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Singh S, Shah H, Dalal A, Shukla A, Bhavani GS, Girisha KM. Two sisters with RSPRY1-related spondyloepimetaphyseal dysplasia. Am J Med Genet A 2024:e63601. [PMID: 38562122 DOI: 10.1002/ajmg.a.63601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024]
Abstract
Biallelic variants in RSPRY1 have been found to result in spondyloepimetaphyseal dysplasia. Two siblings presenting with short stature, facial dysmorphism, progressive vertebral defects, small epiphysis, cupping and fraying of metaphyses, brachydactyly, and short metatarsals harbored a homozygous missense variant c.1652G>A;p.(Cys551Tyr) in the RSPRY1 gene. The phenotype in our patients resembles spondyloepimetaphyseal dysplasia, Faden-Alkuraya type. Thus, our study provides further evidence to support the association of RSPRY1 variants with spondyloepimetaphyseal dysplasia. We observed joint dislocation as a novel clinical feature of this condition.
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Affiliation(s)
- Swati Singh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University Muscat, Oman
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2
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Singh S, Jacob P, Patil SJ, Muranjan M, Shah H, Girisha KM, Bhavani GS. Indian patients with CHST3-related chondrodysplasia with congenital joint dislocations. Am J Med Genet A 2024; 194:e63422. [PMID: 37876363 DOI: 10.1002/ajmg.a.63422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023]
Abstract
CHST3-related chondrodysplasia with congenital joint dislocations (CDCJD, #MIM 143095), is a rare genetic skeletal disorder caused by biallelic loss of function variants in CHST3. CHST3 is critical for the sulfation of chondroitin sulfate. This study delineates the clinical presentation of nine individuals featuring the key symptoms of CDCJD; congenital joint (knee and elbow) dislocations, short trunk short stature progressive vertebral anomalies, and metacarpal shortening. Additional manifestations include irregular distal femoral epiphysis, supernumerary carpal ossification centers, bifid humerus, club foot, and cardiac abnormalities. Sanger sequencing was carried out to investigate molecular etiology in eight patients and exome sequencing in one. Genetic testing revealed five homozygous variants in CHST3 (four were novel and one was previously reported). All these variants are located on sulfotransferase domain of CHST3 protein and were classified as pathogenic/ likely pathogenic. We thus report on nine individuals with CHST3-related chondrodysplasia with congenital joint dislocations from India and suggest monitoring the health of cardiac valves in this condition.
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Affiliation(s)
- Swati Singh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, Karnataka, India
| | - Mamta Muranjan
- Department of Pediatrics, Genetic Division, Seth GS Medical College, King Edward Memorial Hospital, Mumbai, Maharashtra, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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3
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Kakar N, Rehman FU, Kaur R, Bhavani GS, Goyal M, Shah H, Kaur K, Sodhi KS, Kubisch C, Borck G, Panigrahi I, Girisha KM, Kornak U, Spielmann M. Multi-gene panel sequencing in highly consanguineous families and patients with congenital forms of skeletal dysplasias. Clin Genet 2024. [PMID: 38378010 DOI: 10.1111/cge.14509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Skeletal dysplasias (SKDs) are a heterogeneous group of more than 750 genetic disorders characterized by abnormal development, growth, and maintenance of bones or cartilage in the human skeleton. SKDs are often caused by variants in early patterning genes and in many cases part of multiple malformation syndromes and occur in combination with non-skeletal phenotypes. The aim of this study was to investigate the underlying genetic cause of congenital SKDs in highly consanguineous Pakistani families, as well as in sporadic and familial SKD cases from India using multigene panel sequencing analysis. Therefore, we performed panel sequencing of 386 bone-related genes in 7 highly consanguineous families from Pakistan and 27 cases from India affected with SKDs. In the highly consanguineous families, we were able to identify the underlying genetic cause in five out of seven families, resulting in a diagnostic yield of 71%. Whereas, in the sporadic and familial SKD cases, we identified 12 causative variants, corresponding to a diagnostic yield of 44%. The genetic heterogeneity in our cohorts was very high and we were able to detect various types of variants, including missense, nonsense, and frameshift variants, across multiple genes known to cause different types of SKDs. In conclusion, panel sequencing proved to be a highly effective way to decipher the genetic basis of SKDs in highly consanguineous families as well as sporadic and or familial cases from South Asia. Furthermore, our findings expand the allelic spectrum of skeletal dysplasias.
