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Bönnemann CG, Krishnamoorthy KS, Johnston JJ, Lee MM, Fowler DJ, Biesecker LG, Holmes LB. Clinical and molecular heterogeneity of syndromic hypothalamic hamartoma. Am J Med Genet A 2023; 191:2337-2343. [PMID: 37435845 PMCID: PMC10524239 DOI: 10.1002/ajmg.a.63306] [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: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 07/13/2023]
Abstract
Two children are presented who have a distinct syndrome of multiple buccolingual frenula, a stiff and short fifth finger with small nails, a hypothalamic hamartoma, mild to moderate neurological impairment, and mild endocrinological symptoms. No variant assessed to be pathogenic or likely pathogenic was detected in the GLI3 gene in either child. This syndrome appears to be distinct from the inherited Pallister-Hall syndrome associated with GLI3 variants, which is characterized by hypothalamic hamartoma, mesoaxial polydactyly, and other anomalies. In the individuals described here, manifestations outside of the central nervous system were milder and the mesoaxial polydactyly, which is common in individuals with Pallister-Hall syndrome, was absent. Instead, these children had multiple buccolingual frenula together with the unusual appearance of the fifth digit. It remains unclear whether these two individuals represent a separate nosologic entity or if they represent a milder manifestation of one of the more severe syndromes associated with a hypothalamic hamartoma.
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Affiliation(s)
- Carsten G Bönnemann
- Pediatric Neurology, The Neurology Service, Massachusetts General Hospital, Boston, Massachusetts, United States
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
- Sidney Kimmel Medical College, Philadelphia, Pennsylvania, United States
| | - Kalpathy S Krishnamoorthy
- Pediatric Neurology, The Neurology Service, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Jennifer J Johnston
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Mary M Lee
- Pediatric Endocrinology, Mass General for Children, Boston, Massachusetts, United States
- Nemours Children's Health, DV, Wilmington, Delaware, United States
| | - Darren J Fowler
- Medical Genetics and Metabolism Unit, Mass General for Children, Boston, Massachusetts, United States
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Lewis B Holmes
- Medical Genetics and Metabolism Unit, Mass General for Children, Boston, Massachusetts, United States
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2
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Park MA, Zaw T, Yoder SJ, Gomez M, Genilo-Delgado M, Basinski T, Katende E, Dam A, Mok SRS, Monteiro A, Mohammadi A, Jeong DK, Jiang K, Centeno BA, Hodul P, Malafa M, Fleming J, Chen DT, Mo Q, Teer JK, Permuth JB. A pilot study to evaluate tissue- and plasma-based DNA driver mutations in a cohort of patients with pancreatic intraductal papillary mucinous neoplasms. G3 (BETHESDA, MD.) 2022; 13:6861874. [PMID: 36454217 PMCID: PMC9911050 DOI: 10.1093/g3journal/jkac314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
Intraductal papillary mucinous neoplasms (IPMNs) are precursor lesions to pancreatic ductal adenocarcinoma that are challenging to manage due to limited imaging, cytologic, and molecular markers that accurately classify lesions, grade of dysplasia, or focus of invasion preoperatively. The objective of this pilot study was to determine the frequency and type of DNA mutations in a cohort of surgically resected, pathologically confirmed IPMN, and to determine if concordant mutations are detectable in paired pretreatment plasma samples. Formalin-fixed paraffin-embedded (FFPE) tissue from 46 surgically resected IPMNs (31 low-grade, 15 high-grade) and paired plasma from a subset of 15 IPMN cases (10 low-grade, 5 high-grade) were subjected to targeted mutation analysis using a QIAseq Targeted DNA Custom Panel. Common driver mutations were detected in FFPE from 44 of 46 (95.6%) IPMN cases spanning all grades; the most common DNA mutations included: KRAS (80%), RNF43 (24%), and GNAS (43%). Of note, we observed a significant increase in the frequency of RNF43 mutations from low-grade to high-grade IPMNs associated or concomitant with invasive carcinoma (trend test, P = 0.01). Among the subset of cases with paired plasma, driver mutations identified in the IPMNs were not detected in circulation. Overall, our results indicate that mutational burden for IPMNs is a common occurrence, even in low-grade IPMNs. Furthermore, although blood-based biopsies are an attractive, noninvasive method for detecting somatic DNA mutations, the QIAseq panel was not sensitive enough to detect driver mutations that existed in IPMN tissue using paired plasma in the volume we were able to retrieve for this retrospective study.
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Affiliation(s)
| | | | - Sean J Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Maria Gomez
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Maria Genilo-Delgado
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Toni Basinski
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Esther Katende
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Aamir Dam
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Shaffer R S Mok
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Alvaro Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Amir Mohammadi
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Daniel K Jeong
- Department of Diagnostic Imaging and Interventional Radiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Kun Jiang
- Department of Anatomic Pathology, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | - Barbara A Centeno
- Department of Anatomic Pathology, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | - Pamela Hodul
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Jason Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Dung-Tsa Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | | | - Jennifer B Permuth
- Corresponding author: Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA.
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3
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Lui JC, Raimann A, Hojo H, Dong L, Roschger P, Kikani B, Wintergerst U, Fratzl-Zelman N, Jee YH, Haeusler G, Baron J. A neomorphic variant in SP7 alters sequence specificity and causes a high-turnover bone disorder. Nat Commun 2022; 13:700. [PMID: 35121733 PMCID: PMC8816926 DOI: 10.1038/s41467-022-28318-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/20/2022] [Indexed: 12/14/2022] Open
Abstract
SP7/Osterix is a transcription factor critical for osteoblast maturation and bone formation. Homozygous loss-of-function mutations in SP7 cause osteogenesis imperfecta type XII, but neomorphic (gain-of-new-function) mutations of SP7 have not been reported in humans. Here we describe a de novo dominant neomorphic missense variant (c.926 C > G:p.S309W) in SP7 in a patient with craniosynostosis, cranial hyperostosis, and long bone fragility. Histomorphometry shows increased osteoblasts but decreased bone mineralization. Mice with the corresponding variant also show a complex skeletal phenotype distinct from that of Sp7-null mice. The mutation alters the binding specificity of SP7 from AT-rich motifs to a GC-consensus sequence (typical of other SP family members) and produces an aberrant gene expression profile, including increased expression of Col1a1 and endogenous Sp7, but decreased expression of genes involved in matrix mineralization. Our study identifies a pathogenic mechanism in which a mutation in a transcription factor shifts DNA binding specificity and provides important in vivo evidence that the affinity of SP7 for AT-rich motifs, unique among SP proteins, is critical for normal osteoblast differentiation.
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Affiliation(s)
- Julian C Lui
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Adalbert Raimann
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Pulmonology, Allergology and Endocrinology, Medical University of Vienna, Vienna, Austria
- Vienna Bone and Growth Center, Vienna, Austria
| | - Hironori Hojo
- Center for Disease and Integrative Medicine, University of Tokyo, Tokyo, Japan
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Paul Roschger
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of OEGK and AUVA Trauma Centre Meidling, 1st Medical Department, Hanusch Hospital, Vienna, Austria
| | - Bijal Kikani
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Uwe Wintergerst
- Department of Pediatrics, Hospital of Braunau, Braunau, Austria
| | - Nadja Fratzl-Zelman
- Vienna Bone and Growth Center, Vienna, Austria
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of OEGK and AUVA Trauma Centre Meidling, 1st Medical Department, Hanusch Hospital, Vienna, Austria
| | - Youn Hee Jee
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Gabriele Haeusler
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Pulmonology, Allergology and Endocrinology, Medical University of Vienna, Vienna, Austria
- Vienna Bone and Growth Center, Vienna, Austria
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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4
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Sumathipala D, Strømme P, Fattahi Z, Lüders T, Sheng Y, Kahrizi K, Einarsen IH, Sloan JL, Najmabadi H, van den Heuvel L, Wevers RA, Guerrero-Castillo S, Mørkrid L, Valayannopoulos V, Backe PH, Venditti CP, van Karnebeek CD, Nilsen H, Frengen E, Misceo D. ZBTB11 dysfunction: spectrum of brain abnormalities, biochemical signature and cellular consequences. Brain 2022; 145:2602-2616. [PMID: 35104841 PMCID: PMC9337812 DOI: 10.1093/brain/awac034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Bi-allelic pathogenic variants in ZBTB11 have been associated with intellectual developmental disorder, autosomal recessive 69 (MRT69; OMIM 618383). We report five patients from three families with novel, bi-allelic variants in ZBTB11. We have expanded the clinical phenotype of MRT69, documenting varied severity of atrophy affecting different brain regions and described combined malonic and methylmalonic aciduria as a biochemical manifestation. As ZBTB11 encodes for a transcriptional regulator, we performeded chromatin immunoprecipitation-sequencing targeting ZBTB11 in fibroblasts from patients and controls. Chromatin immunoprecipitation-sequencing revealed binding of wild-type ZBTB11 to promoters in 238 genes, among which genes encoding proteins involved in mitochondrial functions and RNA processing are over-represented. Mutated ZBTB11 showed reduced binding to 61 of the targeted genes, indicating that the variants act as loss of function. Most of these genes are related to mitochondrial functions. Transcriptome analysis of the patient fibroblasts revealed dysregulation of mitochondrial functions. In addition, we uncovered that reduced binding of the mutated ZBTB11 to ACSF3 leads to decreased ACSF3 transcript level, explaining combined malonic and methylmalonic aciduria. Collectively, these results expand the clinical spectrum of ZBTB11-related neurological disease and give insight into the pathophysiology in which the dysfunctional ZBTB11 affect mitochondrial functions and RNA processing contributing to the neurological and biochemical phenotypes.
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Affiliation(s)
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Torben Lüders
- Department of Clinical Molecular Biology, Section of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ingunn Holm Einarsen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Jennifer L Sloan
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Lambert van den Heuvel
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands,United for Metabolic Disease—UMD, The Netherlands
| | - Sergio Guerrero-Castillo
- University Children’s Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Paul Hoff Backe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Charles P Venditti
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Clara D van Karnebeek
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands,United for Metabolic Disease—UMD, The Netherlands,Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Section of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | | | - Doriana Misceo
- Correspondence to: Doriana Misceo Department of Medical Genetics Oslo University Hospital and University of Oslo Postboks 4956 Nydalen, 0424 Oslo, Norway E-mail:
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5
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Rudd ML, Hansen NF, Zhang X, Urick ME, Zhang S, Merino MJ, Mullikin JC, Brody LC, Bell DW. KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas. PLoS One 2022; 17:e0251286. [PMID: 35081118 PMCID: PMC8791453 DOI: 10.1371/journal.pone.0251286] [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: 05/04/2021] [Accepted: 11/05/2021] [Indexed: 12/24/2022] Open
Abstract
Endometrioid endometrial carcinomas (EECs) are the most common histological subtype of uterine cancer. Late-stage disease is an adverse prognosticator for EEC. The purpose of this study was to analyze EEC exome mutation data to identify late-stage-specific statistically significantly mutated genes (SMGs), which represent candidate driver genes potentially associated with disease progression. We exome sequenced 15 late-stage (stage III or IV) non-ultramutated EECs and paired non-tumor DNAs; somatic variants were called using Strelka, Shimmer, SomaticSniper and MuTect. Additionally, somatic mutation calls were extracted from The Cancer Genome Atlas (TCGA) data for 66 late-stage and 270 early-stage (stage I or II) non-ultramutated EECs. MutSigCV (v1.4) was used to annotate SMGs in the two late-stage cohorts and to derive p-values for all mutated genes in the early-stage cohort. To test whether late-stage SMGs are statistically significantly mutated in early-stage tumors, q-values for late-stage SMGs were re-calculated from the MutSigCV (v1.4) early-stage p-values, adjusting for the number of late-stage SMGs tested. We identified 14 SMGs in the combined late-stage EEC cohorts. When the 14 late-stage SMGs were examined in the TCGA early-stage data, only Krüppel-like factor 3 (KLF3) and Paired box 6 (PAX6) failed to reach significance as early-stage SMGs, despite the inclusion of enough early-stage cases to ensure adequate statistical power. Within TCGA, nonsynonymous mutations in KLF3 and PAX6 were, respectively, exclusive or nearly exclusive to the microsatellite instability (MSI)-hypermutated molecular subgroup and were dominated by insertions-deletions at homopolymer tracts. In conclusion, our findings are hypothesis-generating and suggest that KLF3 and PAX6, which encode transcription factors, are MSI target genes and late-stage-specific SMGs in EEC.
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Affiliation(s)
- Meghan L. Rudd
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy F. Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaolu Zhang
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mary Ellen Urick
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Suiyuan Zhang
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maria J. Merino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - James C. Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lawrence C. Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daphne W. Bell
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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6
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Donkervoort S, Krause N, Dergai M, Yun P, Koliwer J, Gorokhova S, Geist Hauserman J, Cummings BB, Hu Y, Smith R, Uapinyoying P, Ganesh VS, Ghosh PS, Monaghan KG, Edassery SL, Ferle PE, Silverstein S, Chao KR, Snyder M, Ellingwood S, Bharucha‐Goebel D, Iannaccone ST, Dal Peraro M, Foley AR, Savas JN, Bolduc V, Fasshauer D, Bönnemann CG, Schwake M. BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy. EMBO Mol Med 2021; 13:e13787. [PMID: 34779586 PMCID: PMC8649873 DOI: 10.15252/emmm.202013787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022] Open
Abstract
BET1 is required, together with its SNARE complex partners GOSR2, SEC22b, and Syntaxin-5 for fusion of endoplasmic reticulum-derived vesicles with the ER-Golgi intermediate compartment (ERGIC) and the cis-Golgi. Here, we report three individuals, from two families, with severe congenital muscular dystrophy (CMD) and biallelic variants in BET1 (P1 p.(Asp68His)/p.(Ala45Valfs*2); P2 and P3 homozygous p.(Ile51Ser)). Due to aberrant splicing and frameshifting, the variants in P1 result in low BET1 protein levels and impaired ER-to-Golgi transport. Since in silico modeling suggested that p.(Ile51Ser) interferes with binding to interaction partners other than SNARE complex subunits, we set off and identified novel BET1 interaction partners with low affinity for p.(Ile51Ser) BET1 protein compared to wild-type, among them ERGIC-53. The BET1/ERGIC-53 interaction was validated by endogenous co-immunoprecipitation with both proteins colocalizing to the ERGIC compartment. Mislocalization of ERGIC-53 was observed in P1 and P2's derived fibroblasts; while in the p.(Ile51Ser) P2 fibroblasts specifically, mutant BET1 was also mislocalized along with ERGIC-53. Thus, we establish BET1 as a novel CMD/epilepsy gene and confirm the emerging role of ER/Golgi SNAREs in CMD.
