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Shokrollahi N, Tehrani Fateh S, Nouri M, Behnam A, Moghimi P, Sadeghi H, Mirfakhraie R, Roudgari H, Jamshidi S, Miryounesi M, Ghasemi MR. The first Iranian patient with You-Hoover-Fong syndrome and a review of the literature on 27 cases: expanding the genotypic and phenotypic spectrum. Neurol Sci 2024; 45:3979-3987. [PMID: 38421525 DOI: 10.1007/s10072-024-07413-y] [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: 08/29/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND The ultra-rare autosomal recessive genetic disorder, You-Hoover-Fong Syndrome (YHFS), is caused by defects in the TELO2 gene and is characterized by intellectual disability, developmental delay, and ocular impairments. This study aims to contribute to a better understanding of YHFS by reviewing previous cases and introducing a novel variant in a new case. METHODS Whole exome sequencing (WES) was conducted on the proband to identify genetic variants, and Sanger sequencing was used to confirm variants within the family. This article presents a comprehensive collection of reported cases of YHFS, incorporating both molecular and clinical data, through an extensive literature search and analysis of English-language studies published until June 2023. RESULTS Using WES, a novel homozygous missense variant, c.1799A > G (p. Tyr600Cys), was identified in the TELO2 gene in a 4-year-old Iranian male patient. Novel clinical features, including choanal atresia and clubfoot, were also identified. A comprehensive literature review identified 27 patients with YHFS, with 20 variants in the TELO2 gene. Missense pathogenic variants were the most common type of pathogenic variant, and the most common features were microcephaly and intellectual impairment. CONCLUSION This study presents the first case of pathogenic variants in TELO2 gene in Iran, expands the genotypic and phenotypic spectrum of YHFS and contributes to the growing body of literature pertaining to YHFS. Furthermore, our findings highlight the importance of genetic testing for non-consanguineous carrier screening, as compound heterozygosity may be a significant factor in the development of YHFS. Further research is needed to clarify the molecular mechanisms underlying YHFS pathogenesis.
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Affiliation(s)
- Nima Shokrollahi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Nouri
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirmohammad Behnam
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parinaz Moghimi
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Roudgari
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sanaz Jamshidi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad-Reza Ghasemi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Garg P, Jamal F, Srivastava P. Comparative Transcriptomics Data Profiling Reveals E2F Targets as an Important Biological Pathway Overexpressed in Intellectual Disability Disorder. Bioinform Biol Insights 2024; 18:11779322231224665. [PMID: 38357659 PMCID: PMC10865946 DOI: 10.1177/11779322231224665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
Intellectual disability (ID) is an early childhood neurodevelopmental disorder that is characterized by impaired intellectual functioning and adaptive behavior. It is one of the major concerns in the field of neurodevelopmental disorders across the globe. Diversified approaches have been put forward to overcome this problem. Among all these approaches, high throughput transcriptomic analysis has taken an important dimension. The identification of genes causing ID rapidly increased over the past 3 to 5 years owing to the use of sophisticated high throughput sequencing platforms. Early monitoring and preventions are much important for such disorder as their progression occurs during fetal development. This study is an attempt to identify differentially expressed genes (DEGs) and upregulated biological processes involved in development of ID patients through comparative analysis of available transcriptomics data. A total of 7 transcriptomic studies were retrieved from National Center for Biotechnology Information (NCBI) and were subjected to quality check and trimming prior to alignment. The normalization and differential expression analysis were carried out using DESeq2 and EdgeR packages of Rstudio to identify DEGs in ID. In progression of the study, functional enrichment analysis of the results obtained from both DESeq2 and EdgeR was done using gene set enrichment analysis (GSEA) tool to identify major upregulated biological processes involved in ID. Our findings concluded that monitoring the level of E2F targets, estrogen, and genes related to oxidative phosphorylation, DNA repair, and glycolysis during the developmental stage of an individual can help in the early detection of ID disorder.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr Rammanohar Lohia Avadh University, Ayodhya, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
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Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D. Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Mol Cell 2023; 83:2792-2809.e9. [PMID: 37478847 PMCID: PMC10530064 DOI: 10.1016/j.molcel.2023.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
To maintain genome integrity, cells must accurately duplicate their genome and repair DNA lesions when they occur. To uncover genes that suppress DNA damage in human cells, we undertook flow-cytometry-based CRISPR-Cas9 screens that monitored DNA damage. We identified 160 genes whose mutation caused spontaneous DNA damage, a list enriched in essential genes, highlighting the importance of genomic integrity for cellular fitness. We also identified 227 genes whose mutation caused DNA damage in replication-perturbed cells. Among the genes characterized, we discovered that deoxyribose-phosphate aldolase DERA suppresses DNA damage caused by cytarabine (Ara-C) and that GNB1L, a gene implicated in 22q11.2 syndrome, promotes biogenesis of ATR and related phosphatidylinositol 3-kinase-related kinases (PIKKs). These results implicate defective PIKK biogenesis as a cause of some phenotypes associated with 22q11.2 syndrome. The phenotypic mapping of genes that suppress DNA damage therefore provides a rich resource to probe the cellular pathways that influence genome maintenance.
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Affiliation(s)
- Yichao Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel Tabet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Linjiang Lao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sumin Feng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Atina G Coté
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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Zhao Y, Han Y, Li N, Fu W, Luo G, Tan Y, Qian X. Novel compound heterozygous mutations in TELO2 in an infant with You-Hoover-Fong syndrome: A case report and literature review. Open Life Sci 2023; 18:20220602. [PMID: 37215500 PMCID: PMC10199318 DOI: 10.1515/biol-2022-0602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/03/2023] [Accepted: 03/26/2023] [Indexed: 05/24/2023] Open
Abstract
We report here the clinical diagnosis and treatment and genetic mutations of an infant with You-Hoover-Fong syndrome (YHFS). The relevant literature review was conducted. A female infant aged 17 months was admitted to Nanhai Affiliated Maternity and Children's Hospital of Guangzhou University of Chinese Medicine due to "global development delay complicated with postnatal growth retardation for more than 1 year." The infant was diagnosed with YHFS due to the onset of extremely severe mental retardation, microcephaly, abnormal hearing, severe protein-energy malnutrition, congenital cataract, cleft palate (I°), congenital atrial septal defect, brain atrophy, hydrocephalus, and brain hypoplasia. The whole exon sequencing revealed two compound heterozygous mutations, including a likely pathogenic TELO2 variant, c.2245A > T (p.K749X) from her mother and an uncertain variant, c.2299C > T (p.R767C) from her father, validated by Sanger sequencing. After bilateral cataract surgery, the infant obtained better visual acuity and showed more responses and interactions with her parents. Diagnosis and treatment of this case prompt that these TELO2 variants have not been reported, deepening the understanding of the molecular and genetic mechanism of YHFS in clinical practice.