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Affiliation(s)
- Naseebullah Kakar
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Fazal Ur Rehman
- Department of Pathology, Bolan Medical College, Quetta, Pakistan
| | - Ramandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Manisha Goyal
- Pediatrics Genetic & Research Laboratory, Department of Pediatrics, Lok Nayak Hospital, New Delhi, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | | | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guntram Borck
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
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Sithambaram S, Jacob P, Neethukrishna K, Bhavani GS, Dalal A, Shah H, Girisha KM. PRKACA-related, atrial defects-polydactyly-multiple congenital malformation syndrome in an Indian patient. Am J Med Genet A 2024:e63566. [PMID: 38357848 DOI: 10.1002/ajmg.a.63566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/16/2024]
Abstract
PRKACA-related, atrial defects-polydactyly-multiple congenital malformation syndrome is a recently described skeletal ciliopathy, which is caused by disease-causing variants in PRKACA. The primary phenotypic description includes atrial septal defects, and limb anomalies including polydactyly and short limbs. To date, only four molecularly proven patients have been reported in the literature with a recurrent variant, c.409G>A p.Gly137Arg in PRKACA. In this study, we report the fifth affected individual with the same variant and review the clinical features and radiographic findings of this rare syndrome.
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Affiliation(s)
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Hitesh Shah
- Department of Pediatric Orthopaedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
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Pande S, Majethia P, Nair K, Rao LP, Mascarenhas S, Kaur N, do Rosario MC, Neethukrishna K, Chaurasia A, Hunakunti B, Jadhav N, Xavier S, Kumar J, Bhat V, Bhavani GS, Narayanan DL, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Aroor S, Bhat Y R, Lewis LE, Sharma S, Bajaj S, Sankhyan N, Siddiqui S, Nayak SS, Bielas S, Girisha KM, Shukla A. De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India. Eur J Hum Genet 2023:10.1038/s41431-023-01513-7. [PMID: 38114583 DOI: 10.1038/s41431-023-01513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/21/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
The contribution of de novo variants as a cause of intellectual disability (ID) is well established in several cohorts reported from the developed world. However, the genetic landscape as well as the appropriate testing strategies for identification of de novo variants of these disorders remain largely unknown in low-and middle-income countries like India. In this study, we delineate the clinical and genotypic spectrum of 54 families (55 individuals) with syndromic ID harboring rare de novo variants. We also emphasize on the effectiveness of singleton exome sequencing as a valuable tool for diagnosing these disorders in resource limited settings. Overall, 46 distinct disorders were identified encompassing 46 genes with 51 single-nucleotide variants and/or indels and two copy-number variants. Pathogenic variants were identified in CREBBP, TSC2, KMT2D, MECP2, IDS, NIPBL, NSD1, RIT1, SOX10, BRWD3, FOXG1, BCL11A, KDM6B, KDM5C, SETD5, QRICH1, DCX, SMARCD1, ASXL1, ASXL3, AKT3, FBN2, TCF12, WASF1, BRAF, SMARCA4, SMARCA2, TUBG1, KMT2A, CTNNB1, DLG4, MEIS2, GATAD2B, FBXW7, ANKRD11, ARID1B, DYNC1H1, HIVEP2, NEXMIF, ZBTB18, SETD1B, DYRK1A, SRCAP, CASK, L1CAM, and KRAS. Twenty-four of these monogenic disorders have not been previously reported in the Indian population. Notably, 39 out of 53 (74%) disease-causing variants are novel. These variants were identified in the genes mainly encoding transcriptional and chromatin regulators, serine threonine kinases, lysosomal enzymes, molecular motors, synaptic proteins, neuronal migration machinery, adhesion molecules, structural proteins and signaling molecules.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sruthy Xavier
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jeevan Kumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B L Yatheesha