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Affiliation(s)
- Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Niklas Krause
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Mykola Dergai
- Department of Fundamental NeurosciencesUniversity of LausanneLausanneSwitzerland
| | - Pomi Yun
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Judith Koliwer
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Svetlana Gorokhova
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Service de Génétique MédicaleHôpital de la Timone, APHMMarseilleFrance
- INSERM, U1251‐MMGAix‐Marseille UniversitéMarseilleFrance
| | - Janelle Geist Hauserman
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Beryl B Cummings
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | | | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Research for Genetic MedicineChildren's National Medical CenterWashingtonDCUSA
| | - Vijay S Ganesh
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
- Department of NeurologyBrigham & Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Partha S Ghosh
- Department of NeurologyBoston Children's HospitalBostonMAUSA
| | | | - Seby L Edassery
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Pia E Ferle
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Sarah Silverstein
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Rutgers New Jersey School of MedicineNewarkNJUSA
- Undiagnosed Diseases ProgramNational Human Genome Research InstituteNational Institute of HealthBethesdaMDUSA
| | - Katherine R Chao
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Molly Snyder
- Department of NeurologyChildren's HealthDallasTXUSA
| | | | - Diana Bharucha‐Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Division of NeurologyChildren’s National Medical CenterWashingtonDCUSA
| | - Susan T Iannaccone
- Division of Pediatric NeurologyDepartments of Pediatrics, Neurology and NeurotherapeuticsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Matteo Dal Peraro
- Institute of BioengineeringSchool of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Jeffrey N Savas
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Véronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Dirk Fasshauer
- Department of Fundamental NeurosciencesUniversity of LausanneLausanneSwitzerland
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Michael Schwake
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
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7
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Dursun A, Yalnizoglu D, Yilmaz DY, Oguz KK, Gülbakan B, Koşukcu C, Akar HT, Kahraman AB, Acar NV, Günbey C, Yildiz Y, Ozgul RK. Biallelic mutations in ELFN1 gene associated with developmental and epileptic encephalopathy and joint laxity. Eur J Med Genet 2021; 64:104340. [PMID: 34509675 DOI: 10.1016/j.ejmg.2021.104340] [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: 01/25/2021] [Revised: 07/06/2021] [Accepted: 09/05/2021] [Indexed: 11/26/2022]
Abstract
ELFN1, a transmembrane leucine rich repeat protein, is involved in signal transduction in both neural cells and ROD ON-bipolar synaptogenesis. We present three siblings with developmental and epileptic encephalopathy and co-morbidities due to ELFN1 gene mutation; this is the first report in literature defining the human phenotype of ELFN1 gene mutation. Clinical, electrophysiological, and radiological findings along with comprehensive genetic studies of the patients and their family members are presented. Developmental and epileptic encephalopathy, autistic features, pyramidal signs, joint laxity, and dysmorphic features are the characteristic findings of this new clinical entity, involving mainly nervous system and possibly connective tissue. Whole exome sequence analysis followed by Sanger sequencing in all family members revealed disease-causing 8 bp frameshift mutation depicted as NM_001128636.2: c.42_49delGGCCGCCA; p. (Ala15Profs*241) in ELFN1. The variant, located in the signal peptide domain in the ELFN1 gene, was found to be homozygous in three patients, and heterozygous in the parents and three healthy siblings. Segregation analysis in family members together with pathogenicity assessment tools strongly supported the damaging effect of the frameshift variant on the function of the ELFN1 protein. Mutations in ELFN1 gene may be considered in patients with neonatal and infantile-onset epileptic encephalopathy before the full clinical picture is apparent.
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Affiliation(s)
- Ali Dursun
- Hacettepe University Faculty of Medicine, Department of Pediatric Metabolism, Ankara, Turkey.
| | - Dilek Yalnizoglu
- Hacettepe University Faculty of Medicine, Department of Pediatric Neurology, Ankara, Turkey
| | | | - Kader Karli Oguz
- Hacettepe University Faculty of Medicine, Department of Radiology, Ankara, Turkey
| | - Basri Gülbakan
- Hacettepe University Institute of Child Health, Ankara, Turkey
| | - Can Koşukcu
- Hacettepe University Institute of Health Sciences, Department of Bioinformatics, Ankara, Turkey
| | - Halil Tuna Akar
- Hacettepe University Faculty of Medicine, Department of Pediatric Metabolism, Ankara, Turkey
| | - Ayça Burcu Kahraman
- Hacettepe University Faculty of Medicine, Department of Pediatric Metabolism, Ankara, Turkey
| | | | - Ceren Günbey
- Hacettepe University Faculty of Medicine, Department of Pediatric Neurology, Ankara, Turkey
| | - Yilmaz Yildiz
- Hacettepe University Faculty of Medicine, Department of Pediatric Metabolism, Ankara, Turkey
| | - R Koksal Ozgul
- Hacettepe University Institute of Child Health, Ankara, Turkey
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8
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Jee YH, Gangat M, Yeliosof O, Temnycky AG, Vanapruks S, Whalen P, Gourgari E, Bleach C, Yu CH, Marshall I, Yanovski JA, Link K, Ten S, Baron J, Radovick S. Evidence That the Etiology of Congenital Hypopituitarism Has a Major Genetic Component but Is Infrequently Monogenic. Front Genet 2021; 12:697549. [PMID: 34456972 PMCID: PMC8386283 DOI: 10.3389/fgene.2021.697549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/12/2021] [Indexed: 01/31/2023] Open
Abstract
Purpose Congenital hypopituitarism usually occurs sporadically. In most patients, the etiology remains unknown. Methods We studied 13 children with sporadic congenital hypopituitarism. Children with non-endocrine, non-familial idiopathic short stature (NFSS) (n = 19) served as a control group. Exome sequencing was performed in probands and both unaffected parents. A burden testing approach was used to compare the number of candidate variants in the two groups. Results First, we assessed the frequency of rare, predicted-pathogenic variants in 42 genes previously reported to be associated with pituitary gland development. The average number of variants per individual was greater in probands with congenital hypopituitarism than those with NFSS (1.1 vs. 0.21, mean variants/proband, P = 0.03). The number of probands with at least 1 variant in a pituitary-associated gene was greater in congenital hypopituitarism than in NFSS (62% vs. 21%, P = 0.03). Second, we assessed the frequency of rare, predicted-pathogenic variants in the exome (to capture undiscovered causes) that were inherited in a fashion that could explain the sporadic occurrence of the proband's condition with a monogenic etiology (de novo mutation, autosomal recessive, or X-linked recessive) with complete penetrance. There were fewer monogenic candidates in the probands with congenital hypopituitarism than those with NFSS (1.3 vs. 2.5 candidate variants/proband, P = 0.024). We did not find any candidate variants (0 of 13 probands) in genes previously reported to explain the phenotype in congenital hypopituitarism, unlike NFSS (8 of 19 probands, P = 0.01). Conclusion Our findings provide evidence that the etiology of sporadic congenital hypopituitarism has a major genetic component but may be infrequently monogenic with full penetrance, suggesting a more complex etiology.
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Affiliation(s)
- Youn Hee Jee
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Mariam Gangat
- Division of Pediatric Endocrinology Rutgers Robert Wood Johnson Medical School Child Health Institute of New Jersey, New Brunswick, NJ, United States
| | - Olga Yeliosof
- Division of Pediatric Endocrinology Rutgers Robert Wood Johnson Medical School Child Health Institute of New Jersey, New Brunswick, NJ, United States
| | - Adrian G Temnycky
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Selena Vanapruks
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Philip Whalen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Evgenia Gourgari
- Division of Pediatric Endocrinology, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Cortney Bleach
- Division of Pediatric Endocrinology, Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Christine H Yu
- Section of Adult and Pediatric Endocrinology and Metabolism, University of Chicago, Chicago, IL, United States
| | - Ian Marshall
- Division of Pediatric Endocrinology Rutgers Robert Wood Johnson Medical School Child Health Institute of New Jersey, New Brunswick, NJ, United States
| | - Jack A Yanovski
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Kathleen Link
- Division of Pediatric Endocrinology, Pediatric Subspecialists of Virginia, Fairfax, VA, United States
| | - Svetlana Ten
- Pediatric Endocrinology, Richmond University Medical Center, Staten Island, NY, United States
| | - Jeffrey Baron
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sally Radovick
- Division of Pediatric Endocrinology Rutgers Robert Wood Johnson Medical School Child Health Institute of New Jersey, New Brunswick, NJ, United States
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9
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van de Locht M, Donkervoort S, de Winter JM, Conijn S, Begthel L, Kusters B, Mohassel P, Hu Y, Medne L, Quinn C, Moore SA, Foley AR, Seo G, Hwee DT, Malik FI, Irving T, Ma W, Granzier HL, Kamsteeg EJ, Immadisetty K, Kekenes-Huskey P, Pinto JR, Voermans N, Bönnemann CG, Ottenheijm CA. Pathogenic variants in TNNC2 cause congenital myopathy due to an impaired force response to calcium. J Clin Invest 2021; 131:145700. [PMID: 33755597 DOI: 10.1172/jci145700] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
Troponin C (TnC) is a critical regulator of skeletal muscle contraction; it binds Ca2+ to activate muscle contraction. Surprisingly, the gene encoding fast skeletal TnC (TNNC2) has not yet been implicated in muscle disease. Here, we report 2 families with pathogenic variants in TNNC2. Patients present with a distinct, dominantly inherited congenital muscle disease. Molecular dynamics simulations suggested that the pathomechanisms by which the variants cause muscle disease include disruption of the binding sites for Ca2+ and for troponin I. In line with these findings, physiological studies in myofibers isolated from patients' biopsies revealed a markedly reduced force response of the sarcomeres to [Ca2+]. This pathomechanism was further confirmed in experiments in which contractile dysfunction was evoked by replacing TnC in myofibers from healthy control subjects with recombinant, mutant TnC. Conversely, the contractile dysfunction of myofibers from patients was repaired by replacing endogenous, mutant TnC with recombinant, wild-type TnC. Finally, we tested the therapeutic potential of the fast skeletal muscle troponin activator tirasemtiv in patients' myofibers and showed that the contractile dysfunction was repaired. Thus, our data reveal that pathogenic variants in TNNC2 cause congenital muscle disease, and they provide therapeutic angles to repair muscle contractility.
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Affiliation(s)
- Martijn van de Locht
- Deptartment of Physiology, Amsterdam UMC (location VUmc), Amsterdam, Netherlands
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Josine M de Winter
- Deptartment of Physiology, Amsterdam UMC (location VUmc), Amsterdam, Netherlands
| | - Stefan Conijn
- Deptartment of Physiology, Amsterdam UMC (location VUmc), Amsterdam, Netherlands
| | - Leon Begthel
- Deptartment of Physiology, Amsterdam UMC (location VUmc), Amsterdam, Netherlands
| | - Benno Kusters
- Department of Neurology and Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Livija Medne
- Division of Human Genetics, Department of Pediatrics, Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Colin Quinn
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Gwimoon Seo
- Protein Expression Facility, Institute of Molecular Biophysics, The Florida State University, Tallahassee, Florida, USA
| | - Darren T Hwee
- Research and Early Development, Cytokinetics Inc., South San Francisco, California, USA
| | - Fady I Malik
- Research and Early Development, Cytokinetics Inc., South San Francisco, California, USA
| | - Thomas Irving
- BioCAT, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Weikang Ma
- BioCAT, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Henk L Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Erik-Jan Kamsteeg
- Department of Neurology and Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kalyan Immadisetty
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois, USA
| | - Peter Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois, USA
| | - José R Pinto
- Department of Biomedical Sciences, The Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Nicol Voermans
- Department of Neurology and Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Coen Ac Ottenheijm
- Deptartment of Physiology, Amsterdam UMC (location VUmc), Amsterdam, Netherlands.,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
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10
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Zhou Y, Sood R, Wang Q, Carrington B, Park M, Young AC, Birnbaum D, Liu Z, Ashizawa T, Mullikin JC, Koubeissi MZ, Liu P. Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion. Epilepsia Open 2021; 6:102-111. [PMID: 33681653 PMCID: PMC7918340 DOI: 10.1002/epi4.12450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 11/07/2020] [Accepted: 11/14/2020] [Indexed: 01/13/2023] Open
Abstract
Objective Our goal was to perform detailed clinical and genomic analysis of a large multigenerational Chinese family with 21 individuals showing symptoms of Familial Cortical Myoclonic Tremor with Epilepsy (FCMTE) that we have followed for over 20 years. Methods Patients were subjected to clinical evaluation, routine EEG, and structural magnetic resonance imaging. Whole exome sequencing, repeat-primed PCR, long-range PCR, and PacBio sequencing were performed to characterize the disease-causing mutation in this family. Results All evaluated patients manifested adult-onset seizures and presented with progressive myoclonic postural tremors starting after the third or fourth decade of life. Seizures typically diminished markedly in frequency with implementation of antiseizure medications but did not completely cease. The electroencephalogram of affected individuals showed generalized or multifocal spikes and slow wave complexes. An expansion of TTTTA motifs with addition of TTTCA motifs in intron 4 of SAMD12 was identified to segregate with the disease phenotype in this family. Furthermore, we found that the mutant allele is unstable and can undergo both contraction and expansion by changes in the number of repeat motifs each time it is passed to the next generation. The size of mutant allele varied from 5 to 5.5 kb with 549-603 copies of TTTTA and 287-343 copies of TTTCA repeat motifs in this family. Significance Our study provides a detailed description of clinical progression of FCMTE symptoms and its management with antiseizure medications. Our method of repeat analysis by PacBio sequencing of long-range PCR products does not require high-quality DNA and hence can be easily applied to other families to elucidate any correlation between the repeat size and phenotypic variables, such as, age of onset, and severity of symptoms.