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Affiliation(s)
- Yong Zhao
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
| | - Yu Han
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
| | - Nuo Li
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
| | - Wenjie Fu
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
| | - Guanjun Luo
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
| | - Yuan Tan
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
| | - Xuguang Qian
- Department of Children Rehabilitation, Nanhai Women and Children’s Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine, No. 6, Guiping West Road, Nanhai District, Foshan, Guangdong Province, 528200, China
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5
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Bhadra S, Xu YJ. TTT (Tel2-Tti1-Tti2) Complex, the Co-Chaperone of PIKKs and a Potential Target for Cancer Chemotherapy. Int J Mol Sci 2023; 24:ijms24098268. [PMID: 37175973 PMCID: PMC10178989 DOI: 10.3390/ijms24098268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The heterotrimeric Tel2-Tti1-Tti2 or TTT complex is essential for cell viability and highly observed in eukaryotes. As the co-chaperone of ATR, ATM, DNA-PKcs, mTOR, SMG1, and TRRAP, the phosphatidylinositol 3-kinase-related kinases (PIKKs) and a group of large proteins of 300-500 kDa, the TTT plays crucial roles in genome stability, cell proliferation, telomere maintenance, and aging. Most of the protein kinases in the kinome are targeted by co-chaperone Cdc37 for proper folding and stability. Like Cdc37, accumulating evidence has established the mechanism by which the TTT interacts with chaperone Hsp90 via R2TP (Rvb1-Rvb2-Tah1-Pih1) complex or other proteins for co-translational maturation of the PIKKs. Recent structural studies have revealed the α-solenoid structure of the TTT and its interactions with the R2TP complex, which shed new light on the co-chaperone mechanism and provide new research opportunities. A series of mutations of the TTT have been identified that cause disease syndrome with neurodevelopmental defects, and misregulation of the TTT has been shown to contribute to myeloma, colorectal, and non-small-cell lung cancers. Surprisingly, Tel2 in the TTT complex has recently been found to be a target of ivermectin, an antiparasitic drug that has been used by millions of patients. This discovery provides mechanistic insight into the anti-cancer effect of ivermectin and thus promotes the repurposing of this Nobel-prize-winning medicine for cancer chemotherapy. Here, we briefly review the discovery of the TTT complex, discuss the recent studies, and describe the perspectives for future investigation.
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Affiliation(s)
- Sankhadip Bhadra
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Yong-Jie Xu
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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6
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Serey-Gaut M, Cortes M, Makrythanasis P, Suri M, Taylor AMR, Sullivan JA, Asleh AN, Mitra J, Dar MA, McNamara A, Shashi V, Dugan S, Song X, Rosenfeld JA, Cabrol C, Iwaszkiewicz J, Zoete V, Pehlivan D, Akdemir ZC, Roeder ER, Littlejohn RO, Dibra HK, Byrd PJ, Stewart GS, Geckinli BB, Posey J, Westman R, Jungbluth C, Eason J, Sachdev R, Evans CA, Lemire G, VanNoy GE, O'Donnell-Luria A, Mau-Them FT, Juven A, Piard J, Nixon CY, Zhu Y, Ha T, Buckley MF, Thauvin C, Essien Umanah GK, Van Maldergem L, Lupski JR, Roscioli T, Dawson VL, Dawson TM, Antonarakis SE. Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly. Am J Hum Genet 2023; 110:499-515. [PMID: 36724785 PMCID: PMC10027477 DOI: 10.1016/j.ajhg.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Telomere maintenance 2 (TELO2), Tel2 interacting protein 2 (TTI2), and Tel2 interacting protein 1 (TTI1) are the three components of the conserved Triple T (TTT) complex that modulates activity of phosphatidylinositol 3-kinase-related protein kinases (PIKKs), including mTOR, ATM, and ATR, by regulating the assembly of mTOR complex 1 (mTORC1). The TTT complex is essential for the expression, maturation, and stability of ATM and ATR in response to DNA damage. TELO2- and TTI2-related bi-allelic autosomal-recessive (AR) encephalopathies have been described in individuals with moderate to severe intellectual disability (ID), short stature, postnatal microcephaly, and a movement disorder (in the case of variants within TELO2). We present clinical, genomic, and functional data from 11 individuals in 9 unrelated families with bi-allelic variants in TTI1. All present with ID, and most with microcephaly, short stature, and a movement disorder. Functional studies performed in HEK293T cell lines and fibroblasts and lymphoblastoid cells derived from 4 unrelated individuals showed impairment of the TTT complex and of mTOR pathway activity which is improved by treatment with Rapamycin. Our data delineate a TTI1-related neurodevelopmental disorder and expand the group of disorders related to the TTT complex.
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Affiliation(s)
- Margaux Serey-Gaut
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France.
| | - Marisol Cortes
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Periklis Makrythanasis
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland; Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Mohnish Suri
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alexander M R Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Ayat N Asleh
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jaba Mitra
- Department of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Mohamad A Dar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amy McNamara
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Sarah Dugan
- Providence Medical Group Genetic Clinics, Spokane, WA, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christelle Cabrol
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; EA481 Integrative and Cognitive Neuroscience Research Unit, University of Franche-Comte, Besancon, France
| | - Zeynep Coban Akdemir
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; University Texas Health Science Center, Houston, TX 77030, USA
| | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Okashah Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harpreet K Dibra
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Philip J Byrd
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Bilgen B Geckinli
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul 34722, Turkey
| | - Jennifer Posey
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Westman
- Providence Medical Group Genetic Clinics, Spokane, WA, USA
| | | | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia
| | - Gabrielle Lemire
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Grace E VanNoy
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Frédéric Tran Mau-Them
- UF6254 Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Aurélien Juven
- UF6254 Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Juliette Piard
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Cheng Yee Nixon
- Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia
| | - Ying Zhu
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Christel Thauvin
- INSERM UMR1231 GAD, Bourgogne Franche-Comté University, Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, Dijon, France
| | - George K Essien Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lionel Van Maldergem
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France; Clinical Investigation Center 1431, National Institute of Health and Medical Research (INSERM), CHU, Besancon, France; EA481 Integrative and Cognitive Neuroscience Research Unit, University of Franche-Comte, Besancon, France
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stylianos E Antonarakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland; Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland.