- Dheemahi Child Neurology and Development Center, Shivamogga, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | | | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Secunderabad, Hyderabad, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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Jacob P, Bhavani GS, Udupa P, Wang Z, Hariharan SV, Delampady K, Dalal A, Kamath N, Ikegawa S, Shenoy RD, Handattu K, Shah H, Girisha KM. Exome Sequencing in Monogenic Forms of Rickets. Indian J Pediatr 2023; 90:1182-1190. [PMID: 36692815 PMCID: PMC10627992 DOI: 10.1007/s12098-022-04393-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/27/2022] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To understand the phenotypic and genotypic spectrum of genetic forms of rickets in 10 families. METHODS Detailed clinical, radiographic, and biochemical evaluation of 10 families with phenotypes suggestive of a genetic cause of rickets was performed. Molecular testing using exome sequencing aided in the diagnosis of six different forms of known genetic causes. RESULTS Eleven disease-causing variants including five previously reported variants (CYP27B1:c.1319_1325dup, p.(Phe443Profs*24), VDR:c.1171C>T, p.(Arg391Cys), PHEX: c.1586_1586+1del, PHEX: c.1482+5G>C, PHEX: c.58C>T, p.(Arg20*)) and six novel variants (CYP27B1:c.974C>T, p.(Thr325Met), CYP27B1: c.1376G>A, p.(Arg459His), CYP2R1: c.595C>T, p.(Arg199*), CYP2R1:c.1330G>C, p.(Gly444Arg),SLC34A3:c.1336-11_1336-1del, SLC2A2: c.589G>C, p.(Val197Leu)) in the genes known to cause monogenic rickets were identified. CONCLUSION The authors hereby report a case series of individuals from India with a molecular diagnosis of rickets and provide the literature review which would help in enhancing the clinical and molecular profile for rapid and differential diagnosis of rickets.
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Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Zheng Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Sankar V Hariharan
- Department of Pediatrics, Genetics Clinic, SAT Hospital, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Kishan Delampady
- Department of Endocrinology, AJ Hospital & Research Center, Mangalore, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting & Diagnostics, Hyderabad, Telangana, India
| | - Nutan Kamath
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shiro Ikegawa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Rathika D Shenoy
- Department of Pediatrics, K S Hegde Medical Academy, Nitte University, Mangalore, Karnataka, India
| | - Koushik Handattu
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India.
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7
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Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023; 8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2-64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants' impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
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Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilie F Rustad
- Department of Medial Genetics, Oslo University Hospital, Oslo, Norway
| | - Vernon Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, Norway
| | - Laura Orellana
- Protein Dynamics and Mutation lab, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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8
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Udupa P, Shrikondawar AN, Nayak SS, Shah H, Ranjan A, Girisha KM, Bhavani GS, Ghosh DK. Deep intronic mutation in CRTAP results in unstable isoforms of the protein to induce type I collagen aggregation in a lethal type of osteogenesis imperfecta type VII. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166741. [PMID: 37146916 DOI: 10.1016/j.bbadis.2023.166741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Genetic mutations are involved in Mendelian disorders. Unbuffered intronic mutations in gene variants can generate aberrant splice sites in mutant transcripts, resulting in mutant isoforms of proteins with modulated expression, stability, and function in diseased cells. Here, we identify a deep intronic variant, c.794_1403A>G, in CRTAP by genome sequencing of a male fetus with osteogenesis imperfecta (OI) type VII. The mutation introduces cryptic splice sites in intron-3 of CRTAP, resulting in two mature mutant transcripts with cryptic exons. While transcript-1 translates to a truncated isoform (277 amino acids) with thirteen C-terminal non-wild-type amino acids, transcript-2 translates to a wild-type protein sequence, except that this isoform contains an in-frame fusion of non-wild-type twenty-five amino acids in a tetratricopeptide repeat sequence. Both mutant isoforms of CRTAP are unstable due to the presence of a unique 'GWxxI' degron, which finally leads to loss of proline hydroxylation and aggregation of type I collagen. Although type I collagen aggregates undergo autophagy, the overall proteotoxicity resulted in death of the proband cells by senescence. In summary, we present a genetic disease pathomechanism by linking a novel deep intronic mutation in CRTAP to unstable mutant isoforms of the protein in lethal OI type VII.