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Affiliation(s)
- Yongxing Zhou
- Department of NeurologyMedStar St Mary’s Hospital/Georgetown University HospitalMedStar Medical GroupLeonardtownMDUSA
| | - Raman Sood
- Translational and Functional Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Qun Wang
- Epilepsy CenterDepartment of NeurologyBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
| | - Blake Carrington
- Translational and Functional Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Morgan Park
- NIH Intramural Sequencing CenterNational Human Genome Research InstituteNational Institutes of HealthRockvilleMDUSA
| | - Alice C. Young
- NIH Intramural Sequencing CenterNational Human Genome Research InstituteNational Institutes of HealthRockvilleMDUSA
| | - Daniel Birnbaum
- Department of NeurologyEinstein Medical CenterPhiladelphiaPAUSA
| | - Zhao Liu
- Division of Pediatric NeurologyChildren's Hospital of IllinoisUniversity of Illinois College of MedicineChicagoILUSA
| | - Tetsuo Ashizawa
- Houston Methodist Neurological Institute and Research InstituteHoustonTXUSA
| | - James C. Mullikin
- NIH Intramural Sequencing CenterNational Human Genome Research InstituteNational Institutes of HealthRockvilleMDUSA
| | - Mohamad Z. Koubeissi
- Epilepsy CenterDepartment of NeurologyGeorge Washington UniversityWashingtonDCUSA
| | - Paul Liu
- Translational and Functional Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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11
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Gonzalez-Calderon G, Liu R, Carvajal R, Teer JK. A negative storage model for precise but compact storage of genetic variation data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5820061. [PMID: 32293013 PMCID: PMC7157186 DOI: 10.1093/database/baz158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/21/2019] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Falling sequencing costs and large initiatives are resulting in increasing amounts of data available for investigator use. However, there are informatics challenges in being able to access genomic data. Performance and storage are well-appreciated issues, but precision is critical for meaningful analysis and interpretation of genomic data. There is an inherent accuracy vs. performance trade-off with existing solutions. The most common approach (Variant-only Storage Model, VOSM) stores only variant data. Systems must therefore assume that everything not variant is reference, sacrificing precision and potentially accuracy. A more complete model (Full Storage Model, FSM) would store the state of every base (variant, reference and missing) in the genome thereby sacrificing performance. A compressed variation of the FSM can store the state of contiguous regions of the genome as blocks (Block Storage Model, BLSM), much like the file-based gVCF model. We propose a novel approach by which this state is encoded such that both performance and accuracy are maintained. The Negative Storage Model (NSM) can store and retrieve precise genomic state from different sequencing sources, including clinical and whole exome sequencing panels. Reduced storage requirements are achieved by storing only the variant and missing states and inferring the reference state. We evaluate the performance characteristics of FSM, BLSM and NSM and demonstrate dramatic improvements in storage and performance using the NSM approach.
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Affiliation(s)
- Guillermo Gonzalez-Calderon
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
| | - Ruizheng Liu
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
| | - Rodrigo Carvajal
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
| | - Jamie K Teer
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA.,Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
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12
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Wang X, Yu X, Krauthammer M, Hugo W, Duan C, Kanetsky PA, Teer JK, Thompson ZJ, Kalos D, Tsai KY, Smalley KSM, Sondak VK, Chen YA, Conejo-Garcia JR. The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma. Cancer Epidemiol Biomarkers Prev 2020; 29:1792-1799. [PMID: 32611582 PMCID: PMC7483810 DOI: 10.1158/1055-9965.epi-20-0307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/29/2020] [Accepted: 06/22/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND MUC16 is a mucin marker that is frequently mutated in melanoma, but whether MUC16 mutations could be useful as a surrogate biomarker for tumor mutation burden (TMB) remains unclear. METHODS This study rigorously evaluates the MUC16 mutation as a clinical biomarker in cutaneous melanoma by utilizing genomic and clinical data from patient samples from The Cancer Genome Atlas (TCGA) and two independent validation cohorts. We further extended the analysis to studies with patients treated with immunotherapies. RESULTS Analysis results showed that samples with MUC16 mutations had a higher TMB than the samples of wild-type, with strong statistical significance (P < 0.001) in all melanoma cohorts tested. Associations between MUC16 mutations and TMB remained statistically significant after adjusting for potential confounding factors in the TCGA cohort [OR, 9.28 (95% confidence interval (CI), 5.18-17.39); P < 0.001], Moffitt cohort [OR, 31.95 (95% CI, 8.71-163.90); P < 0.001], and Yale cohort [OR, 8.09 (95% CI, 3.12-23.79); P < 0.01]. MUC16 mutations were also found to be associated with overall survival in the TCGA [HR, 0.62; (95% CI, 0.45-0.85); P < 0.01] and Moffitt cohorts [HR, 0.49 (95% CI, 0.28-0.87); P = 0.014]. Strikingly, MUC16 is the only top frequently mutated gene for which prognostic significance was observed. MUC16 mutations were also found valuable in predicting anti-CTLA-4 and anti-PD-1 therapy responses. CONCLUSIONS MUC16 mutation appears to be a useful predictive marker of global TMB and patient survival in melanoma. IMPACT This is, to the best of our knowledge, the first systematic evaluation of MUC16 mutation as a clinical biomarker and a predictive biomarker for immunotherapy in melanoma.
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Affiliation(s)
- Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - Willy Hugo
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Chunzhe Duan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Zachary J Thompson
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Denise Kalos
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kenneth Y Tsai
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Keiran S M Smalley
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Vernon K Sondak
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Jose R Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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13
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Pemov A, Dewan R, Hansen NF, Chandrasekharappa SC, Ray-Chaudhury A, Jones K, Luo W, Heiss JD, Mullikin JC, Chittiboina P, Stewart DR, Asthagiri AR. Comparative clinical and genomic analysis of neurofibromatosis type 2-associated cranial and spinal meningiomas. Sci Rep 2020; 10:12563. [PMID: 32724039 PMCID: PMC7387487 DOI: 10.1038/s41598-020-69074-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022] Open
Abstract
Neurofibromatosis type 2 (NF2) is an autosomal dominant Mendelian tumor predisposition disorder caused by germline pathogenic variants in the tumor suppressor NF2. Meningiomas are the second most common neoplasm in NF2, often occurring in multiple intracranial and spinal locations within the same patient. In this prospective longitudinal study, we assessed volumes and growth rates of ten spinal and ten cranial benign meningiomas in seven NF2 patients that concluded with surgical resection and performed whole-exome sequencing and copy-number variant (CNV) analysis of the tumors. Our comparison of the volume and the growth rate of NF2-associated spinal and cranial meningiomas point to the differences in timing of tumor initiation and/or to the differences in tumor progression (e.g., non-linear, saltatory growth) at these two anatomical locations. Genomic investigation of these tumors revealed that somatic inactivation of NF2 is the principal and perhaps the only driver of tumor initiation; and that tumor progression likely occurs via accumulation of CNVs, rather than point mutations. Results of this study contribute to a better understanding of NF2-associated meningiomas clinical behavior and their genetic underpinnings.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Ramita Dewan
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.,Neuromuscular Disease Research Section, National Institute On Aging, NIH, Bethesda, MD, USA
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Abhik Ray-Chaudhury
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Kristine Jones
- Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wen Luo
- Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John D Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.,NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Rockville, MD, USA
| | - Prashant Chittiboina
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA.
| | - Ashok R Asthagiri
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA. .,Department of Neurological Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA.
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14
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Li C, Wang N, Schäffer AA, Liu X, Zhao Z, Elliott G, Garrett L, Choi NT, Wang Y, Wang Y, Wang C, Wang J, Chan D, Su P, Cui S, Yang Y, Gao B. Mutations in COMP cause familial carpal tunnel syndrome. Nat Commun 2020; 11:3642. [PMID: 32686688 PMCID: PMC7371736 DOI: 10.1038/s41467-020-17378-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 06/21/2020] [Indexed: 02/06/2023] Open
Abstract
Carpal tunnel syndrome (CTS) is the most common peripheral nerve entrapment syndrome, affecting a large proportion of the general population. Genetic susceptibility has been implicated in CTS, but the causative genes remain elusive. Here, we report the identification of two mutations in cartilage oligomeric matrix protein (COMP) that segregate with CTS in two large families with or without multiple epiphyseal dysplasia (MED). Both mutations impair the secretion of COMP by tenocytes, but the mutation associated with MED also perturbs its secretion in chondrocytes. Further functional characterization of the CTS-specific mutation reveals similar histological and molecular changes of tendons/ligaments in patients’ biopsies and the mouse models. The mutant COMP fails to oligomerize properly and is trapped in the ER, resulting in ER stress-induced unfolded protein response and cell death, leading to inflammation, progressive fibrosis and cell composition change in tendons/ligaments. The extracellular matrix (ECM) organization is also altered. Our studies uncover a previously unrecognized mechanism in CTS pathogenesis. Familial carpal tunnel syndrome (CTS) is common, but causal genes are not characterized. Here the authors report two CTS-related mutations in two large families that impair secretion of COMP in tenocytes, leading to ER stress-induced unfolded protein response, inflammation and fibrosis in patients and mouse models.
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Affiliation(s)
- Chunyu Li
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Ni Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alejandro A Schäffer
- National Center for Biotechnology Information and National Cancer Institute, National Institutes of Health, Bethesda, MD, US
| | - Xilin Liu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhuo Zhao
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Gene Elliott
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US
| | - Lisa Garrett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US
| | - Nga Ting Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yueshu Wang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yufa Wang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Cheng Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peiqiang Su
- Department of Orthopaedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shusen Cui
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
| | - Yingzi Yang
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US. .,Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Harvard University, Boston, MA, US.
| | - Bo Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US.
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15
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Tunca C, Şeker T, Akçimen F, Coşkun C, Bayraktar E, Palvadeau R, Zor S, Koçoğlu C, Kartal E, Şen NE, Hamzeiy H, Özoğuz Erimiş A, Norman U, Karakahya O, Olgun G, Akgün T, Durmuş H, Şahin E, Çakar A, Başar Gürsoy E, Babacan Yıldız G, İşak B, Uluç K, Hanağası H, Bilgiç B, Turgut N, Aysal F, Ertaş M, Boz C, Kotan D, İdrisoğlu H, Soysal A, Uzun Adatepe N, Akalın MA, Koç F, Tan E, Oflazer P, Deymeer F, Taştan Ö, Çiçek AE, Kavak E, Parman Y, Başak AN. Revisiting the complex architecture of ALS in Turkey: Expanding genotypes, shared phenotypes, molecular networks, and a public variant database. Hum Mutat 2020; 41:e7-e45. [PMID: 32579787 DOI: 10.1002/humu.24055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/05/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022]
Abstract
The last decade has proven that amyotrophic lateral sclerosis (ALS) is clinically and genetically heterogeneous, and that the genetic component in sporadic cases might be stronger than expected. This study investigates 1,200 patients to revisit ALS in the ethnically heterogeneous yet inbred Turkish population. Familial ALS (fALS) accounts for 20% of our cases. The rates of consanguinity are 30% in fALS and 23% in sporadic ALS (sALS). Major ALS genes explained the disease cause in only 35% of fALS, as compared with ~70% in Europe and North America. Whole exome sequencing resulted in a discovery rate of 42% (53/127). Whole genome analyses in 623 sALS cases and 142 population controls, sequenced within Project MinE, revealed well-established fALS gene variants, solidifying the concept of incomplete penetrance in ALS. Genome-wide association studies (GWAS) with whole genome sequencing data did not indicate a new risk locus. Coupling GWAS with a coexpression network of disease-associated candidates, points to a significant enrichment for cell cycle- and division-related genes. Within this network, literature text-mining highlights DECR1, ATL1, HDAC2, GEMIN4, and HNRNPA3 as important genes. Finally, information on ALS-related gene variants in the Turkish cohort sequenced within Project MinE was compiled in the GeNDAL variant browser (www.gendal.org).
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Affiliation(s)
- Ceren Tunca
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey.,Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Tuncay Şeker
- Genomize Inc., Boğaziçi University Technology Development Region, Istanbul, Turkey
| | - Fulya Akçimen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Cemre Coşkun
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Elif Bayraktar
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Robin Palvadeau
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Seyit Zor
- Genomize Inc., Boğaziçi University Technology Development Region, Istanbul, Turkey
| | - Cemile Koçoğlu
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Ece Kartal
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Nesli Ece Şen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Aslıhan Özoğuz Erimiş
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Utku Norman
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Oğuzhan Karakahya
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Gülden Olgun
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Tahsin Akgün
- Department of Anesthesiology and Reanimation, American Hospital, Istanbul, Turkey
| | - Hacer Durmuş
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Erdi Şahin
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Arman Çakar
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Esra Başar Gürsoy
- Department of Neurology, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Gülsen Babacan Yıldız
- Department of Neurology, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Barış İşak
- Department of Neurology, Marmara University School of Medicine, Istanbul, Turkey
| | - Kayıhan Uluç
- Department of Neurology, Marmara University School of Medicine, Istanbul, Turkey
| | - Haşmet Hanağası
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Başar Bilgiç
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Nilda Turgut
- Department of Neurology, Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Fikret Aysal
- Department of Neurology, Medipol University School of Medicine, Istanbul, Turkey
| | - Mustafa Ertaş
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Cavit Boz
- Department of Neurology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - Dilcan Kotan
- Department of Neurology, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Halil İdrisoğlu
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Aysun Soysal
- Department of Neurology, Bakırköy Research and Training Hospital for Neurologic and Psychiatric Diseases, Istanbul, Turkey
| | - Nurten Uzun Adatepe
- Department of Neurology, Cerrahpaşa Medical School, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mehmet Ali Akalın
- Department of Neurology, Cerrahpaşa Medical School, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Filiz Koç
- Department of Neurology, Çukurova University Medical School, Adana, Turkey
| | - Ersin Tan
- Department of Neurology, Hacettepe University Medical School, Ankara, Turkey
| | - Piraye Oflazer
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Feza Deymeer
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Öznur Taştan
- Department of Computer Science and Engineering, Sabancı University, Istanbul, Turkey
| | - A Ercüment Çiçek
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.,Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Erşen Kavak
- Genomize Inc., Boğaziçi University Technology Development Region, Istanbul, Turkey
| | - Yeşim Parman
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey.,Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
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16
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Kosaki R, Kubota M, Uehara T, Suzuki H, Takenouchi T, Kosaki K. Consecutive medical exome analysis at a tertiary center: Diagnostic and health-economic outcomes. Am J Med Genet A 2020; 182:1601-1607. [PMID: 32369273 DOI: 10.1002/ajmg.a.61589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 11/08/2022]
Abstract
The utility of whole exome analysis has been extensively demonstrated in research settings, but its clinical utility as a first-tier genetic test has not been well documented from diagnostic and health economic standpoints in real-life clinical settings. We performed medical exome analyses focusing on a clinically interpretable portion of the genome (4,813 genes) as a first-tier genetic test for 360 consecutive patients visiting a genetics clinic at a tertiary children's hospital in Japan, over a 3-year period. Bioinformatics analyses were conducted using standard software. A molecular diagnosis was made in 171 patients involving a total of 107 causative genes. Among these 107 causative genes, 57 genes were classified as genes with potential organ-specific interventions and management strategies. Clinically relevant results were obtained in 26% of the total cohort and 54% of the patients with a definitive molecular diagnosis. Performing the medical exome analysis at the time of the initial visit to the tertiary center, rather than after visits to pertinent specialists, brain MRI examination, and G-banded chromosome testing, would have reduced the financial cost by 197 euros according to retrospective calculation under multiple assumption. The present study demonstrated a high diagnostic yield (47.5%) for singleton medical exome analysis as a first-tier test in a real-life setting. Medical exome analysis yielded clinically relevant information in a quarter of the total patient cohort. The application of genomic testing during the initial visit to a tertiary medical center could be a rational approach to the diagnosis of patients with suspected genetic disorders.