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7
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Albokhari D, Pritchard AB, Beil A, Muss C, Bupp C, Grange DK, Delplancq G, Heeley J, Zuteck M, Morrow MM, Kuentz P, Palculict TB, Hoover-Fong JE. TELO2-related syndrome (You-Hoover-Fong syndrome): Description of 14 new affected individuals and review of the literature. Am J Med Genet A 2023; 191:1261-1272. [PMID: 36797513 DOI: 10.1002/ajmg.a.63142] [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: 06/06/2022] [Revised: 10/18/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023]
Abstract
You-Hoover-Fong syndrome (YHFS) is an autosomal recessive condition caused by pathogenic variants in the TELO2 gene. Affected individuals were reported to have global developmental delay, intellectual disability, microcephaly, dysmorphic facial features, ocular involvement including cortical visual impairment, strabismus, cataract and rotatory nystagmus, movement disorder, hypertonia and spasticity, balance disturbance and ataxia, and abnormal sleep pattern. Other features reported include poor growth, cleft palate, cardiac malformations, epilepsy, scoliosis, and hearing loss. To date, 12 individuals with YHFS have been reported in the literature. Here we describe 14 new individuals with YHFS from 10 families. Their clinical presentation provides additional support of the phenotype recognized previously and delineates the clinical spectrum associated with YHFS syndrome. In addition, we present a review of the literature including follow-up data on four previously reported individuals with YHFS.
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Affiliation(s)
- Daniah Albokhari
- Department of Pediatrics, Taibah University College of Medicine, Medina, Saudi Arabia.,Mckusick-Nathan Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Amanda Barone Pritchard
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Adelyn Beil
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Candace Muss
- Department of Genetics, Nemours Children's Hospital, Wilmington, Delaware, USA
| | - Caleb Bupp
- Spectrum Health, Helen Devos Children's Hospital, Medical Genetics and Genomics, Grand Rapids, Michigan, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Geoffroy Delplancq
- Oncobiologie Génétique Bioinformatique, PCBio, Centre Hospitalier Universitaire de Besançon, Besançon, France.,Service de Neuropédiatrie, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Jennifer Heeley
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Melissa Zuteck
- Spectrum Health, Helen Devos Children's Hospital, Medical Genetics and Genomics, Grand Rapids, Michigan, USA
| | | | - Paul Kuentz
- Oncobiologie Génétique Bioinformatique, PCBio, Centre Hospitalier Universitaire de Besançon, Besançon, France.,INSERM - Université de Bourgogne Franche-Comté, UMR 1231 Equipe GAD, Génétique des Anomalies du Développement, FHU TRANSLAD, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | | | - Julie E Hoover-Fong
- Mckusick-Nathan Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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8
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VpdC is a ubiquitin-activated phospholipase effector that regulates Legionella vacuole expansion during infection. Proc Natl Acad Sci U S A 2022; 119:e2209149119. [PMID: 36413498 PMCID: PMC9860323 DOI: 10.1073/pnas.2209149119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intravacuolar pathogens need to gradually expand their surrounding vacuole to accommodate the growing number of bacterial offspring during intracellular replication. Here we found that Legionella pneumophila controls vacuole expansion by fine-tuning the generation of lysophospholipids within the vacuolar membrane. Upon allosteric activation by binding to host ubiquitin, the type IVB (Dot/Icm) effector VpdC converts phospholipids into lysophospholipids which, at moderate concentrations, are known to promote membrane fusion but block it at elevated levels by generating excessive positive membrane curvature. Consequently, L. pneumophila overproducing VpdC were prevented from adequately expanding their surrounding membrane, trapping the replicating bacteria within spatially confined vacuoles and reducing their capability to proliferate intracellularly. Quantitative lipidomics confirmed a VpdC-dependent increase in several types of lysophospholipids during infection, and VpdC production in transiently transfected cells caused tubulation of organelle membranes as well as mitochondria fragmentation, processes that can be phenocopied by supplying cells with exogenous lysophospholipids. Together, these results demonstrate an important role for bacterial phospholipases in vacuolar expansion.
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9
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Novel Homozygous TTI2 Variant Causing Autosomal Recessive Syndromic Intellectual Disability and Primary Microcephaly from Pakistan: A Case Report (Exome Report). Case Rep Genet 2022; 2022:2766957. [PMID: 35990009 PMCID: PMC9391182 DOI: 10.1155/2022/2766957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
We describe a male patient with a novel TTI2 variant, which has not been previously associated with a human phenotype. His features include intellectual disability, primary microcephaly, delayed psychomotor development, speech delay, short stature, dysmorphic facial features, esotropia, kyphoscoliosis, and behavior abnormalities (Figure). Next generation sequencing revealed autosomal recessive TTI2 variant with uncertain significance, denoted as c.21_22insAAGCGCTCTG (p.Glu8Lysfs × 12). TTI2 encodes a regulator of DNA damage response and helps maintain steady levels of the PIKK family of protein kinases. No disease-causing variants in other genes potentially linked to his clinical presentation were identified. We report a novel loss-of-function homozygous variant in TTI2 that leads to syndromic intellectual disability and primary microcephaly.
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10
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Fielder SM, Rosenfeld JA, Burrage LC, Emrick L, Lalani S, Attali R, Bembenek JN, Hoang H, Baldridge D, Silverman GA, Schedl T, Pak SC. Functional analysis of a novel de novo variant in PPP5C associated with microcephaly, seizures, and developmental delay. Mol Genet Metab 2022; 136:65-73. [PMID: 35361529 DOI: 10.1016/j.ymgme.2022.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/13/2022] [Indexed: 11/27/2022]
Abstract
We describe a proband evaluated through the Undiagnosed Diseases Network (UDN) who presented with microcephaly, developmental delay, and refractory epilepsy with a de novo p.Ala47Thr missense variant in the protein phosphatase gene, PPP5C. This gene has not previously been associated with a Mendelian disease, and based on the population database, gnomAD, the gene has a low tolerance for loss-of-function variants (pLI = 1, o/e = 0.07). We functionally evaluated the PPP5C variant in C. elegans by knocking the variant into the orthologous gene, pph-5, at the corresponding residue, Ala48Thr. We employed assays in three different biological processes where pph-5 was known to function through opposing the activity of genes, mec-15 and sep-1. We demonstrated that, in contrast to control animals, the pph-5 Ala48Thr variant suppresses the neurite growth phenotype and the GABA signaling defects of mec-15 mutants, and the embryonic lethality of sep-1 mutants. The Ala48Thr variant did not display dominance and behaved similarly to the reference pph-5 null, indicating that the variant is likely a strong hypomorph or complete loss-of-function. We conclude that pph-5 Ala48Thr is damaging in C. elegans. By extension in the proband, PPP5C p.Ala47Thr is likely damaging, the de novo dominant presentation is consistent with haplo-insufficiency, and the PPP5C variant is likely responsible for one or more of the proband's phenotypes.
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Affiliation(s)
- Sara M Fielder
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Ruben Attali
- Genomic Research Department, Emedgene Technologies, 6744332 Tel Aviv, Israel
| | - Joshua N Bembenek
- Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Hieu Hoang
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Dustin Baldridge
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Gary A Silverman
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Tim Schedl
- Department of Genetics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Stephen C Pak
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA.