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Affiliation(s)
- Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akshaykumar Nanaji Shrikondawar
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India; Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
| | - Debasish Kumar Ghosh
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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9
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Udupa P, Ghosh DK, Kausthubham N, Shah H, Bartakke S, Dalal A, Girisha KM, Bhavani GS. Genome sequencing identifies a large non-coding region deletion of SNX10 causing autosomal recessive osteopetrosis. J Hum Genet 2023; 68:287-290. [PMID: 36526684 PMCID: PMC10040338 DOI: 10.1038/s10038-022-01104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Autosomal recessive osteopetrosis (ARO) is a rare genetic disorder caused by impaired osteoclast activity. In this study, we describe a 4-year-old boy with increased bone density due to osteopetrosis, autosomal recessive 8. Using genome sequencing, we identified a large deletion in the 5'-untranslated region (UTR) of SNX10 (sorting nexin 10), where the regulatory region of this gene is located. This large deletion resulted in the absence of the SNX10 transcript and led to abnormal osteoclast activity. SNX10 is one of the nine genes known to cause ARO, shown to interact with V-ATPase (vacuolar type H( + )-ATPase), as it plays an important role in bone resorption. Our study highlights the importance of regulatory regions in the 5'-UTR of SNX10 for its expression while also demonstrating the importance of genome sequencing for detecting large deletion of the regulatory region of SNX10.
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Affiliation(s)
- Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Debasish Kumar Ghosh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sandip Bartakke
- Department of Clinical Hematology, Aditya Birla Memorial Hospital, Pune, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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10
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Schnabel F, Schuler E, Al-Maawali A, Chaurasia A, Syrbe S, Al-Kindi A, Bhavani GS, Shukla A, Altmüller J, Nürnberg P, Banka S, Girisha KM, Li Y, Wollnik B, Yigit G. Homozygous loss-of-function variants in FILIP1 cause autosomal recessive arthrogryposis multiplex congenita with microcephaly. Hum Genet 2023; 142:543-552. [PMID: 36943452 PMCID: PMC10060356 DOI: 10.1007/s00439-023-02528-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/21/2023] [Indexed: 03/23/2023]
Abstract
Arthrogryposis multiplex congenita forms a broad group of clinically and etiologically heterogeneous disorders characterized by congenital joint contractures that involve at least two different parts of the body. Neurological and muscular disorders are commonly underlying arthrogryposis. Here, we report five affected individuals from three independent families sharing an overlapping phenotype with congenital contractures affecting shoulder, elbow, hand, hip, knee and foot as well as scoliosis, reduced palmar and plantar skin folds, microcephaly and facial dysmorphism. Using exome sequencing, we identified homozygous truncating variants in FILIP1 in all patients. FILIP1 is a regulator of filamin homeostasis required for the initiation of cortical cell migration in the developing neocortex and essential for the differentiation process of cross-striated muscle cells during myogenesis. In summary, our data indicate that bi-allelic truncating variants in FILIP1 are causative of a novel autosomal recessive disorder and expand the spectrum of genetic factors causative of arthrogryposis multiplex congenita.
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Affiliation(s)
- Franziska Schnabel
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, 04103, Leipzig, Germany
| | - Elisabeth Schuler
- Division of Paediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Steffen Syrbe
- Division of Paediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Adila Al-Kindi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines To Networks of Excitable Cells" (MBExC), University of Göttingen, 37073, Göttingen, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany.
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany.