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Affiliation(s)
- Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Masaya Kubota
- Department of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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17
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Arumilli M, Layer RM, Hytönen MK, Lohi H. webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering. Front Genet 2020; 11:152. [PMID: 32194629 PMCID: PMC7063093 DOI: 10.3389/fgene.2020.00152] [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: 09/06/2019] [Accepted: 02/10/2020] [Indexed: 01/02/2023] Open
Abstract
Summary Genotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions. Results webGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups. Availability webGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt.
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Affiliation(s)
- Meharji Arumilli
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genetics Research Program, The Folkhälsan Research Center, Helsinki, Finland
| | - Ryan M Layer
- Department of Computer Science, University of Colorado, Boulder, CO, United States.,The BioFrontiers Institute, University of Colorado, Boulder, CO, United States
| | - Marjo K Hytönen
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genetics Research Program, The Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Genetics Research Program, The Folkhälsan Research Center, Helsinki, Finland
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18
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Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS. Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines. Gigascience 2020; 9:giaa007. [PMID: 32025702 PMCID: PMC7002876 DOI: 10.1093/gigascience/giaa007] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/02/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Accurately identifying single-nucleotide polymorphisms (SNPs) from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP-calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia, and Klebsiella. RESULTS We evaluated the performance of 209 SNP-calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic bacteria such as Escherichia coli but less dominant for clonal species such as Mycobacterium tuberculosis. CONCLUSIONS The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest-performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often used the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup, or Strelka.
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Affiliation(s)
- Stephen J Bush
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - David W Eyre
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SH, UK
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
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19
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Kalaskar VK, Alur RP, Li LK, Thomas JW, Sergeev YV, Blain D, Hufnagel RB, Cogliati T, Brooks BP. High-throughput custom capture sequencing identifies novel mutations in coloboma-associated genes: Mutation in DNA-binding domain of retinoic acid receptor beta affects nuclear localization causing ocular coloboma. Hum Mutat 2019; 41:678-695. [PMID: 31816153 PMCID: PMC7027867 DOI: 10.1002/humu.23954] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 10/04/2019] [Accepted: 11/09/2019] [Indexed: 12/11/2022]
Abstract
Uveal coloboma is a potentially blinding congenital ocular malformation caused by the failure of optic fissure closure during the fifth week of human gestation. We performed custom capture high‐throughput screening of 38 known coloboma‐associated genes in 66 families. Suspected causative novel variants were identified in TFAP2A and CHD7, as well as two previously reported variants of uncertain significance in RARB and BMP7. The variant in RARB, unlike previously reported disease mutations in the ligand‐binding domain, was a missense change in the highly conserved DNA‐binding domain predicted to affect the protein's DNA‐binding ability. In vitro studies revealed lower steady‐state protein levels, reduced transcriptional activity, and incomplete nuclear localization of the mutant RARB protein compared with wild‐type. Zebrafish studies showed that human RARB messenger RNA partially reduced the ocular phenotype caused by morpholino knockdown of rarga gene, a zebrafish homolog of human RARB. Our study indicates that sequence alterations in known coloboma genes account for a small percentage of coloboma cases and that mutations in the RARB DNA‐binding domain could result in human disease.
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Affiliation(s)
- Vijay K Kalaskar
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Ramakrishna P Alur
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - LeeAnn K Li
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - James W Thomas
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Yuri V Sergeev
- Protein Biochemistry and Molecular Modeling Group, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Delphine Blain
- Ophthalmic Clinical Genetics Section, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Robert B Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Tiziana Cogliati
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Brian P Brooks
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland.,Ophthalmic Clinical Genetics Section, OGVFB, NEI, NIH, Bethesda, Maryland
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20
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Dutil J, Teer JK, Golubeva V, Yoder S, Tong WL, Arroyo N, Karam R, Echenique M, Matta JL, Monteiro AN. Germline variants in cancer genes in high-risk non-BRCA patients from Puerto Rico. Sci Rep 2019; 9:17769. [PMID: 31780696 PMCID: PMC6882826 DOI: 10.1038/s41598-019-54170-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/05/2019] [Indexed: 12/30/2022] Open
Abstract
Inherited pathogenic variants in genes that confer moderate to high risk of breast cancer may explain up to 50% of familial breast cancer. This study aimed at identifying inherited pathogenic variants in breast cancer cases from Puerto Rico that were not linked to BRCA1 or BRCA2. Forty-eight breast cancer patients that met the clinical criteria for BRCA testing but had received a negative BRCA1/2 result were recruited. Fifty-three genes previously implicated in hereditary cancer predisposition were captured using the BROCA Agilent cancer risk panel followed by massively parallel sequencing. Missense variants of uncertain clinical significance in CHEK2 were evaluated using an in vitro kinase assays to determine their impact on function. Pathogenic variants were identified in CHEK2, MUTYH, and RAD51B in four breast cancer patients, which represented 8.3% of the cohort. We identified three rare missense variants of uncertain significance in CHEK2 and two variants (p.Pro484Leu and p.Glu239Lys) showed markedly decreased kinase activity in vitro comparable to a known pathogenic variant. Interestingly, the local ancestry at the RAD51B locus in the carrier of p.Arg47* was predicted to be of African origin. In this cohort, 12.5% of the BRCA-negative breast cancer patients were found to carry a known pathogenic variant or a variant affecting protein activity. This study reveals an unmet clinical need of genetic testing that could benefit a significant proportion of at-risk Latinas. It also highlights the complexity of Hispanic populations as pathogenic factors may originate from any of the ancestral populations that make up their genetic backgrounds.
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Affiliation(s)
- Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR, USA.
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Volha Golubeva
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sean Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wei Lue Tong
- University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Nelly Arroyo
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR, USA
| | | | - Miguel Echenique
- Auxilio Cancer Center, Auxilio Mutuo Hospital, San Juan, PR, USA
| | - Jaime L Matta
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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21
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Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB. Proteogenomic landscape of squamous cell lung cancer. Nat Commun 2019; 10:3578. [PMID: 31395880 PMCID: PMC6687710 DOI: 10.1038/s41467-019-11452-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
How genomic and transcriptomic alterations affect the functional proteome in lung cancer is not fully understood. Here, we integrate DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 squamous cell lung cancer (SCC) patients. We identify three proteomic subtypes, two of which (Inflamed, Redox) comprise 87% of tumors. The Inflamed subtype is enriched with neutrophils, B-cells, and monocytes and expresses more PD-1. Redox tumours are enriched for oxidation-reduction and glutathione pathways and harbor more NFE2L2/KEAP1 alterations and copy gain in the 3q2 locus. Proteomic subtypes are not associated with patient survival. However, B-cell-rich tertiary lymph node structures, more common in Inflamed, are associated with better survival. We identify metabolic vulnerabilities (TP63, PSAT1, and TFRC) in Redox. Our work provides a powerful resource for lung SCC biology and suggests therapeutic opportunities based on redox metabolism and immune cell infiltrates. Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.
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Affiliation(s)
- Paul A Stewart
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Robbert J C Slebos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Victoria Izumi
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Matthew Chambers
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Ling Cen
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Fredrik Pettersson
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Yonghong Zhang
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Zhihua Chen
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Chia-Ho Cheng
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Ram Thapa
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Zachary Thompson
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Katherine M Fellows
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jewel M Francis
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - James J Saller
- Department of Anatomical Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Tania Mesa
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Chaomei Zhang
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Gina M DeNicola
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Amer A Beg
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Theresa A Boyle
- Department of Anatomical Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Yian Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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22
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Bosio M, Drechsel O, Rahman R, Muyas F, Rabionet R, Bezdan D, Domenech Salgado L, Hor H, Schott JJ, Munell F, Colobran R, Macaya A, Estivill X, Ossowski S. eDiVA-Classification and prioritization of pathogenic variants for clinical diagnostics. Hum Mutat 2019; 40:865-878. [PMID: 31026367 PMCID: PMC6767450 DOI: 10.1002/humu.23772] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023]
Abstract
Mendelian diseases have shown to be an and efficient model for connecting genotypes to phenotypes and for elucidating the function of genes. Whole‐exome sequencing (WES) accelerated the study of rare Mendelian diseases in families, allowing for directly pinpointing rare causal mutations in genic regions without the need for linkage analysis. However, the low diagnostic rates of 20–30% reported for multiple WES disease studies point to the need for improved variant pathogenicity classification and causal variant prioritization methods. Here, we present the exome Disease Variant Analysis (eDiVA; http://ediva.crg.eu), an automated computational framework for identification of causal genetic variants (coding/splicing single‐nucleotide variants and small insertions and deletions) for rare diseases using WES of families or parent–child trios. eDiVA combines next‐generation sequencing data analysis, comprehensive functional annotation, and causal variant prioritization optimized for familial genetic disease studies. eDiVA features a machine learning‐based variant pathogenicity predictor combining various genomic and evolutionary signatures. Clinical information, such as disease phenotype or mode of inheritance, is incorporated to improve the precision of the prioritization algorithm. Benchmarking against state‐of‐the‐art competitors demonstrates that eDiVA consistently performed as a good or better than existing approach in terms of detection rate and precision. Moreover, we applied eDiVA to several familial disease cases to demonstrate its clinical applicability.
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Affiliation(s)
- Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Oliver Drechsel
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Francesc Muyas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institut de Recerca Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Daniela Bezdan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura Domenech Salgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hyun Hor
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Jacques Schott
- L'Institut du Thorax, INSERM, CNRS, Univ Nantes, Nantes, France.,Service de Cardiologie, L'institut du thorax, CHU Nantes, Nantes, France
| | | | - Roger Colobran
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Alfons Macaya
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Xavier Estivill
- Sidra Medicine, Doha, Qatar.,Women's Health Dexeus, Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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23
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Female genitourinary tract melanoma: mutation analysis with clinicopathologic correlation: a single-institution experience. Melanoma Res 2019; 28:586-591. [PMID: 30028779 DOI: 10.1097/cmr.0000000000000480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Female genitourinary tract melanoma (FGTM) is a rare and often-fatal form of mucosal melanoma. We describe our institutional experience with 55 cases of FGTM, 16 of which were evaluated with next-generation sequencing targeting 151 cancer-associated genes. Tumors tended to be thicker than conventional melanoma at presentation (median: 3.2 mm), were frequently ulcerated (50%), and characterized by incomplete initial resections. Regional lymph nodes showed tumor involvement at presentation in 28% of cases. With a median follow-up of 23.6 months, the median recurrence free survival was 14.5 months and the median overall survival was 29.6 months. Genomic analysis revealed mutually exclusive mutations in TP53 and KIT in 25%, while 19% of cases showed BRAF mutation. NRAS mutation was found in 13% of cases. Mutation in ATRX, previously undescribed in mucosal melanoma, was seen in three (10%) of 16 patients. Only invasive melanoma cases were included in statistical analyses. Patients with three or more mutations had marginally worse overall survival rates than those with two or less (P=0.07). Further studies are required for potential adjuvant treatment modalities to improve survival outcomes of FGTM.
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24
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Sharma P, Reichert M, Lu Y, Markello TC, Adams DR, Steinbach PJ, Fuqua BK, Parisi X, Kaler SG, Vulpe CD, Anderson GJ, Gahl WA, Malicdan MCV. Biallelic HEPHL1 variants impair ferroxidase activity and cause an abnormal hair phenotype. PLoS Genet 2019; 15:e1008143. [PMID: 31125343 PMCID: PMC6534290 DOI: 10.1371/journal.pgen.1008143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/16/2019] [Indexed: 11/18/2022] Open
Abstract
Maintenance of the correct redox status of iron is functionally important for critical biological processes. Multicopper ferroxidases play an important role in oxidizing ferrous iron, released from the cells, into ferric iron, which is subsequently distributed by transferrin. Two well-characterized ferroxidases, ceruloplasmin (CP) and hephaestin (HEPH) facilitate this reaction in different tissues. Recently, a novel ferroxidase, Hephaestin like 1 (HEPHL1), also known as zyklopen, was identified. Here we report a child with compound heterozygous mutations in HEPHL1 (NM_001098672) who presented with abnormal hair (pili torti and trichorrhexis nodosa) and cognitive dysfunction. The maternal missense mutation affected mRNA splicing, leading to skipping of exon 5 and causing an in-frame deletion of 85 amino acids (c.809_1063del; p.Leu271_ala355del). The paternal mutation (c.3176T>C; p.Met1059Thr) changed a highly conserved methionine that is part of a typical type I copper binding site in HEPHL1. We demonstrated that HEPHL1 has ferroxidase activity and that the patient's two mutations exhibited loss of this ferroxidase activity. Consistent with these findings, the patient's fibroblasts accumulated intracellular iron and exhibited reduced activity of the copper-dependent enzyme, lysyl oxidase. These results suggest that the patient's biallelic variants are loss-of-function mutations. Hence, we generated a Hephl1 knockout mouse model that was viable and had curly whiskers, consistent with the hair phenotype in our patient. These results enhance our understanding of the function of HEPHL1 and implicate altered ferroxidase activity in hair growth and hair disorders.
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Affiliation(s)
- Prashant Sharma
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marie Reichert
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yan Lu
- Iron Metabolism Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas C. Markello
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland, United States of America
| | - David R. Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brie K. Fuqua
- Department of Medicine, University of California, Los Angeles, United States of America
| | - Xenia Parisi
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen G. Kaler
- Section on Translational Neuroscience, Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher D. Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Gregory J. Anderson
- Iron Metabolism Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland, United States of America
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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25
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Valka J, Vesela J, Votavova H, Dostalova-Merkerova M, Urbanova Z, Jonasova A, Cermak J, Belickova M. Genetic Variant Screening of DNA Repair Genes in Myelodysplastic Syndrome Identifies a Novel Mutation in the XRCC2 Gene. Oncol Res Treat 2019; 42:263-268. [PMID: 30861523 DOI: 10.1159/000497209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/23/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND We aimed to detect single nucleotide polymorphisms (SNPs) and mutations in DNA repair genes and their possible association with myelodysplastic syndrome (MDS). METHODS Targeted enrichment resequencing of 84 DNA repair genes was initially performed on a screening cohort of MDS patients. Real-time polymerase chain reaction was used for genotyping selected SNPs in the validation cohort of patients. RESULTS A heterozygous frameshift mutation in the XRCC2 gene was identified. It leads to the formation of a truncated non-functional protein and decreased XRCC2 expression level. Decreased expression levels of all DNA repair genes functionally connected with mutated XRCC2 were also present. Moreover, a synonymous substitution in the PRKDC gene and 2 missense mutations in the SMUG1 and XRCC1 genes were also found. In the screening cohort, 6 candidate SNPs were associated with the tendency to develop MDS: rs4135113 (TDG, p = 0.03), rs12917 (MGMT, p = 0.003), rs2230641 (CCNH, p = 0.01), rs2228529 and rs2228526 (ERCC6, p = 0.04 and p = 0.03), and rs1799977 (MLH1, p = 0.04). In the validation cohort, only a polymorphism in MLH1 was significantly associated with development of MDS in patients with poor cytogenetics (p = 0.0004). CONCLUSION Our study demonstrates that genetic variants are present in DNA repair genes of MDS patients and may be associated with susceptibility to MDS.