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11
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French CE, Dolling H, Mégy K, Sanchis-Juan A, Kumar A, Delon I, Wakeling M, Mallin L, Agrawal S, Austin T, Walston F, Park SM, Parker A, Piyasena C, Bradbury K, Ellard S, Rowitch DH, Raymond FL. Refinements and considerations for trio whole genome sequence analysis when investigating Mendelian Diseases presenting in early childhood. HGG ADVANCES 2022; 3:100113. [PMID: 35586607 PMCID: PMC9108978 DOI: 10.1016/j.xhgg.2022.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
To facilitate early deployment of whole-genome sequencing (WGS) for severely ill children, a standardized pipeline for WGS analysis with timely turnaround and primary care pediatric uptake is needed. We developed a bioinformatics pipeline for comprehensive gene-agnostic trio WGS analysis of children suspected of having an undiagnosed monogenic disease that included detection and interpretation of primary genetic mechanisms of disease, including SNVs/indels, CNVs/SVs, uniparental disomy (UPD), imprinted genes, short tandem repeat expansions, mobile element insertions, SMN1/2 copy number calling, and mitochondrial genome variants. We assessed primary care practitioner experience and competence in a large cohort of 521 families (comprising 90% WGS trios). Children were identified by primary practitioners for recruitment, and we used the UK index of multiple deprivation to confirm lack of patient socio-economic status ascertainment bias. Of the 521 children sequenced, 176 (34%) received molecular diagnoses, with rates as high as 45% for neurology clinics. Twenty-three of the diagnosed cases (13%) required bespoke methods beyond routine SNV/CNV analysis. In our multidisciplinary clinician user experience assessment, both pediatricians and clinical geneticists expressed strong support for rapid WGS early in the care pathway, but requested further training in determining patient selection, consenting, and variant interpretation. Rapid trio WGS provides an efficacious single-pass screening test for children when deployed by primary practitioners in clinical settings that carry high a priori risk for rare pediatric disease presentations.
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Affiliation(s)
- Courtney E. French
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Boston Children’s Hospital, Boston, MA 02115, USA
| | - Helen Dolling
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Centre for Family Research, Department of Psychology, University of Cambridge, Cambridge CB2 3RQ, UK
| | - Karyn Mégy
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alba Sanchis-Juan
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ajay Kumar
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Isabelle Delon
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX4 4PY, UK
| | - Lucy Mallin
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Shruti Agrawal
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Topun Austin
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Florence Walston
- Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich NR4 7UY, UK
| | - Soo-Mi Park
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alasdair Parker
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | | | | | | | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX4 4PY, UK
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - David H. Rowitch
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - F. Lucy Raymond
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Corresponding author
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12
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Senko AN, Overall RW, Silhavy J, Mlejnek P, Malínská H, Hüttl M, Marková I, Fabel KS, Lu L, Stuchlik A, Williams RW, Pravenec M, Kempermann G. Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose. PLoS Genet 2022; 18:e1009638. [PMID: 35377872 PMCID: PMC9060359 DOI: 10.1371/journal.pgen.1009638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 05/02/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Neurogenesis in the adult hippocampus contributes to learning and memory in the healthy brain but is dysregulated in metabolic and neurodegenerative diseases. The molecular relationships between neural stem cell activity, adult neurogenesis, and global metabolism are largely unknown. Here we applied unbiased systems genetics methods to quantify genetic covariation among adult neurogenesis and metabolic phenotypes in peripheral tissues of a genetically diverse family of rat strains, derived from a cross between the spontaneously hypertensive (SHR/OlaIpcv) strain and Brown Norway (BN-Lx/Cub). The HXB/BXH family is a very well established model to dissect genetic variants that modulate metabolic and cardiovascular diseases and we have accumulated deep phenome and transcriptome data in a FAIR-compliant resource for systematic and integrative analyses. Here we measured rates of precursor cell proliferation, survival of new neurons, and gene expression in the hippocampus of the entire HXB/BXH family, including both parents. These data were combined with published metabolic phenotypes to detect a neurometabolic quantitative trait locus (QTL) for serum glucose and neuronal survival on Chromosome 16: 62.1-66.3 Mb. We subsequently fine-mapped the key phenotype to a locus that includes the Telo2-interacting protein 2 gene (Tti2)-a chaperone that modulates the activity and stability of PIKK kinases. To verify the hypothesis that differences in neurogenesis and glucose levels are caused by a polymorphism in Tti2, we generated a targeted frameshift mutation on the SHR/OlaIpcv background. Heterozygous SHR-Tti2+/- mutants had lower rates of hippocampal neurogenesis and hallmarks of dysglycemia compared to wild-type littermates. Our findings highlight Tti2 as a causal genetic link between glucose metabolism and structural brain plasticity. In humans, more than 800 genomic variants are linked to TTI2 expression, seven of which have associations to protein and blood stem cell factor concentrations, blood pressure and frontotemporal dementia.
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Affiliation(s)
- Anna N. Senko
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Rupert W. Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Malínská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Marková
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Klaus S. Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Ales Stuchlik
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
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13
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Structure of the Human TELO2-TTI1-TTI2 Complex. J Mol Biol 2021; 434:167370. [PMID: 34838521 DOI: 10.1016/j.jmb.2021.167370] [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: 06/28/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022]
Abstract
Phosphatidylinositol 3-kinase-related protein kinases (PIKKs) play critical roles in various metabolic pathways related to cell proliferation and survival. The TELO2-TTI1-TTI2 (TTT) complex has been proposed to recognize newly synthesized PIKKs and to deliver them to the R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) and the heat shock protein 90 chaperone, thereby supporting their folding and assembly. Here, we determined the cryo-EM structure of the TTT complex at an average resolution of 4.2 Å. We describe the full-length structures of TTI1 and TELO2, and a partial structure of TTI2. All three proteins form elongated helical repeat structures. TTI1 provides a platform on which TELO2 and TTI2 bind to its central region and C-terminal end, respectively. The TELO2 C-terminal domain (CTD) is required for the interaction with TTI1 and recruitment of Ataxia-telangiectasia mutated (ATM). The N- and C-terminal segments of TTI1 recognize the FRAP-ATM-TRRAP (FAT) domain and the N-terminal HEAT repeats of ATM, respectively. The TELO2 CTD and TTI1 N- and C-terminal segments are required for cell survival in response to ionizing radiation.
