(s)
- Yi Shi
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Yingrui Li
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Dingding Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Hao Zhang
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Yuanfeng Li
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Fang Lu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Xiaoqi Liu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Fei He
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Bo Gong
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Li Cai
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Ruiqiang Li
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Shihuang Liao
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Shi Ma
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - He Lin
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jing Cheng
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | | | - Ying Shan
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Bin Chen
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jianbin Hu
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Xin Jin
- Innovative Program for Undergraduate Students, School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China
| | - Peiquan Zhao
- The Department of Ophthalmology, Xinhua Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Yiye Chen
- The Department of Ophthalmology, Xinhua Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Yong Zhang
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Ying Lin
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Xi Li
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Yingchuan Fan
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Huanming Yang
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Jun Wang
- Beijing Genome Institute at Shenzhen, Shenzhen, China
| | - Zhenglin Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- * E-mail:
| |
Collapse
|
41
|
Bedeschi MF, Colombo L, Mari F, Hofmann K, Rauch A, Gentilin B, Renieri A, Clerici D. Unmasking of a Recessive SCARF2 Mutation by a 22q11.12 de novo Deletion in a Patient with Van den Ende-Gupta Syndrome. Mol Syndromol 2011; 1:239-245. [PMID: 22140376 DOI: 10.1159/000328135] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2011] [Indexed: 11/19/2022] Open
Abstract
Van den Ende-Gupta syndrome (VDEGS) is a congenital condition characterized by craniofacial and skeletal manifestations, specifically blepharophimosis, malar and maxillary hypoplasia, distinctive nose, arachnocamptodactyly, and long slender bones of the hands and feet. To date, only 24 patients have been described. It is generally thought that the syndrome is transmitted by an autosomal recessive mode of inheritance, although evidence for genetic heterogeneity has recently been presented. We report on a girl followed from birth up to 3 years of life with a set of peculiar minor anomalies, arachnocamptodactyly of hands and feet, characteristic of VDEGS in association with a 22q11.12 deletion. Recently, the VDEGS gene was mapped to the DiGeorge syndrome region on 22q11.2, and homozygous mutations in the SCARF2 gene were identified. We now report the first patient with VDEGS due to compound heterozygosity for the common 22q11.2 microdeletion and a hemizygous SCARF2 splice site mutation.
Collapse
Affiliation(s)
- M F Bedeschi
- Medical Genetic Unit, Università degli Studi di Milano, Milano
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Revisiting Mendelian disorders through exome sequencing. Hum Genet 2011; 129:351-70. [PMID: 21331778 DOI: 10.1007/s00439-011-0964-2] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 02/03/2011] [Indexed: 12/25/2022]
Abstract
Over the past several years, more focus has been placed on dissecting the genetic basis of complex diseases and traits through genome-wide association studies. In contrast, Mendelian disorders have received little attention mainly due to the lack of newer and more powerful methods to study these disorders. Linkage studies have previously been the main tool to elucidate the genetics of Mendelian disorders; however, extremely rare disorders or sporadic cases caused by de novo variants are not amendable to this study design. Exome sequencing has now become technically feasible and more cost-effective due to the recent advances in high-throughput sequence capture methods and next-generation sequencing technologies which have offered new opportunities for Mendelian disorder research. Exome sequencing has been swiftly applied to the discovery of new causal variants and candidate genes for a number of Mendelian disorders such as Kabuki syndrome, Miller syndrome and Fowler syndrome. In addition, de novo variants were also identified for sporadic cases, which would have not been possible without exome sequencing. Although exome sequencing has been proven to be a promising approach to study Mendelian disorders, several shortcomings of this method must be noted, such as the inability to capture regulatory or evolutionary conserved sequences in non-coding regions and the incomplete capturing of all exons.
Collapse
|