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Affiliation(s)
- Jan Valka
- Institute of Hematology and Blood Transfusion, Prague, Czechia, .,Charles University,1st Faculty of Medicine, Prague, Czechia,
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | - Hana Votavova
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | | | - Zuzana Urbanova
- Institute of Hematology and Blood Transfusion, Prague, Czechia.,Charles University,1st Faculty of Medicine, Prague, Czechia
| | - Anna Jonasova
- First Internal Clinic - Clinic of Hematology, General University Hospital, Prague, Czechia
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czechia
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26
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Kuo ME, Theil AF, Kievit A, Malicdan MC, Introne WJ, Christian T, Verheijen FW, Smith DEC, Mendes MI, Hussaarts-Odijk L, van der Meijden E, van Slegtenhorst M, Wilke M, Vermeulen W, Raams A, Groden C, Shimada S, Meyer-Schuman R, Hou YM, Gahl WA, Antonellis A, Salomons GS, Mancini GMS. Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. Am J Hum Genet 2019; 104:520-529. [PMID: 30824121 DOI: 10.1016/j.ajhg.2019.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes responsible for charging tRNA molecules with cognate amino acids. Consistent with the essential function and ubiquitous expression of ARSs, mutations in 32 of the 37 ARS-encoding loci cause severe, early-onset recessive phenotypes. Previous genetic and functional data suggest a loss-of-function mechanism; however, our understanding of the allelic and locus heterogeneity of ARS-related disease is incomplete. Cysteinyl-tRNA synthetase (CARS) encodes the enzyme that charges tRNACys with cysteine in the cytoplasm. To date, CARS variants have not been implicated in any human disease phenotype. Here, we report on four subjects from three families with complex syndromes that include microcephaly, developmental delay, and brittle hair and nails. Each affected person carries bi-allelic CARS variants: one individual is compound heterozygous for c.1138C>T (p.Gln380∗) and c.1022G>A (p.Arg341His), two related individuals are compound heterozygous for c.1076C>T (p.Ser359Leu) and c.1199T>A (p.Leu400Gln), and one individual is homozygous for c.2061dup (p.Ser688Glnfs∗2). Measurement of protein abundance, yeast complementation assays, and assessments of tRNA charging indicate that each CARS variant causes a loss-of-function effect. Compared to subjects with previously reported ARS-related diseases, individuals with bi-allelic CARS variants are unique in presenting with a brittle-hair-and-nail phenotype, which most likely reflects the high cysteine content in human keratins. In sum, our efforts implicate CARS variants in human inherited disease, expand the locus and clinical heterogeneity of ARS-related clinical phenotypes, and further support impaired tRNA charging as the primary mechanism of recessive ARS-related disease.
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Affiliation(s)
- Molly E Kuo
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Anneke Kievit
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - May Christine Malicdan
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy J Introne
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Frans W Verheijen
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Desiree E C Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands
| | - Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands
| | - Lidia Hussaarts-Odijk
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Eric van der Meijden
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Catherine Groden
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shino Shimada
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ya Ming Hou
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands; Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, 1081 HZ Amsterdam, the Netherlands.
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
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27
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Yalnızoǧlu D, Özgül RK, Oǧuz KK, Özer B, Yücel-Yılmaz D, Gürbüz B, Serdaroǧlu E, Erol İ, Topçu M, Dursun A. Expanding the phenotype of phospholipid remodelling disease due to MBOAT7 gene defect. J Inherit Metab Dis 2019; 42:381-388. [PMID: 30701556 DOI: 10.1002/jimd.12016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/26/2018] [Accepted: 11/02/2018] [Indexed: 11/07/2022]
Abstract
MBOAT7 gene codes O-acyltransferase domain containing seven proteins which is one of four enzymes involved in remodeling of phosphoinositol phosphate (PIP) in LANDs cycle. We present clinical, neuroimaging, and genetic findings of 12 patients from 7 families with MBOAT7 gene defect, a recently defined novel phospholipid remodelling disease. To the best of our knowledge, our case series is the second report on patients with MBOAT7 gene defect. The patients present with global developmental delay particularly in speech and language skills, intellectual disability, stereotypical behavior, ataxic gait, early onset epilepsy with well response to medical treatment, strabismus and similar facial features. Common neuroimaging findings of the patients were folium dysgenesis of the cerebellum with a particular appearance, mild-to-moderate cerebellar atrophy, T2 hyperintensity of bilateral globus pallidius and dentate nuclei, enlarged perivascular areas, and mild thinning of the corpus callosum. Genome-wide genotyping and exome sequencing identified five different types of homozygous mutations in the MBOAT7 gene in all seven families which are p.Arg87*, p.Leu227ProfsX65, p.Gln376Lys, p.Trp426*, and chr19:54.666.173-54.677.766/11594 bp del. We conclude that clinical and neuroimaging findings of MBOAT7 gene defect may suggest the diagnosis and guide genetic tests.
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Affiliation(s)
- Dilek Yalnızoǧlu
- Department of Pediatrics, Division of Neurology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - R Köksal Özgül
- Hacettepe University Institute of Child Health, Ankara, Turkey
| | - Kader K Oǧuz
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Buǧra Özer
- Advanced Genomics and Bioinformatics Research Center (IGBAM), BILGEM, The Scientific and Technological Research Council of Turkey (TUBITAK), Kocaeli, Turkey
| | | | - Berrak Gürbüz
- Department of Pediatrics, Division of Metabolism, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Esra Serdaroǧlu
- Department of Pediatrics, Division of Neurology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - İlknur Erol
- Department of Pediatrics, Division of Neurology, Baskent University Faculty of Medicine, Adana, Turkey
| | - Meral Topçu
- Department of Pediatrics, Division of Neurology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Dursun
- Department of Pediatrics, Division of Metabolism, Hacettepe University Faculty of Medicine, Ankara, Turkey
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28
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Gu F, Wu A, Gordon MG, Vlahos L, Macnamara S, Burke E, Malicdan MC, Adams DR, Tifft CJ, Toro C, Gahl WA, Markello TC. A suite of automated sequence analyses reduces the number of candidate deleterious variants and reveals a difference between probands and unaffected siblings. Genet Med 2019; 21:1772-1780. [PMID: 30700791 PMCID: PMC6669106 DOI: 10.1038/s41436-019-0434-0] [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: 05/31/2018] [Accepted: 01/03/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Develop an automated exome analysis workflow that can produce a very small number of candidate variants yet still detect different numbers of deleterious variants between probands and unaffected siblings. METHODS Ninety-seven outbred nuclear families from the Undiagnosed Diseases Program/Network included single probands and the corresponding unaffected sibling(s). Single-nucleotide polymorphism (SNP) chip and exome analyses were performed on all, with proband and unaffected sibling considered independently as the target. The total burden of candidate genetic variants was summed for probands and siblings over all considered disease models. RESULTS Exome analysis workflow include automated programs for ethnicity-matched genotype calling, salvage pathway for Mendelian inconsistency, compound heterozygous recessive detection, BAM file regional curation, population frequency filtering, pedigree-aware BAM file noise evaluation, and exon deletion filtration. This workflow relied heavily on BAM file analysis. A greater average pathogenic variant number was found compared with unaffected siblings. This was significant (p < 0.05) when using published recommended thresholds, and implies that causal variants are retained in many probands' lists. CONCLUSION Using Mendelian and non-Mendelian models, this agnostic exome analysis shows a difference between a small group of probands and their unaffected siblings. This workflow produces candidate lists small enough to pursue with laboratory validation.
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Affiliation(s)
- Fangning Gu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Anchi Wu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - M Grace Gordon
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lukas Vlahos
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Shane Macnamara
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Burke
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - May C Malicdan
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Thomas C Markello
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
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Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies. Eur J Hum Genet 2019; 27:582-593. [PMID: 30622326 DOI: 10.1038/s41431-018-0298-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/25/2018] [Indexed: 12/24/2022] Open
Abstract
The Integrator complex subunit 1 (INTS1) is a component of the integrator complex that comprises 14 subunits and associates with RPB1 to catalyze endonucleolytic cleavage of nascent snRNAs and assist RNA polymerase II in promoter-proximal pause-release on protein-coding genes. We present five patients, including two sib pairs, with biallelic sequence variants in INTS1. The patients manifested absent or severely limited speech, an abnormal gait, hypotonia and cataracts. Exome sequencing revealed biallelic variants in INTS1 in all patients. One sib pair demonstrated a missense variant, p.(Arg77Cys), and a frameshift variant, p.(Arg1800Profs*20), another sib pair had a homozygous missense variant, p.(Pro1874Leu), and the fifth patient had a frameshift variant, p.(Leu1764Cysfs*16) and a missense variant, p.(Leu2164Pro). We also report additional clinical data on three previously described individuals with a homozygous, loss of function variant, p.(Ser1784*) in INTS1 that shared cognitive delays, cataracts and dysmorphic features with these patients. Several of the variants affected the protein C-terminus and preliminary modeling showed that the p.(Pro1874Leu) and p.(Leu2164Pro) variants may interfere with INTS1 helix folding. In view of the cataracts observed, we performed in-situ hybridization and demonstrated expression of ints1 in the zebrafish eye. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 to make larvae with biallelic insertion/deletion (indel) variants in ints1. The mutant larvae developed typically through gastrulation, but sections of the eye showed abnormal lens development. The distinctive phenotype associated with biallelic variants in INTS1 points to dysfunction of the integrator complex as a mechanism for intellectual disability, eye defects and craniofacial anomalies.
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Qualls AE, Donkervoort S, Herkert JC, D'gama AM, Bharucha-Goebel D, Collins J, Chao KR, Foley AR, Schoots MH, Jongbloed JDH, Bönnemann CG, Agrawal PB. Novel SPEG mutations in congenital myopathies: Genotype-phenotype correlations. Muscle Nerve 2018; 59:357-362. [PMID: 30412272 DOI: 10.1002/mus.26378] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Centronuclear myopathies (CNMs) are a subtype of congenital myopathies (CMs) characterized by muscle weakness, predominant type 1 fibers, and increased central nuclei. SPEG (striated preferentially expressed protein kinase) mutations have recently been identified in 7 CM patients (6 with CNMs). We report 2 additional patients with SPEG mutations expanding the phenotype and evaluate genotype-phenotype correlations associated with SPEG mutations. METHODS Using whole exome/genome sequencing in CM families, we identified novel recessive SPEG mutations in 2 patients. RESULTS Patient 1, with severe muscle weakness requiring respiratory support, dilated cardiomyopathy, ophthalmoplegia, and findings of nonspecific CM on muscle biopsy carried a homozygous SPEG mutation (p.Val3062del). Patient 2, with milder muscle weakness, ophthalmoplegia, and CNM carried compound heterozygous mutations (p.Leu728Argfs*82) and (p.Val2997Glyfs*52). CONCLUSIONS The 2 patients add insight into genotype-phenotype correlations of SPEG-associated CMs. Clinicians should consider evaluating a CM patient for SPEG mutations even in the absence of CNM features. Muscle Nerve 59:357-362, 2019.
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Affiliation(s)
- Anita E Qualls
- Division of Newborn Medicine, Division of Genetics and Genomics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA
| | - Johanna C Herkert
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alissa M D'gama
- Division of Newborn Medicine, Division of Genetics and Genomics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA
| | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA.,Division of Neurology, Children's National Health System, Washington, DC, USA
| | - James Collins
- Mercy Clinic Pediatric Neurology, Springfield, Missouri, USA
| | - Katherine R Chao
- Center for Mendelian Genomics at the Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA
| | - Mirthe H Schoots
- Department of Pathology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Jan D H Jongbloed
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Division of Genetics and Genomics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA
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Brooks BP, Zein WM, Thompson AH, Mokhtarzadeh M, Doherty DA, Parisi M, Glass IA, Malicdan MC, Vilboux T, Vemulapalli M, Mullikin JC, Gahl WA, Gunay-Aygun M. Joubert Syndrome: Ophthalmological Findings in Correlation with Genotype and Hepatorenal Disease in 99 Patients Prospectively Evaluated at a Single Center. Ophthalmology 2018; 125:1937-1952. [PMID: 30055837 DOI: 10.1016/j.ophtha.2018.05.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Joubert syndrome (JS) is caused by mutations in >34 genes that encode proteins involved with primary (nonmotile) cilia and the cilium basal body. This study describes the varying ocular phenotypes in JS patients, with correlation to systemic findings and genotype. DESIGN Patients were systematically and prospectively examined at the National Institutes of Health (NIH) Clinical Center in the setting of a dedicated natural history clinical trial. PARTICIPANTS Ninety-nine patients with JS examined at a single center. METHODS All patients underwent genotyping for JS, followed by complete age-appropriate ophthalmic examinations at the NIH Clinical Center, including visual acuity (VA), fixation behavior, lid position, motility assessment, slit-lamp biomicroscopy, dilated fundus examination with an indirect ophthalmoscope, and retinoscopy. Color and fundus autofluorescence imaging, Optos wide-field photography (Dunfermline, Scotland, UK), and electroretinography (ERG) were performed when possible. MAIN OUTCOME MEASURES The VA (with longitudinal follow-up where possible), ptosis, extraocular muscle function, retinal and optic nerve status, and retinal function as measured by ERG. RESULTS Among patients with JS with quantifiable VA (68/99), values ranged from 0 logarithm of the minimum angle of resolution (logMAR) (Snellen 20/20) to 1.5 logMAR (Snellen 20/632). Strabismus (71/98), nystagmus (66/99), oculomotor apraxia (60/77), ptosis (30/98), coloboma (28/99), retinal degeneration (20/83), and optic nerve atrophy (8/86) were identified. CONCLUSIONS We recommend regular monitoring for ophthalmological manifestations of JS beginning soon after birth or diagnosis. We demonstrate delayed visual development and note that the amblyogenic time frame may last significantly longer in JS than is typical. In general, patients with coloboma were less likely to display retinal degeneration, and those with retinal degeneration did not have coloboma. Severe retinal degeneration that is early and aggressive is seen in disease caused by specific genes, such as CEP290- and AHI1-associated JS. Retinal degeneration in INPP5E-, MKS1-, and NPHP1-associated JS was generally milder. Finally, ptosis surgery can be helpful in a subset of patients with JS; decisions as to timing and benefit/risk ratio need to be made on an individual basis according to expert consultation.