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14
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Guo Y, Tocchini C, Ciosk R. CLK-2/TEL2 is a conserved component of the nonsense-mediated mRNA decay pathway. PLoS One 2021; 16:e0244505. [PMID: 33444416 PMCID: PMC7808604 DOI: 10.1371/journal.pone.0244505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) controls eukaryotic mRNA quality, inducing the degradation of faulty transcripts. Key players in the NMD pathway were originally identified, through genetics, in Caenorhabditis elegans as smg (suppressor with morphological effect on genitalia) genes. Using forward genetics and fluorescence-based NMD reporters, we reexamined the genetic landscape underlying NMD. Employing a novel strategy for mapping sterile mutations, Het-Map, we identified clk-2, a conserved gene previously implicated in DNA damage signaling, as a player in the nematode NMD. We find that CLK-2 is expressed predominantly in the germline, highlighting the importance of auxiliary factors in tissue-specific mRNA decay. Importantly, the human counterpart of CLK-2/TEL2, TELO2, has been also implicated in the NMD, suggesting a conserved role of CLK-2/TEL2 proteins in mRNA surveillance. Recently, variants of TELO2 have been linked to an intellectual disability disorder, the You-Hoover-Fong syndrome, which could be related to its function in the NMD.
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Affiliation(s)
- Yanwu Guo
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Rafal Ciosk
- Department of Biosciences, University of Oslo, Oslo, Norway
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
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15
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Ciaccio C, Duga V, Pantaleoni C, Esposito S, Moroni I, Pinelli M, Castello R, Nigro V, Chiapparini L, D'Arrigo S. Milder presentation of TELO2-related syndrome in two sisters homozygous for the p.Arg609His pathogenic variant. Eur J Med Genet 2020; 64:104116. [PMID: 33307281 DOI: 10.1016/j.ejmg.2020.104116] [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: 06/24/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 11/17/2022]
Abstract
Biallelic loss of function of TELO2 gene cause a severe syndromic disease mainly characterized by global developmental delay with poor motor and language acquisitions, microcephaly, short stature, minor facial and limbs anomalies, sleep disorder, spasticity, and balance impairment up to ataxia. TELO2-related syndrome, also known as You-Hoover-Fong Syndrome, is extremely rare and since its first description in 2016 only 8 individuals have been reported, all showing a severe disability. The causative gene is member of the big molecular family of genes responsible for cells proliferation and DNA stability. We describe the case of two sisters, carrying the homozygous p. Arg609His variant of the gene, who present a milder phenotype of TELO2-related syndrome. Such variant has been reported once in a more severely affected patient, in compound heterozygous state associated with the p. Pro260Leu variant, suggesting a possible role of the p. Arg609His variant in determining milder phenotypes. Comparing the siblings with all previously reported cases, we offer an overview on the condition and discuss TELO2 genetic interactions, in order to further explore the molecular bases of this recently described disorder.
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Affiliation(s)
- Claudia Ciaccio
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Valentina Duga
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Esposito
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Isabella Moroni
- Child Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Raffaele Castello
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Luisa Chiapparini
- Neuroradiology Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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16
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Advances in the evaluation and management of cortical/cerebral visual impairment in children. Surv Ophthalmol 2020; 65:708-724. [DOI: 10.1016/j.survophthal.2020.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
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17
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Del-Prado-Sánchez C, Armstrong-Moron J, Veiga C, Grixolli-Mazzon S, García-Cazorla À, Juliá-Palacios N, Morales-Ballús M. Cataract in You-Hoover-Fong syndrome: TELO2 deficiency. Ophthalmic Genet 2020; 41:656-658. [PMID: 32940098 DOI: 10.1080/13816810.2020.1821382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Recently, You, Hoover-Fong, and colleagues described a disease caused by a deficiency of the telomere maintenance 2 gene (TELO2) function. The clinical spectrum includes early-onset global delay, dysmorphic facial features, auditory disorder, and reduced vision. MATERIALS AND METHODS We report two siblings, diagnosed with You-Hoover-Fong syndrome at the age of 28 and 14 months. Both were genetically studied to find the cause of their developmental delay and microcephaly. RESULTS The identical compound heterozygous missense mutations in the TELO2gene were found in each. Ophthalmologically, both siblings were diagnosed with progressive congenital bilateral nuclear-lamellar cataracts. CONCLUSIONS We report nuclear-lamellar cataracts in two siblings diagnosed with You-Hoover-Fong syndrome.
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Affiliation(s)
| | | | - Carla Veiga
- Ophthalmology Department, Sant Joan de deu Hospital , Barcelona, Spain
| | | | - Àngels García-Cazorla
- NeurometabolicUnit. Neurology Department, IPR CIBERER and MetabERN. Sant Joan De Deu Hospital , Barcelona, Spain
| | - Natalia Juliá-Palacios
- NeurometabolicUnit. Neurology Department, IPR CIBERER and MetabERN. Sant Joan De Deu Hospital , Barcelona, Spain
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18
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[Syndromic intellectual disability disorder caused by variants in TELO2 or You-Hoover-Fong syndrome]. An Pediatr (Barc) 2020; 94:265-267. [PMID: 32709525 DOI: 10.1016/j.anpedi.2020.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 11/23/2022] Open
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19
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Picher-Martel V, Labrie Y, Rivest S, Lace B, Chrestian N. Whole-exome sequencing identifies homozygous mutation in TTI2 in a child with primary microcephaly: a case report. BMC Neurol 2020; 20:58. [PMID: 32061250 PMCID: PMC7023720 DOI: 10.1186/s12883-020-01643-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/12/2020] [Indexed: 12/31/2022] Open
Abstract
Background Primary microcephaly is defined as reduced occipital-frontal circumference noticeable before 36 weeks of gestation. Large amount of insults might lead to microcephaly including infections, hypoxia and genetic mutations. More than 16 genes are described in autosomal recessive primary microcephaly. However, the cause of microcephaly remains unclear in many cases after extensive investigations and genetic screening. Case presentation Here, we described the case of a boy with primary microcephaly who presented to a neurology clinic with short stature, global development delay, dyskinetic movement, strabismus and dysmorphic features. We performed microcephaly investigations and genetic panels. Then, we performed whole-exome sequencing to identify any genetic cause. Microcephaly investigations and genetic panels were negative, but we found a new D317V homozygous mutation in TELOE-2 interacting protein 2 (TTI2) gene by whole-exome sequencing. TTI2 is implicated in DNA damage response and mutation in that gene was previously described in mental retardation, autosomal recessive 39. Conclusions We described the first French Canadian case with primary microcephaly and global developmental delay secondary to a new D317V homozygous mutation in TTI2 gene. Our report also highlights the importance of TTI2 protein in brain development.