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Affiliation(s)
- Brian P Brooks
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland; National Human Genome Research Institute, Genetics and Molecular Biology Branch, Bethesda, Maryland; Office of the Clinical Director, National Eye Institute, National Institutes of Health, Bethesda, Maryland.
| | - Wadih M Zein
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Amy H Thompson
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland; Columbus Technologies & Services, Inc., Greenbelt, Maryland
| | - Maryam Mokhtarzadeh
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Daniel A Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Melissa Parisi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Ian A Glass
- Department of Pediatrics, University of Washington, Seattle, Washington; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - May C Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Thierry Vilboux
- National Human Genome Research Institute, Genetics and Molecular Biology Branch, Bethesda, Maryland; Inova Translational Medicine Institute, Falls Church, Virginia
| | - Meghana Vemulapalli
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - James C Mullikin
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland; Johns Hopkins University School of Medicine, Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland
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Burns DT, Donkervoort S, Müller JS, Knierim E, Bharucha-Goebel D, Faqeih EA, Bell SK, AlFaifi AY, Monies D, Millan F, Retterer K, Dyack S, MacKay S, Morales-Gonzalez S, Giunta M, Munro B, Hudson G, Scavina M, Baker L, Massini TC, Lek M, Hu Y, Ezzo D, AlKuraya FS, Kang PB, Griffin H, Foley AR, Schuelke M, Horvath R, Bönnemann CG. Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy. Am J Hum Genet 2018; 102:858-873. [PMID: 29727687 PMCID: PMC5986733 DOI: 10.1016/j.ajhg.2018.03.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/06/2018] [Indexed: 12/30/2022] Open
Abstract
The exosome is a conserved multi-protein complex that is essential for correct RNA processing. Recessive variants in exosome components EXOSC3, EXOSC8, and RBM7 cause various constellations of pontocerebellar hypoplasia (PCH), spinal muscular atrophy (SMA), and central nervous system demyelination. Here, we report on four unrelated affected individuals with recessive variants in EXOSC9 and the effect of the variants on the function of the RNA exosome in vitro in affected individuals' fibroblasts and skeletal muscle and in vivo in zebrafish. The clinical presentation was severe, early-onset, progressive SMA-like motor neuronopathy, cerebellar atrophy, and in one affected individual, congenital fractures of the long bones. Three affected individuals of different ethnicity carried the homozygous c.41T>C (p.Leu14Pro) variant, whereas one affected individual was compound heterozygous for c.41T>C (p.Leu14Pro) and c.481C>T (p.Arg161∗). We detected reduced EXOSC9 in fibroblasts and skeletal muscle and observed a reduction of the whole multi-subunit exosome complex on blue-native polyacrylamide gel electrophoresis. RNA sequencing of fibroblasts and skeletal muscle detected significant >2-fold changes in genes involved in neuronal development and cerebellar and motor neuron degeneration, demonstrating the widespread effect of the variants. Morpholino oligonucleotide knockdown and CRISPR/Cas9-mediated mutagenesis of exosc9 in zebrafish recapitulated aspects of the human phenotype, as they have in other zebrafish models of exosomal disease. Specifically, portions of the cerebellum and hindbrain were absent, and motor neurons failed to develop and migrate properly. In summary, we show that variants in EXOSC9 result in a neurological syndrome combining cerebellar atrophy and spinal motoneuronopathy, thus expanding the list of human exosomopathies.
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Szot JO, Cuny H, Blue GM, Humphreys DT, Ip E, Harrison K, Sholler GF, Giannoulatou E, Leo P, Duncan EL, Sparrow DB, Ho JWK, Graham RM, Pachter N, Chapman G, Winlaw DS, Dunwoodie SL. A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e001978. [PMID: 29555671 DOI: 10.1161/circgen.117.001978] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/18/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. METHODS Whole-exome sequencing was performed with the DNA of multiple family members. We utilized a 2-tiered whole-exome variant screening and interpretation procedure. First, we manually curated a high-confidence list of 90 genes known to cause CHD in humans, identified predicted damaging variants in genes on this list, and rated their pathogenicity using American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. RESULTS In 3 families (10%), we found pathogenic variants in known CHD genes TBX5, TFAP2B, and PTPN11, explaining the cardiac lesions. Second, exomes were comprehensively analyzed to identify additional predicted damaging variants that segregate with disease in CHD candidate genes. In 10 additional families (33%), likely disease-causal variants were uncovered in PBX1, CNOT1, ZFP36L2, TEK, USP34, UPF2, KDM5A, KMT2C, TIE1, TEAD2, and FLT4. CONCLUSIONS The pathogenesis of CHD could be explained using our high-confidence CHD gene list for variant filtering in a subset of cases. Furthermore, our unbiased screening procedure of family exomes implicates additional genes and variants in the pathogenesis of CHD, which suggest themselves for functional validation. This 2-tiered approach provides a means of (1) identifying clinically actionable variants and (2) identifying additional disease-causal genes, both of which are essential for improving the molecular diagnosis of CHD.
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Affiliation(s)
- Justin O Szot
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Hartmut Cuny
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gillian M Blue
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - David T Humphreys
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Eddie Ip
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Katrina Harrison
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gary F Sholler
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Eleni Giannoulatou
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Paul Leo
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Emma L Duncan
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Duncan B Sparrow
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Joshua W K Ho
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Robert M Graham
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Nicholas Pachter
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gavin Chapman
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - David S Winlaw
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Sally L Dunwoodie
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.).
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Characteristics of Liver Disease in 100 Individuals With Joubert Syndrome Prospectively Evaluated at a Single Center. J Pediatr Gastroenterol Nutr 2018; 66:428-435. [PMID: 29112083 PMCID: PMC5825259 DOI: 10.1097/mpg.0000000000001816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Joubert Syndrome (JS) is a rare, inherited, ciliopathy defined by cerebellar and brainstem malformations and is variably associated with liver, kidney, and ocular dysfunction. This study characterizes the hepatic findings in JS and identifies factors associated with probable portal hypertension. METHODS Hundred individuals with JS were prospectively evaluated at the National Institutes of Health Clinical Center. Laboratory tests, imaging, and DNA sequencing were performed. Patients were stratified based on the spleen length/patient height ratio as a marker of splenomegaly, used as a surrogate for probable portal hypertension. RESULTS Forty-three patients (43%) had liver involvement based on elevated liver enzymes and/or liver hyperechogenicity and/or splenomegaly. None of the patients had macroscopic liver cysts or bile duct dilatation. Based on the spleen length/patient height ratio, 13 patients were stratified into a probable portal hypertension group. We observed significant elevations in alkaline phosphatase (269 vs 169 U/L, P ≤ 0.001), alanine aminotransferase (92 vs 42 U/L, P = 0.004), aspartate aminotransferase (77 vs 40 U/L, P = 0.002), and gamma-glutamyl transferase (226 vs 51 U/L, P ≤ 0.001) in the probable portal hypertension group. Platelets were lower in the probable portal hypertension cohort (229 vs 299 × 10 cells/μL, P = 0.008), whereas synthetic function was intact in both groups. Probable portal hypertension was also more prevalent in patients with kidney disease (P = 0.001) and colobomas (P = 0.02), as well as mutations in the TMEM67 gene (P = 0.001). CONCLUSIONS In JS, probable portal hypertension is associated with abnormal hepatic enzymes, as well as presence of kidney disease, coloboma, and/or mutation in TMEM67. These findings may allow early identification of JS patients who have or are more likely to develop liver disease.
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Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, Messiaen LM, Piotrowski A. High-Throughput Tabular Data Processor - Platform independent graphical tool for processing large data sets. PLoS One 2018; 13:e0192858. [PMID: 29432475 PMCID: PMC5809091 DOI: 10.1371/journal.pone.0192858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp).
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Affiliation(s)
- Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
- * E-mail: (PM); (AP)
| | - Magdalena Bałut
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | | | - J. Renata Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - David K. Crossman
- Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ludwine M. Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
- * E-mail: (PM); (AP)
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Stokes B, Berger SI, Hall BA, Weiss K, Hadley DW, Murdock DR, Ramanathan S, Clark RD, Roessler E, Kruszka P, Muenke M. SIX3 deletions and incomplete penetrance in families affected by holoprosencephaly. Congenit Anom (Kyoto) 2018; 58:29-32. [PMID: 28670735 PMCID: PMC5750110 DOI: 10.1111/cga.12234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/09/2017] [Accepted: 06/25/2017] [Indexed: 12/27/2022]
Abstract
Holoprosencephaly (HPE) is failure of the forebrain to divide completely during embryogenesis. Incomplete penetrance has not been reported previously in SIX3 whole gene deletions, which are known to cause HPE. Both chromosomal microarray and whole exome sequencing (WES) were used to evaluate families with inherited HPE. Two families showed inherited deletions that contain SIX3 and were incompletely penetrant for HPE. Using WES, we ruled out parental mosaicism, a SIX3 hypomorph, and clinically significant variants in genes that are known to interact with SIX3 as causes of incomplete penetrance. We demonstrate the importance of molecular cascade testing in families with HPE and we answer important questions about incomplete penetrance.
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Affiliation(s)
- Bethany Stokes
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Seth I. Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Beth A. Hall
- Minnesota Perinatal Physicians, Allina Health, Minneapolis Minnesota
| | - Karin Weiss
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Donald W. Hadley
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David R. Murdock
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Subhadra Ramanathan
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Children's Hospital, Loma Linda, California
| | - Robin D. Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Children's Hospital, Loma Linda, California
| | - Erich Roessler
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Malicdan MCV, Vilboux T, Ben-Zeev B, Guo J, Eliyahu A, Pode-Shakked B, Dori A, Kakani S, Chandrasekharappa SC, Ferreira C, Shelestovich N, Marek-Yagel D, Pri-Chen H, Blatt I, Niederhuber JE, He L, Toro C, Taylor RW, Deeken J, Yardeni T, Wallace DC, Gahl WA, Anikster Y. A novel inborn error of the coenzyme Q10 biosynthesis pathway: cerebellar ataxia and static encephalomyopathy due to COQ5 C-methyltransferase deficiency. Hum Mutat 2018; 39:69-79. [PMID: 29044765 PMCID: PMC5722658 DOI: 10.1002/humu.23345] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/27/2017] [Accepted: 09/11/2017] [Indexed: 01/08/2023]
Abstract
Primary coenzyme Q10 (CoQ10 ; MIM# 607426) deficiencies are an emerging group of inherited mitochondrial disorders with heterogonous clinical phenotypes. Over a dozen genes are involved in the biosynthesis of CoQ10 , and mutations in several of these are associated with human disease. However, mutations in COQ5 (MIM# 616359), catalyzing the only C-methylation in the CoQ10 synthetic pathway, have not been implicated in human disease. Here, we report three female siblings of Iraqi-Jewish descent, who had varying degrees of cerebellar ataxia, encephalopathy, generalized tonic-clonic seizures, and cognitive disability. Whole-exome and subsequent whole-genome sequencing identified biallelic duplications in the COQ5 gene, leading to reduced levels of CoQ10 in peripheral white blood cells of all affected individuals and reduced CoQ10 levels in the only muscle tissue available from one affected proband. CoQ10 supplementation led to clinical improvement and increased the concentrations of CoQ10 in blood. This is the first report of primary CoQ10 deficiency caused by loss of function of COQ5, with delineation of the clinical, laboratory, histological, and molecular features, and insights regarding targeted treatment with CoQ10 supplementation.
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Affiliation(s)
- May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, 20892 Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
- Inova Translational Medicine Institute, Falls Church, 22042 Virginia, USA
| | - Bruria Ben-Zeev
- Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
- Department of Pathology, Sheba Medical Center, Tel-Hashomer, 52621, Israel
| | - Jennifer Guo
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, 20892 Maryland, USA
| | - Aviva Eliyahu
- Metabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
| | - Ben Pode-Shakked
- Metabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- The Dr. Pinchas Borenstein Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
| | - Amir Dori
- The Dr. Pinchas Borenstein Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
- Joseph Sagol Neuroscience Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Sravan Kakani
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Settara C. Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Carlos Ferreira
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Natalia Shelestovich
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, USA
| | - Dina Marek-Yagel
- Metabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
- Department of Pathology, Sheba Medical Center, Tel-Hashomer, 52621, Israel
| | - Hadass Pri-Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, 52621, Israel
| | - Ilan Blatt
- Department of Neurology, Sheba Medical Center, Tel-Hashomer, 5621 Israel
| | - John E. Niederhuber
- Inova Translational Medicine Institute, Falls Church, 22042 Virginia, USA
- Johns Hopkins University School of Medicine, 733 North Broadway Street, Baltimore, MD, USA
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, 20892 Maryland, USA
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - John Deeken
- Inova Translational Medicine Institute, Falls Church, 22042 Virginia, USA
| | - Tal Yardeni
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, USA
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, USA
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, 20892 Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Yair Anikster
- Metabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, 5621 Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, 52621, Israel
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Gillis NK, Rotroff DM, Mesa TE, Yao J, Chen Z, Carulli MA, Yoder SJ, Walko CM, Teer JK, McLeod HL. Tumor exome sequencing and copy number alterations reveal potential predictors of intrinsic resistance to multi-targeted tyrosine kinase inhibitors. Oncotarget 2017; 8:115114-115127. [PMID: 29383146 PMCID: PMC5777758 DOI: 10.18632/oncotarget.22914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/05/2017] [Indexed: 12/30/2022] Open
Abstract
Multi-targeted tyrosine kinase inhibitors (TKIs) have broad efficacy and similar FDA-approved indications, suggesting shared molecular drug targets across cancer types. Irrespective of tumor type, 20-30% of patients treated with multi-targeted TKIs demonstrate intrinsic resistance, with progressive disease as a best response. We conducted a retrospective cohort study to identify tumor (somatic) point mutations, insertion/deletions, and copy number alterations (CNA) associated with intrinsic resistance to multi-targeted TKIs. Using a candidate gene approach (n=243), tumor next-generation sequencing and CNA data was associated with resistant and non-resistant outcomes. Resistant individuals (n=11) more commonly harbored somatic point mutations in NTRK1, KDR, TGFBR2, and PTPN11 and CNA in CDK4, CDKN2B, and ERBB2 compared to non-resistant (n=26, p<0.01). Using a random forest classification model for variable reduction and a decision tree classification model, we were able to differentiate intrinsically resistant from non-resistant patients. CNA in CDK4 and CDKN2B were the most important analytical features, implicating the cyclin D pathway as a potentially important factor in resistance to multi-targeted TKIs. Replication of these results in a larger, independent patient cohort has potential to inform personalized prescribing of these widely utilized agents.