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Affiliation(s)
- Vincent Picher-Martel
- Department of psychiatry and neurosciences, Centre de recherche Cervo Brain Research Centre and CHU de Québec, Laval University, 2601 chemin de la canardière, Québec, Qc, G1J 2G3, Canada.
| | - Yvan Labrie
- Centre de recherche du CHU de Québec-Universtié Laval, Québec, Qc, Canada
| | - Serge Rivest
- Centre de recherche CHU de Québec- Universtié Laval, Québec, Qc, Canada
| | - Baiba Lace
- Department of Clinical Genetic, CHU de Québec- Université Laval, Québec, Qc, Canada
| | - Nicolas Chrestian
- Department of Paediatric Neurology, Paediatric Neuromuscular Disorder, Centre Mère Enfant Soleil, Laval University, Québec, Qc, Canada
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20
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Ilyas M, Mir A, Efthymiou S, Houlden H. The genetics of intellectual disability: advancing technology and gene editing. F1000Res 2020; 9. [PMID: 31984132 PMCID: PMC6966773 DOI: 10.12688/f1000research.16315.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) is a neurodevelopmental condition affecting 1–3% of the world’s population. Genetic factors play a key role causing the congenital limitations in intellectual functioning and adaptive behavior. The heterogeneity of ID makes it more challenging for genetic and clinical diagnosis, but the advent of large-scale genome sequencing projects in a trio approach has proven very effective. However, many variants are still difficult to interpret. A combined approach of next-generation sequencing and functional, electrophysiological, and bioinformatics analysis has identified new ways to understand the causes of ID and help to interpret novel ID-causing genes. This approach offers new targets for ID therapy and increases the efficiency of ID diagnosis. The most recent functional advancements and new gene editing techniques involving the use of CRISPR–Cas9 allow for targeted editing of DNA in
in vitro and more effective mammalian and human tissue-derived disease models. The expansion of genomic analysis of ID patients in diverse and ancient populations can reveal rare novel disease-causing genes.
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Affiliation(s)
- Muhammad Ilyas
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan.,Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Asif Mir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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21
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Wang R, Han S, Liu H, Khan A, Xiaerbati H, Yu X, Huang J, Zhang X. Novel Compound Heterozygous Mutations in TTI2 Cause Syndromic Intellectual Disability in a Chinese Family. Front Genet 2019; 10:1060. [PMID: 31737043 PMCID: PMC6830114 DOI: 10.3389/fgene.2019.01060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Telomere maintenance 2 (TELO2)-interacting protein 2 (TTI2) interacts with TTI1 and TELO2 to form the Triple T complex, which is required for various cellular processes, including the double-strand DNA break response, nonsense-mediated mRNA decay, and telomerase assembly. Herein, we identified compound heterozygous mutations in TTI2 using whole-exome sequencing (WES) in a Chinese family with a recessive inheritance pattern of syndromic intellectual disability. The patients displayed intellectual disability, aggressive and self-injurious behaviors, facial dysmorphic features, microcephaly, and skeletal anomalies. In addition, one patient showed cerebral white matter abnormality. Maternal novel indel mutation resulted in a premature termination codon and nonsense-mediated mRNA decay. Paternal reported c.1100C > T mutation changed the highly conserved proline to leucine that located in the DUF2454 domain. Immunoblotting experiments showed significantly decreased TTI2, TTI1, and TELO2 in the patients' lymphocytes. These results indicated that TTI2 loss-of-function mutations might cause an autosomal-recessive syndromic intellectual disability by affecting the Triple T complex. Our report expands the genetic causes of syndromic intellectual disability in the Chinese population.
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Affiliation(s)
- Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongyan Liu
- Medical Genetics Institute, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Habulieti Xiaerbati
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Yu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Department of Pediatrics, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Jia Huang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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22
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Ziegler A, Bader P, McWalter K, Douglas G, Houdayer C, Bris C, Rouleau S, Coutant R, Colin E, Bonneau D. Confirmation that variants in TTI2 are responsible for autosomal recessive intellectual disability. Clin Genet 2019; 96:354-358. [PMID: 31290144 DOI: 10.1111/cge.13603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/21/2019] [Accepted: 06/30/2019] [Indexed: 12/30/2022]
Abstract
TTI2 (MIM 614126) has been described as responsible for autosomal recessive intellectual disability (ID; MRT39, MIM:615541) in only two inbred families. Here, we give an account of two individuals from two unrelated outbred families harbouring compound heterozygous TTI2 pathogenic variants. Together with severe ID, progressive microcephaly, scoliosis and sleeping disorder are the most striking features in the two individuals concerned. TTI2, together with TTI1 and TELO2, encode proteins that constitute the triple T heterotrimeric complex. This TTT complex interacts with the HSP90 and R2TP to form a super-complex that has a chaperone function stabilising and maturing a number of kinases, such as ataxia-telangiectasia mutated and mechanistic target of rapamycin, which are key regulators of cell proliferation and genome maintenance. Pathogenic variants in TTI2 logically result in a phenotype close to that caused by TELO2 variants.
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Affiliation(s)
- Alban Ziegler
- Département de Biochimie et Génétique du CHU d'Angers, Centre Hospitalier Universitaire d'Angers, Angers, France.,Mitolab, UMR INSERM 1083-CNRS 6015, Université d'Angers, Angers, France
| | | | | | - Ganka Douglas
- Exome Sequencing Program, GeneDx, Gaithersburg, Maryland
| | - Clara Houdayer
- Département de Biochimie et Génétique du CHU d'Angers, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Céline Bris
- Département de Biochimie et Génétique du CHU d'Angers, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Stephanie Rouleau
- Service d'Endocrinologie Pédiatrique, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Régis Coutant
- Service d'Endocrinologie Pédiatrique, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Estelle Colin
- Département de Biochimie et Génétique du CHU d'Angers, Centre Hospitalier Universitaire d'Angers, Angers, France.,Mitolab, UMR INSERM 1083-CNRS 6015, Université d'Angers, Angers, France
| | - Dominique Bonneau
- Département de Biochimie et Génétique du CHU d'Angers, Centre Hospitalier Universitaire d'Angers, Angers, France.,Mitolab, UMR INSERM 1083-CNRS 6015, Université d'Angers, Angers, France
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23
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Liu Y, Zhang C, Li L, Ou B, Yuan L, Zhang T, Fan J, Peng Z. Genome-Wide Association Study of Tacrolimus Pharmacokinetics Identifies Novel Single Nucleotide Polymorphisms in the Convalescence and Stabilization Periods of Post-transplant Liver Function. Front Genet 2019; 10:528. [PMID: 31214251 PMCID: PMC6554639 DOI: 10.3389/fgene.2019.00528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/14/2019] [Indexed: 12/15/2022] Open
Abstract
After liver transplantation, the liver function of a patient is gradually restored over a period of time that can be divided into a convalescence period (CP) and a stabilizing period (SP). The plasma concentration of tacrolimus, an immunosuppressant commonly used to prevent organ rejection, varies as a result of variations in its metabolism. The effects of genetic and clinical factors on the plasma concentration of tacrolimus appear to differ in the CP and SP. To establish a model explaining the variation in tacrolimus trough concentration between individuals in the CP and SP, we conducted a retrospective, single-center, discovery study of 115 pairs of patients (115 donors and 115 matched recipients) who had undergone liver transplantation. Donors and recipients were genotyped by a genome-wide association study (GWAS) using an exome chip. Novel exons were identified that influenced tacrolimus trough concentrations and were verified with bootstrap analysis. In donors, two single-nucleotide polymorphisms showed an effect on the CP (rs1927321, rs1057192) and four showed an effect on the SP (rs776746, rs2667662, rs7980521, rs4903096); in recipients, two single-nucleotide polymorphisms showed an effect in the SP (rs7828796, rs776746). Genetic factors played a crucial role in tacrolimus metabolism, accounting for 44.8% in the SP, which was higher than previously reported. In addition, we found that CYP3A5, which is known to affect the metabolism of tacrolimus, only influenced tacrolimus pharmacokinetics in the SP.