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Affiliation(s)
- Nancy K. Gillis
- DeBartolo Family Personalized Medicine Institute, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Center for Pharmacogenomics and Individualized Therapy Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel M. Rotroff
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Tania E. Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jiqiang Yao
- Cancer Informatics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Zhihua Chen
- Cancer Informatics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Sean J. Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Christine M. Walko
- DeBartolo Family Personalized Medicine Institute, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jamie K. Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Howard L. McLeod
- DeBartolo Family Personalized Medicine Institute, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Slavotinek A, Risolino M, Losa M, Cho MT, Monaghan KG, Schneidman-Duhovny D, Parisotto S, Herkert JC, Stegmann APA, Miller K, Shur N, Chui J, Muller E, DeBrosse S, Szot JO, Chapman G, Pachter NS, Winlaw DS, Mendelsohn BA, Dalton J, Sarafoglou K, Karachunski PI, Lewis JM, Pedro H, Dunwoodie SL, Selleri L, Shieh J. De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects. Hum Mol Genet 2017; 26:4849-4860. [PMID: 29036646 PMCID: PMC6455034 DOI: 10.1093/hmg/ddx363] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads. Clinical findings similar to those in Pbx mutant mice were observed in all patients with varying expressivity and severity, including external ear anomalies, abnormal branchial arch derivatives, heart malformations, diaphragmatic hernia, renal hypoplasia and ambiguous genitalia. All patients but one had developmental delays. Previously reported patients with congenital anomalies affecting the kidney and urinary tract exhibited deletions and loss of function variants in PBX1. The sequence variants in our cases included missense substitutions adjacent to the PBX1 homeodomain (p.Arg184Pro, p.Met224Lys, and p.Arg227Pro) or within the homeodomain (p.Arg234Pro, and p.Arg235Gln), whereas p.Ser262Glnfs*2, and p.Arg288* yielded truncated PBX1 proteins. Functional studies on five PBX1 sequence variants revealed perturbation of intrinsic, PBX-dependent transactivation ability and altered nuclear translocation, suggesting abnormal interactions between mutant PBX1 proteins and wild-type TALE or HOX cofactors. It is likely that the mutations directly affect the transcription of PBX1 target genes to impact embryonic development. We conclude that deleterious sequence variants in PBX1 cause intellectual disability and pleiotropic malformations resembling those in Pbx1 mutant mice, arguing for strong conservation of gene function between these two species.
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Affiliation(s)
- Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Maurizio Risolino
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Marta Losa
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biochemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarah Parisotto
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Johanna C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Jacqueline Chui
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Eric Muller
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Suzanne DeBrosse
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Justin O Szot
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Gavin Chapman
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - David S Winlaw
- University of Sydney, Medical School, Sydney, NSW, Australia
- Heart Centre for Children, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Joline Dalton
- Paul and Shelia Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
| | - Kyriakie Sarafoglou
- Department of Pediatrics, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | | | - Jane M Lewis
- Department of Urology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Helio Pedro
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Sally L Dunwoodie
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Plasticity of the MFS1 Promoter Leads to Multidrug Resistance in the Wheat Pathogen Zymoseptoria tritici. mSphere 2017; 2:mSphere00393-17. [PMID: 29085913 PMCID: PMC5656749 DOI: 10.1128/msphere.00393-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 11/20/2022] Open
Abstract
The ascomycete Zymoseptoria tritici is the causal agent of Septoria leaf blotch on wheat. Disease control relies mainly on resistant wheat cultivars and on fungicide applications. The fungus displays a high potential to circumvent both methods. Resistance against all unisite fungicides has been observed over decades. A different type of resistance has emerged among wild populations with multidrug-resistant (MDR) strains. Active fungicide efflux through overexpression of the major facilitator gene MFS1 explains this emerging resistance mechanism. Applying a bulk-progeny sequencing approach, we identified in this study a 519-bp long terminal repeat (LTR) insert in the MFS1 promoter, a relic of a retrotransposon cosegregating with the MDR phenotype. Through gene replacement, we show the insert as a mutation responsible for MFS1 overexpression and the MDR phenotype. Besides this type I insert, we found two different types of promoter inserts in more recent MDR strains. Type I and type II inserts harbor potential transcription factor binding sites, but not the type III insert. Interestingly, all three inserts correspond to repeated elements present at different genomic locations in either IPO323 or other Z. tritici strains. These results underline the plasticity of repeated elements leading to fungicide resistance in Z. tritici and which contribute to its adaptive potential. IMPORTANCE Disease control through fungicides remains an important means to protect crops from fungal diseases and to secure the harvest. Plant-pathogenic fungi, especially Zymoseptoria tritici, have developed resistance against most currently used active ingredients, reducing or abolishing their efficacy. While target site modification is the most common resistance mechanism against single modes of action, active efflux of multiple drugs is an emerging phenomenon in fungal populations reducing additionally fungicides' efficacy in multidrug-resistant strains. We have investigated the mutations responsible for increased drug efflux in Z. tritici field strains. Our study reveals that three different insertions of repeated elements in the same promoter lead to multidrug resistance in Z. tritici. The target gene encodes the membrane transporter MFS1 responsible for drug efflux, with the promoter inserts inducing its overexpression. These results underline the plasticity of repeated elements leading to fungicide resistance in Z. tritici.
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Le Gallo M, Rudd ML, Urick ME, Hansen NF, Merino MJ, Mutch DG, Goodfellow PJ, Mullikin JC, Bell DW. The FOXA2 transcription factor is frequently somatically mutated in uterine carcinosarcomas and carcinomas. Cancer 2017; 124:65-73. [PMID: 28940304 DOI: 10.1002/cncr.30971] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND Uterine carcinosarcomas (UCSs) are a rare but clinically aggressive form of cancer. They are biphasic tumors consisting of both epithelial and sarcomatous components. The majority of uterine carcinosarcomas are clonal, with the carcinomatous cells undergoing metaplasia to give rise to the sarcomatous component. The objective of the current study was to identify novel somatically mutated genes in UCSs. METHODS We whole exome sequenced paired tumor and nontumor DNAs from 14 UCSs and orthogonally validated 464 somatic variants using Sanger sequencing. Fifteen genes that were somatically mutated in at least 2 tumor exomes were Sanger sequenced in another 39 primary UCSs. RESULTS Overall, among 53 UCSs in the current study, the most frequently mutated of these 15 genes were tumor protein p53 (TP53) (75.5%), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) (34.0%), protein phosphatase 2, regulatory subunit A, alpha (PPP2R1A) (18.9%), F-box and WD repeat domain containing 7 (FBXW7) (18.9%), chromodomain helicase DNA binding protein 4 (CHD4) (17.0%), and forkhead box A2 (FOXA2) (15.1%). FOXA2 has not previously been implicated in UCSs and was predominated by frameshift and nonsense mutations. One UCS with a FOXA2 frameshift mutation expressed truncated FOXA2 protein by immunoblotting. Sequencing of FOXA2 in 160 primary endometrial carcinomas revealed somatic mutations in 5.7% of serous, 22.7% of clear cell, 9% of endometrioid, and 11.1% of mixed endometrial carcinomas, the majority of which were frameshift mutations. CONCLUSIONS Collectively, the findings of the current study provide compelling genetic evidence that FOXA2 is a pathogenic driver gene in the etiology of primary uterine cancers, including UCSs. Cancer 2018;124:65-73. © 2017 American Cancer Society.
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Affiliation(s)
- Matthieu Le Gallo
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Meghan L Rudd
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Mary Ellen Urick
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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- National Institutes of Health Intramural Sequencing Center, National Institutes of Health, Rockville, Maryland
| | - Maria J Merino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David G Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri
| | - Paul J Goodfellow
- Department of Obstetrics and Gynecology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Daphne W Bell
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Oprescu SN, Chepa-Lotrea X, Takase R, Golas G, Markello TC, Adams DR, Toro C, Gropman AL, Hou YM, Malicdan MCV, Gahl WA, Tifft CJ, Antonellis A. Compound heterozygosity for loss-of-function GARS variants results in a multisystem developmental syndrome that includes severe growth retardation. Hum Mutat 2017; 38:1412-1420. [PMID: 28675565 DOI: 10.1002/humu.23287] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/17/2017] [Accepted: 06/16/2017] [Indexed: 01/25/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in myriad dominant and recessive disease phenotypes. Glycyl-tRNA synthetase (GARS) is a bifunctional ARS that charges tRNAGly in the cytoplasm and mitochondria. GARS variants have been associated with dominant Charcot-Marie-Tooth disease but have not been convincingly implicated in recessive phenotypes. Here, we describe a patient from the NIH Undiagnosed Diseases Program with a multisystem, developmental phenotype. Whole-exome sequence analysis revealed that the patient is compound heterozygous for one frameshift (p.Glu83Ilefs*6) and one missense (p.Arg310Gln) GARS variant. Using in vitro and in vivo functional studies, we show that both GARS variants cause a loss-of-function effect: the frameshift variant results in depleted protein levels and the missense variant reduces GARS tRNA charging activity. In support of GARS variant pathogenicity, our patient shows striking phenotypic overlap with other patients having ARS-related recessive diseases, including features associated with variants in both cytoplasmic and mitochondrial ARSs; this observation is consistent with the essential function of GARS in both cellular locations. In summary, our clinical, genetic, and functional analyses expand the phenotypic spectrum associated with GARS variants.
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Affiliation(s)
| | - Xenia Chepa-Lotrea
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ryuichi Takase
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gretchen Golas
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Thomas C Markello
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David R Adams
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Camilo Toro
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Andrea L Gropman
- Division of Neurogenetics and Developmental Pediatrics, Children's National Medical Center, Washington, District of Columbia
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - May Christine V Malicdan
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Cynthia J Tifft
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan.,Department of Neurology, University of Michigan, Ann Arbor, Michigan
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Johnston JJ, Lee C, Wentzensen IM, Parisi MA, Crenshaw MM, Sapp JC, Gross JM, Wallingford JB, Biesecker LG. Compound heterozygous alterations in intraflagellar transport protein CLUAP1 in a child with a novel Joubert and oral-facial-digital overlap syndrome. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001321. [PMID: 28679688 PMCID: PMC5495032 DOI: 10.1101/mcs.a001321] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/05/2016] [Indexed: 12/17/2022] Open
Abstract
Disruption of normal ciliary function results in a range of diseases collectively referred to as ciliopathies. Here we report a child with a phenotype that overlapped with Joubert, oral–facial–digital, and Pallister–Hall syndromes including brain, limb, and craniofacial anomalies. We performed exome-sequence analysis on a proband and both parents, filtered for putative causative variants, and Sanger-verified variants of interest. Identified variants in CLUAP1 were functionally analyzed in a Xenopus system to determine their effect on ciliary function. Two variants in CLUAP1 were identified through exome-sequence analysis, Chr16:g.3558407T>G, c.338T>G, p.(Met113Arg) and Chr16:g.3570011C>T, c.688C>T, p.(Arg230Ter). These variants were rare in the Exome Aggregation Consortium (ExAC) data set of 65,000 individuals (one and two occurrences, respectively). Transfection of mutant CLUAP1 constructs into Xenopus embryos showed reduced protein levels p.(Arg230Ter) and reduced intraflagellar transport p.(Met113Arg). The genetic data show that these variants are present in an affected child, are rare in the population, and result in reduced, but not absent, intraflagellar transport. We conclude that biallelic mutations in CLUAP1 resulted in this novel ciliopathy syndrome in the proband.
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Affiliation(s)
- Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78705, USA
| | - Ingrid M Wentzensen
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Melissa A Parisi
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Molly M Crenshaw
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Julie C Sapp
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78705, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
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Myophosphorylase (PYGM) mutations determined by next generation sequencing in a cohort from Turkey with McArdle disease. Neuromuscul Disord 2017; 27:997-1008. [PMID: 28967462 DOI: 10.1016/j.nmd.2017.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/30/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022]
Abstract
This study aimed to identify PYGM mutations in patients with McArdle disease from Turkey by next generation sequencing (NGS). Genomic DNA was extracted from the blood of the McArdle patients (n = 67) and unrelated healthy volunteers (n = 53). The PYGM gene was sequenced with NGS and the observed mutations were validated by direct Sanger sequencing. A diagnostic algorithm was developed for patients with suspected McArdle disease. A total of 16 deleterious PYGM mutations were identified, of which 5 were novel, including 1 splice-site donor, 1 frame-shift, and 3 non-synonymous variants. The p.Met1Val (27-patients/11-families) was the most common PYGM mutation, followed by p.Arg576* (6/4), c.1827+7A>G (5/4), c.772+2_3delTG (5/3), p.Phe710del (4/2), p.Lys754Asnfs (2/1), and p.Arg50* (1/1). A molecular diagnostic flowchart is proposed for the McArdle patients in Turkey, covering the 6 most common PYGM mutations found in Turkey as well as the most common mutation in Europe. The diagnostic algorithm may alleviate the need for muscle biopsies in 77.6% of future patients. A prevalence of any of the mutations to a geographical region in Turkey was not identified. Furthermore, the NGS approach to sequence the entire PYGM gene was successful in detecting a common missense mutation and discovering novel mutations in this population study.
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Zou Y, Donkervoort S, Salo AM, Foley AR, Barnes AM, Hu Y, Makareeva E, Leach ME, Mohassel P, Dastgir J, Deardorff MA, Cohn RD, DiNonno WO, Malfait F, Lek M, Leikin S, Marini JC, Myllyharju J, Bönnemann CG. P4HA1 mutations cause a unique congenital disorder of connective tissue involving tendon, bone, muscle and the eye. Hum Mol Genet 2017; 26:2207-2217. [PMID: 28419360 PMCID: PMC6075373 DOI: 10.1093/hmg/ddx110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/14/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4Hs) play a central role in the formation and stabilization of the triple helical domain of collagens. P4HA1 encodes the catalytic α(I) subunit of the main C-P4H isoenzyme (C-P4H-I). We now report human bi-allelic P4HA1 mutations in a family with a congenital-onset disorder of connective tissue, manifesting as early-onset joint hypermobility, joint contractures, muscle weakness and bone dysplasia as well as high myopia, with evidence of clinical improvement of motor function over time in the surviving patient. Similar to P4ha1 null mice, which die prenatally, the muscle tissue from P1 and P2 was found to have reduced collagen IV immunoreactivity at the muscle basement membrane. Patients were compound heterozygous for frameshift and splice site mutations leading to reduced, but not absent, P4HA1 protein level and C-P4H activity in dermal fibroblasts compared to age-matched control samples. Differential scanning calorimetry revealed reduced thermal stability of collagen in patient-derived dermal fibroblasts versus age-matched control samples. Mutations affecting the family of C-P4Hs, and in particular C-P4H-I, should be considered in patients presenting with congenital connective tissue/myopathy overlap disorders with joint hypermobility, contractures, mild skeletal dysplasia and high myopia.