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Affiliation(s)
- Yuan Liu
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Li
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baochi Ou
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liyun Yuan
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tao Zhang
- Department of Organ Transplant, The Second Affiliated Hospital to Guangzhou Medical University, Guangzhou, China
| | - Junwei Fan
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhihai Peng
- Department of Hepatobiliary Pancreatic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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24
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Studying the effects of haplotype partitioning methods on the RA-associated genomic results from the North American Rheumatoid Arthritis Consortium (NARAC) dataset. J Adv Res 2019; 18:113-126. [PMID: 30891314 PMCID: PMC6403413 DOI: 10.1016/j.jare.2019.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/14/2019] [Indexed: 12/16/2022] Open
Abstract
Haplotype blocks methods plays a complementary role to the single-SNP approaches. CIT, FGT, SSLD, and single-SNP methods should be applied to discover the markers. Selection of the method used for the association has an impact on the biomarkers. SSLD method detected more significant SNPs than CIT, FGT, and single-SNP methods. The 383 SNPs discovered by all methods are significantly associated with RA.
The human genome, which includes thousands of genes, represents a big data challenge. Rheumatoid arthritis (RA) is a complex autoimmune disease with a genetic basis. Many single-nucleotide polymorphism (SNP) association methods partition a genome into haplotype blocks. The aim of this genome wide association study (GWAS) was to select the most appropriate haplotype block partitioning method for the North American Rheumatoid Arthritis Consortium (NARAC) dataset. The methods used for the NARAC dataset were the individual SNP approach and the following haplotype block methods: the four-gamete test (FGT), confidence interval test (CIT), and solid spine of linkage disequilibrium (SSLD). The measured parameters that reflect the strength of the association between the biomarker and RA were the P-value after Bonferroni correction and other parameters used to compare the output of each haplotype block method. This work presents a comparison among the individual SNP approach and the three haplotype block methods to select the method that can detect all the significant SNPs when applied alone. The GWAS results from the NARAC dataset obtained with the different methods are presented. The individual SNP, CIT, FGT, and SSLD methods detected 541, 1516, 1551, and 1831 RA-associated SNPs respectively, and the individual SNP, FGT, CIT, and SSLD methods detected 65, 156, 159, and 450 significant SNPs respectively, that were not detected by the other methods. Three hundred eighty-three SNPs were discovered by the haplotype block methods and the individual SNP approach, while 1021 SNPs were discovered by all three haplotype block methods. The 383 SNPs detected by all the methods are promising candidates for studying RA susceptibility. A hybrid technique involving all four methods should be applied to detect the significant SNPs associated with RA in the NARAC dataset, but the SSLD method may be preferred because of its advantages when only one method was used.
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Affiliation(s)
- Mohamed N Saad
- Biomedical Engineering Department, Faculty of Engineering, Minia University, Minia, Egypt
| | - Mai S Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology, 6th of October City, Egypt
| | - Ayman M Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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25
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Paganini L, Hadi LA, Chetta M, Rovina D, Fontana L, Colapietro P, Bonaparte E, Pezzani L, Marchisio P, Tabano SM, Costanza J, Sirchia SM, Riboni L, Milani D, Miozzo M. A HS6ST2 gene variant associated with X-linked intellectual disability and severe myopia in two male twins. Clin Genet 2018; 95:368-374. [PMID: 30471091 PMCID: PMC6392117 DOI: 10.1111/cge.13485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Abstract
X-linked intellectual disability (XLID) refers to a clinically and genetically heterogeneous neurodevelopmental disorder, in which males are more heavily affected than females. Among the syndromic forms of XLID, identified by additional clinical signs as part of the disease spectrum, the association between XLID and severe myopia has been poorly characterized. We used whole exome sequencing (WES) to study two Italian male twins presenting impaired intellectual function and adaptive behavior, in association with severe myopia and mild facial dysmorphisms. WES analysis detected the novel, maternally inherited, mutation c.916G > C (G306R) in the X-linked heparan sulfate 6-O-sulfotransferase 2 (HS6ST2) gene. HS6ST2 transfers sulfate from adenosine 3'-phosphate, 5'-phosphosulfate to the sixth position of the N-sulphoglucosamine residue in heparan sulfate (HS) proteoglycans. Low HS sulfation levels are associated with defective optic disc and stalk morphogenesis during mammalian visual system development. The c.916G>C variant affects the HS6ST2 substrate binding site, and its effect was considered "deleterious" by in-silico tools. An in-vitro enzymatic assay showed that the HS6ST2 mutant isoform had significantly reduced sulphotransferase activity. Taken together, the results suggest that mutant HS6ST2 is possibly involved in the development of myopia and cognitive impairment, characteristics of the probands reported here.
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Affiliation(s)
- Leda Paganini
- Division of pathology, Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Loubna A Hadi
- Department of Medical Biotechnology and Translational Medicine, LITA-Segrate, Università degli Studi di Milano, Milan, Italy
| | | | - Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Laura Fontana
- Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Patrizia Colapietro
- Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Eleonora Bonaparte
- Division of pathology, Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lidia Pezzani
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Marchisio
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia M Tabano
- Division of pathology, Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Jole Costanza
- Division of pathology, Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia M Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Laura Riboni
- Department of Medical Biotechnology and Translational Medicine, LITA-Segrate, Università degli Studi di Milano, Milan, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Monica Miozzo
- Division of pathology, Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
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26
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Mealy MA, Nam TS, Pardo SJ, Pardo CA, Sobreira NL, Avramopoulos D, Valle D, Burns KH, Levy M. Familial monophasic acute transverse myelitis due to the pathogenic variant in VPS37A. NEUROLOGY-GENETICS 2018; 4:e213. [PMID: 29473047 PMCID: PMC5820602 DOI: 10.1212/nxg.0000000000000213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/20/2017] [Indexed: 12/30/2022]
Abstract
Objective To identify genetic differences among siblings with a family history of idiopathic transverse myelitis (ITM). Methods We compared whole-exome sequencing (WES) on germline samples from the 2 affected sisters with ITM with 3 of their healthy siblings. Results The 2 sisters with ITM both had acute onset of sensory loss in the legs, weakness, and bowel/bladder dysfunction. The first developed ITM at age 15 years with a clinical nadir of complete paralysis, which slowly recovered over a few years. MRI demonstrated a persistent T2 lesion in the lower thoracic cord. The second developed ITM at age 50 years with a nadir of sensory loss from T6 down and paraparesis in the legs, associated with an MRI lesion at T6. She also made a partial recovery with treatment. Both sisters are homozygous for a missense variant in VPS37A (c.700C>A, p.Leu234Ile) identified by WES. We performed targeted sequencing of VPS37A in an additional 86 samples from patients with ITM and 175 with other diseases to investigate the p.Leu234Ile variant. We identified another patient with ITM homozygous for the same rare variant. No patients with multiple sclerosis, neuromyelitis optica, other neurologic conditions, or any healthy controls in public databases were homozygous for this variant. Conclusions A rare missense variant in VPS37A may predispose to development of ITM. Further studies are necessary to determine the frequency of this variant in the patient population and the mechanism through which it contributes to the risk of disease.
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Affiliation(s)
- Maureen A Mealy
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Tai-Seung Nam
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Santiago J Pardo
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Carlos A Pardo
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Nara L Sobreira
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Dimitrios Avramopoulos
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - David Valle
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Kathleen H Burns
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
| | - Michael Levy
- Department of Neurology (M.A.M., S.J.P., C.A.P., M.L.), Institute of Genetic Medicine (N.L.S., D.A., D.V., K.H.B.), and Department of Pathology (K.H.B.), Johns Hopkins University, Baltimore, MD; and Department of Neurology (T.-S.N.), Chonnam National University Medical School, Gwangju, South Korea
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27
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Moosa S, Altmüller J, Lyngbye T, Christensen R, Li Y, Nürnberg P, Yigit G, Vogel I, Wollnik B. Novel compound heterozygous mutations in TELO2 in a patient with severe expression of You-Hoover-Fong syndrome. Mol Genet Genomic Med 2017; 5:580-584. [PMID: 28944240 PMCID: PMC5606883 DOI: 10.1002/mgg3.287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/03/2022] Open
Abstract
Background Very recently, compound heterozygous loss‐of‐function mutations in TELO2 were shown to underlie the newly‐described You‐Hoover‐Fong syndrome. TELO2 forms part of the co‐chaperone triple T complex (TTT complex), which plays an important role in the maturation and stabilization of the phosphatidylinositol 3‐kinase‐related protein kinases (PIKKs). Patients with mutations in TELO2 present with microcephaly and associated intellectual disability, postnatal growth retardation and dysmorphic features. Here, we describe Danish sisters with two novel mutations in TELO2. In particular, we highlight the clinical features of the 22‐year index patient, which are more severe than the original patients described, thereby expanding the clinical spectrum of YHFS. Methods The index patient was clinically examined and subsequently exome sequencing on her DNA was performed using the NimbleGen SeqCap EZ Human Exome Library v2.0 enrichment kit on an Illumina HiSeq2000 sequencer. Results Two novel, compound heterozygous mutations in TELO2 were identified in the index patient and her deceased older sister. Both have clinical features in keeping with the original YHFS patients, although the index patient seems to represent the severe end of the clinical spectrum with very marked prenatal onset growth retardation and microcephaly, severe global developmental delay and facial dysmorphic features. Additional clinical findings include eye anomalies (bilateral congenital cataracts, retinitis pigmentosa, convergent squint), bilateral conductive hearing loss, an abnormal kidney and seizures. Conclusion This report of Danish siblings with YHFS serves to expand the presentation of this new syndrome to include features in keeping with a form of microcephalic primordial dwarfism on the severe end of the clinical spectrum, and adds two novel mutations to the TELO2 mutational spectrum.
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Affiliation(s)
- Shahida Moosa
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
| | - Janine Altmüller
- Institute of Human GeneticsUniversity of CologneCologneGermany.,Cologne Center for GenomicsUniversity of CologneCologneGermany
| | - Troels Lyngbye
- The Centre for Deafblindness and Hearing LossAalborgDenmark
| | - Rikke Christensen
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
| | - Yun Li
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
| | - Peter Nürnberg
- Cologne Center for GenomicsUniversity of CologneCologneGermany
| | - Gökhan Yigit
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
| | - Ida Vogel
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
| | - Bernd Wollnik
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
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Baldridge D, Heeley J, Vineyard M, Manwaring L, Toler TL, Fassi E, Fiala E, Brown S, Goss CW, Willing M, Grange DK, Kozel BA, Shinawi M. The Exome Clinic and the role of medical genetics expertise in the interpretation of exome sequencing results. Genet Med 2017; 19:1040-1048. [PMID: 28252636 PMCID: PMC5581723 DOI: 10.1038/gim.2016.224] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/13/2016] [Indexed: 02/03/2023] Open
Abstract
Purpose Evaluation of the clinician’s role in optimal interpretation of clinical exome sequencing (ES) results. Methods Retrospective chart review of the first 155 patients who underwent clinical ES in our Exome Clinic and direct interaction with the ordering geneticist to evaluate the process of interpretation of results. Results The most common primary indication was neurodevelopmental problems (~66%), followed by multiple congenital anomalies (~10%). The overall diagnostic yield was 36% based on sequencing data. After assessment by the medical geneticist, incorporation of detailed phenotypic and molecular data, and utilization of additional diagnostic modalities, the final diagnostic yield was increased to 43%. Seven patients of our cohort were included in initial case series that described novel genetic syndromes, and 23% of patients were involved in subsequent research studies directly related to their results or involved in efforts to move beyond clinical ES for diagnosis. The clinical management was directly altered due to the ES findings in 12% of definitively diagnosed cases. Conclusions Our results emphasize the usefulness of ES, demonstrate the significant role of the medical geneticist in the diagnostic process of patients undergoing ES, and illustrate the benefits of post-analytical diagnostic work-up in solving the “diagnostic odyssey.”
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Affiliation(s)
- Dustin Baldridge
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer Heeley
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Current affiliation: Mercy Clinic-Kids Genetics, Mercy Children's Hospital St. Louis, St. Louis, Missouri, USA
| | - Marisa Vineyard
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Linda Manwaring
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tomi L Toler
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elise Fiala
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sarah Brown
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charles W Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Marcia Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Beth A Kozel
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Current affiliation: National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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Sobreira NL, Valle D. Lessons learned from the search for genes responsible for rare Mendelian disorders. Mol Genet Genomic Med 2016; 4:371-5. [PMID: 27468413 PMCID: PMC4947856 DOI: 10.1002/mgg3.233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nara L Sobreira
- McKusick-Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMaryland 21205; Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMaryland 21205
| | - David Valle
- McKusick-Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMaryland 21205; Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMaryland 21205
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