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Affiliation(s)
- Yaqun Zou
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Antti M. Salo
- Oulu Center for Cell-Matrix Research, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - A. Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Aileen M. Barnes
- Section on Heritable Disorders of Bone and Extracellular Matrix, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Elena Makareeva
- Section on Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Meganne E. Leach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Children’s National Health System, Washington, DC, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jahannaz Dastgir
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew A. Deardorff
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald D. Cohn
- Division of Clinical and Metabolic Genetics, Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wendy O. DiNonno
- Department of Maternal-Fetal Medicine, Eastern Virginia Medical School, VA, USA
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital and Ghent University, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sergey Leikin
- Section on Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joan C. Marini
- Section on Heritable Disorders of Bone and Extracellular Matrix, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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Donkervoort S, Chan SHS, Hayes LH, Bradley N, Nguyen D, Leach ME, Mohassel P, Hu Y, Thangarajh M, Bharucha-Goebel D, Kan A, Ho RSL, Reyes CA, Nance J, Moore SA, Foley AR, Bönnemann CG. Cytoplasmic body pathology in severe ACTA1-related myopathy in the absence of typical nemaline rods. Neuromuscul Disord 2017; 27:531-536. [PMID: 28416349 PMCID: PMC5918412 DOI: 10.1016/j.nmd.2017.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/24/2017] [Accepted: 02/24/2017] [Indexed: 02/07/2023]
Abstract
Mutations in ACTA1 cause a group of myopathies with expanding clinical and histopathological heterogeneity. We describe three patients with severe ACTA1-related myopathy who have muscle fiber cytoplasmic bodies but no classic nemaline rods. Patient 1 is a five-year-old boy who presented at birth with severe weakness and respiratory failure, requiring mechanical ventilation. Whole exome sequencing identified a heterozygous c.282C>A (p.Asn94Lys) ACTA1 mutation. Patients 2 and 3 were twin boys with hypotonia, severe weakness, and respiratory insufficiency at birth requiring mechanical ventilation. Both died at 6 months of age. The same heterozygous c.282C>A (p.Asn94Lys) ACTA1 mutation was identified by whole exome sequencing. We conclude that clinically severe ACTA1-related myopathy can present with muscle morphological findings suggestive of cytoplasmic body myopathy in the absence of definite nemaline rods. The Asn94Lys mutation in skeletal muscle sarcomeric α-actin may be linked to this histological appearance. These novel ACTA1 cases also illustrate the successful application of whole exome sequencing in directly arriving at a candidate genetic diagnosis in patients with unexpected phenotypic and histologic features for a known neuromuscular gene.
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Affiliation(s)
- Sandra Donkervoort
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - Sophelia H S Chan
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR
| | - Leslie H Hayes
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA; Boston Children's Hospital, Boston, MA, USA
| | - Nathaniel Bradley
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - David Nguyen
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - Meganne E Leach
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA; Children's National Health System, Washington, DC, USA
| | - Payam Mohassel
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - Ying Hu
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | | | - Diana Bharucha-Goebel
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA; Children's National Health System, Washington, DC, USA
| | - Amanda Kan
- Department of Pathology and Clinical Biochemistry, The Queen Mary Hospital, Hong Kong SAR
| | - Ronnie S L Ho
- Department of Pathology and Clinical Biochemistry, The Queen Mary Hospital, Hong Kong SAR
| | | | - Jessica Nance
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - A Reghan Foley
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - Carsten G Bönnemann
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA.
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Donkervoort S, Bharucha-Goebel D, Yun P, Hu Y, Mohassel P, Hoke A, Zein WM, Ezzo D, Atherton AM, Modrcin AC, Dasouki M, Foley AR, Bönnemann CG. HSP and deafness: Neurocristopathy caused by a novel mosaic SOX10 mutation. Neurol Genet 2017; 3:e151. [PMID: 28534044 PMCID: PMC5432370 DOI: 10.1212/nxg.0000000000000151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/22/2017] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To identify the underlying genetic cause in 2 sisters affected with progressive lower extremity spasticity, neuropathy, and early-onset deafness. METHODS Whole-exome sequencing was performed, and segregation testing of variants was investigated using targeted Sanger sequencing. An inherited paternal mosaic mutation was further evaluated through quantitative analysis of the ratio of mutant vs wild-type allele in genomic DNA from various tissues, including blood, dermal fibroblasts, and saliva. RESULTS A novel heterozygous nonsense mutation (c.1140C>A; p.Y380X) in SOX10 was identified in the affected sisters. Paternal mosaicism was suspected based on a small chromatogram peak, which was less than the heterozygous peak of the mutated allele. Consistent with mosaicism, the mosaic paternal samples had notable variability in the ratio of mutant vs wild-type allele in various tissues (compared with the fully heterozygous daughter), with the highest paternal mutant levels in saliva (32.7%) and lowest in dermal fibroblasts (13.9%). Targeted clinical re-examination of the father revealed a sensorimotor neuropathy that was previously clinically unrecognized. CONCLUSIONS These findings expand the phenotypic spectrum of SOX10-related neurocristopathy. Mutations in SOX10 should be considered in patients presenting with a complicated form of hereditary spastic paraplegia that includes neuropathy and deafness. Diagnostic workup may be complicated, as SOX10 mutations can present in a mosaic state, with a mild clinical manifestation.
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Affiliation(s)
- Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Pomi Yun
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Ahmet Hoke
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Wadih M Zein
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Daniel Ezzo
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Andrea M Atherton
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Ann C Modrcin
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Majed Dasouki
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section (S.D., D.B.-G., P.Y., Y.H., P.M., D.E., A.R.F., C.G.B.), and National Eye Institute (W.M.Z.), National Institutes of Health, Bethesda, MD; Children's National Medical Center (D.B.-G.), Washington, DC; Department of Neurology (A.H.), The Johns Hopkins University School of Medicine, Baltimore, MD; Children's Mercy Hospital (A.M.A., A.C.M.), Kansas City, MO; and Department of Neurology (M.D.), University of Kansas Medical Center, Kansas City, KS
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48
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Le Gallo M, Rudd ML, Urick ME, Hansen NF, Zhang S, Lozy F, Sgroi DC, Vidal Bel A, Matias-Guiu X, Broaddus RR, Lu KH, Levine DA, Mutch DG, Goodfellow PJ, Salvesen HB, Mullikin JC, Bell DW. Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing. Cancer 2017; 123:3261-3268. [PMID: 28485815 DOI: 10.1002/cncr.30745] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND The molecular pathogenesis of clear cell endometrial cancer (CCEC), a tumor type with a relatively unfavorable prognosis, is not well defined. We searched exome-wide for novel somatically mutated genes in CCEC and assessed the mutational spectrum of known and candidate driver genes in a large cohort of cases. METHODS We conducted whole exome sequencing of paired tumor-normal DNAs from 16 cases of CCEC (12 CCECs and the CCEC components of 4 mixed histology tumors). Twenty-two genes-of-interest were Sanger-sequenced from another 47 cases of CCEC. Microsatellite instability (MSI) and microsatellite stability (MSS) were determined by genotyping 5 mononucleotide repeats. RESULTS Two tumor exomes had relatively high mutational loads and MSI. The other 14 tumor exomes were MSS and had 236 validated nonsynonymous or splice junction somatic mutations among 222 protein-encoding genes. Among the 63 cases of CCEC in this study, we identified frequent somatic mutations in TP53 (39.7%), PIK3CA (23.8%), PIK3R1 (15.9%), ARID1A (15.9%), PPP2R1A (15.9%), SPOP (14.3%), and TAF1 (9.5%), as well as MSI (11.3%). Five of 8 mutations in TAF1, a gene with no known role in CCEC, localized to the putative histone acetyltransferase domain and included 2 recurrently mutated residues. Based on patterns of MSI and mutations in 7 genes, CCEC subsets molecularly resembled serous endometrial cancer (SEC) or endometrioid endometrial cancer (EEC). CONCLUSION Our findings demonstrate molecular similarities between CCEC and SEC and EEC and implicate TAF1 as a novel candidate CCEC driver gene. Cancer 2017;123:3261-8. © 2017 American Cancer Society.
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Affiliation(s)
- Matthieu Le Gallo
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Meghan L Rudd
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Mary Ellen Urick
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Suiyuan Zhang
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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- National Institutes of Health Intramural Sequencing Center, National Institutes of Health, Bethesda, Maryland
| | - Fred Lozy
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Dennis C Sgroi
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - August Vidal Bel
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain.,Department of Pathology, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari de Bellvitge, Barcelona, Spain.,Department of Pathology and Molecular Genetics/Oncological Pathology Group, Hospital Universitari Arnau de Vilanova, Universitat de Lleida, IRB Lleida, Lleida, Spain
| | - Russell R Broaddus
- Division of Surgery, Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Karen H Lu
- Division of Surgery, Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Douglas A Levine
- Gynecologic Oncology, Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York
| | - David G Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri
| | - Paul J Goodfellow
- Department of Obstetrics and Gynecology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Helga B Salvesen
- Department of Clinical Science, Center for Cancer Biomarkers, University of Bergen, Bergen, Norway.,Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,National Institutes of Health Intramural Sequencing Center, National Institutes of Health, Bethesda, Maryland
| | - Daphne W Bell
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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49
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Bryan MM, Tolman NJ, Simon KL, Huizing M, Hufnagel RB, Brooks BP, Speransky V, Mullikin JC, Gahl WA, Malicdan MCV, Gochuico BR. Clinical and molecular phenotyping of a child with Hermansky-Pudlak syndrome-7, an uncommon genetic type of HPS. Mol Genet Metab 2017; 120:378-383. [PMID: 28259707 PMCID: PMC5395203 DOI: 10.1016/j.ymgme.2017.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 01/22/2023]
Abstract
PURPOSE Hermansky-Pudlak syndrome (HPS) is a rare inherited disorder with ten reported genetic types; each type has defects in subunits of either Adaptor Protein-3 complex or Biogenesis of Lysosome-related Organelles Complex (BLOC)-1, -2, or -3. Very few patients with BLOC-1 deficiency (HPS-7, -8, and -9 types) have been diagnosed. We report results of comprehensive clinical testing and molecular analyses of primary fibroblasts from a new case of HPS-7. RESULTS A 6-year old Paraguayan male presented with hypopigmentation, ocular albinism, nystagmus, reduced visual acuity, and easy bruising. He also experienced delayed motor and language development as a very young child; head and chest trauma resulted in intracranial hemorrhage with subsequent right hemiparesis and lung scarring. There was no clinical evidence of immunodeficiency or colitis. Whole mount transmission electron microscopy revealed absent platelet delta granules; platelet aggregation testing was abnormal. Exome sequencing revealed a homozygous nonsense mutation in the Dystrobrevin binding protein 1 (DTNBP1) gene [NM_032122.4: c.307C>T; p.Gln103*], previously reported in a Portuguese adult. The gene encodes the dysbindin subunit of BLOC-1. Dysbindin protein expression was negligible in our patient's dermal fibroblasts, while his DTNBP1 mRNA level was similar to that of a normal control. CONCLUSIONS Comprehensive clinical evaluation of the first pediatric case reported with HPS-7 reveals oculocutaneous albinism and platelet storage pool deficiency; his phenotype is consistent with findings in other patients with BLOC-1 disorders. This patient's markedly reduced Dysbindin protein expression in HPS-7 resulted from a mechanism other than nonsense mediated decay.
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Affiliation(s)
- Melanie M Bryan
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Nathanial J Tolman
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Karen L Simon
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Marjan Huizing
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Vladislav Speransky
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Institutes of Health, 5625 Fishers Lane, Rockville, MD 20852, USA
| | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA; NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, 9000 Rockville Pike, National Institutes of Health, Bethesda, MD 20892, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, 9000 Rockville Pike, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Bernadette R Gochuico
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
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50
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Cox AJ, Darbro BW, Laxer RM, Velez G, Bing X, Finer AL, Erives A, Mahajan VB, Bassuk AG, Ferguson PJ. Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO). PLoS One 2017; 12:e0169687. [PMID: 28301468 PMCID: PMC5354242 DOI: 10.1371/journal.pone.0169687] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022] Open
Abstract
Chronic recurrent multifocal osteomyelitis (CRMO) is a rare, pediatric, autoinflammatory disease characterized by bone pain due to sterile osteomyelitis, and is often accompanied by psoriasis or inflammatory bowel disease. There are two syndromic forms of CRMO, Majeed syndrome and DIRA, for which the genetic cause is known. However, for the majority of cases of CRMO, the genetic basis is unknown. Via whole-exome sequencing, we detected a homozygous mutation in the filamin-binding domain of FBLIM1 in an affected child with consanguineous parents. Microarray analysis of bone marrow macrophages from the CRMO murine model (cmo) determined that the Fblim1 ortholog is the most differentially expressed gene, downregulated over 20-fold in the cmo mouse. We sequenced FBLIM1 in 96 CRMO subjects and found a second proband with a novel frameshift mutation in exon 6 and a rare regulatory variant. In SaOS2 cells, overexpressing the regulatory mutation showed the flanking region acts as an enhancer, and the mutation ablates enhancer activity. Our data implicate FBLIM1 in the pathogenesis of sterile bone inflammation and our findings suggest CRMO is a disorder of chronic inflammation and imbalanced bone remodeling.
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Affiliation(s)
- Allison J. Cox
- Department of Pediatrics, The University of Iowa, Iowa City, IA, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA, United States of America
| | - Benjamin W. Darbro
- Department of Pediatrics, The University of Iowa, Iowa City, IA, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA, United States of America
| | - Ronald M. Laxer
- Division of Pediatric Rheumatology, Departments of Pediatrics and Medicine, University of Toronto and The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabriel Velez
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, United States of America
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA, United States of America
- Omics Laboratory, University of Iowa, Iowa City, IA, United States of America
| | - Xinyu Bing
- Department of Pediatrics, The University of Iowa, Iowa City, IA, United States of America
| | - Alexis L. Finer
- Department of Pediatrics, The University of Iowa, Iowa City, IA, United States of America
| | - Albert Erives
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA, United States of America
- Department of Biology, The University of Iowa, Iowa City, IA, United States of America
| | - Vinit B. Mahajan
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA, United States of America
- Omics Laboratory, University of Iowa, Iowa City, IA, United States of America
| | - Alexander G. Bassuk
- Department of Pediatrics, The University of Iowa, Iowa City, IA, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA, United States of America
| | - Polly J. Ferguson
- Department of Pediatrics, The University of Iowa, Iowa City, IA, United States of America
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