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11
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Varshney K, Narayanachar SG, Girisha KM, Bhavani GS, Narayanan D, Phadke S, Nampoothiri S, Udupi GA, Raghupathy P, Nair M, Geetha TS, Bhat M. Clinical, radiological and molecular studies in 24 individuals with Dyggve-Melchior-Clausen dysplasia and Smith-McCort dysplasia from India. J Med Genet 2023; 60:204-211. [PMID: 35477554 DOI: 10.1136/jmedgenet-2021-108098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/10/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Dyggve-Melchior-Clausen dysplasia (DMC) and Smith-McCort dysplasia (SMC types 1 and 2) are rare spondyloepimetaphyseal dysplasias with identical radiological findings. The presence of intellectual disability in DMC and normal intellect in SMC differentiates the two. DMC and SMC1 are allelic and caused by homozygous or compound heterozygous variants in DYM. SMC2 is caused by variations in RAB33B. Both DYM and RAB33B are important in intravesicular transport and function in the Golgi apparatus. METHODS Detailed clinical phenotyping and skeletal radiography followed by molecular testing were performed in all affected individuals. Next-generation sequencing and Sanger sequencing were used to confirm DYM and RAB33B variants. Sanger sequencing of familial variants was done in all parents. RESULTS 24 affected individuals from seven centres are described. 18 had DMC and 6 had SMC2. Parental consanguinity was present in 15 of 19 (79%). Height <3 SD and gait abnormalities were seen in 20 and 14 individuals, respectively. The characteristic radiological findings of lacy iliac crests and double-humped vertebral bodies were seen in 96% and 88% of the affected. Radiological findings became attenuated with age. 23 individuals harboured biallelic variants in either DYM or RAB33B. Fourteen different variants were identified, out of which 10 were novel. The most frequently occurring variants in this group were c.719 C>A (3), c.1488_1489del (2), c.1484dup (2) and c.1563+2T>C (2) in DYM and c.400C>T (2) and c.186del (2) in RAB33B. The majority of these have not been reported previously. CONCLUSION This large cohort from India contributes to the increasing knowledge of clinical and molecular findings in these rare 'Golgipathies'.
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Affiliation(s)
- Kruti Varshney
- Department of Clinical Genetics, Centre for Human Genetics, Bangalore, Karnataka, India
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Dhanyalakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shubha Phadke
- Department of Medical Genetics, SGPGIMS, Lucknow, Uttar Pradesh, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Reseacrh Centre, Kochi, Kerala, India
| | - Gautham Arunachal Udupi
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
| | - Palany Raghupathy
- Department of Paediatric Endocrinology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Mohandas Nair
- Department of Paediatrics, Government Medical College, Kozhikode, Kerala, India
| | | | - Meenakshi Bhat
- Department of Clinical Genetics, Centre for Human Genetics, Bangalore, Karnataka, India
- Department of Paediatric Genetics, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
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12
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Ghosh DK, Udupa P, Shrikondawar AN, Bhavani GS, Shah H, Ranjan A, Girisha KM. Mutant MESD links cellular stress to type I collagen aggregation in osteogenesis imperfecta type XX. Matrix Biol 2023; 115:81-106. [PMID: 36526215 PMCID: PMC7615836 DOI: 10.1016/j.matbio.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/19/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Aberrant forms of endoplasmic reticulum (ER)-resident chaperones are implicated in loss of protein quality control in rare diseases. Here we report a novel mutation (p.Asp233Asn) in the ER retention signal of MESD by whole exome sequencing of an individual diagnosed with osteogenesis imperfecta (OI) type XX. While MESDD233N has similar stability and chaperone activity as wild-type MESD, its mislocalization to cytoplasm leads to imbalance of ER proteostasis, resulting in improper folding and aggregation of proteins, including LRP5 and type I collagen. Aggregated LRP5 loses its plasma membrane localization to disrupt the expression of WNT-responsive genes, such as BMP2, BMP4, in proband fibroblasts. We show that MESD is a direct chaperone of pro-α1(I) [COL1A1], and absence of MESDD233N in ER results in cytosolic type I collagen aggregates that remain mostly not secreted. While cytosolic type I collagen aggregates block the intercellular nanotubes, decreased extracellular type I collagen also results in loss of interaction of ITGB1 with type I collagen and weaker attachment of fibroblasts to matrix. Although proband fibroblasts show increased autophagy to degrade the aggregated type I collagen, an overall cellular stress overwhelms the proband fibroblasts. In summary, we present an essential chaperone function of MESD for LRP5 and type I collagen and demonstrating how the D233N mutation in MESD correlates with impaired WNT signaling and proteostasis in OI.
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Affiliation(s)
- Debasish Kumar Ghosh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akshaykumar Nanaji Shrikondawar
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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13
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Moreno Traspas R, Teoh TS, Wong PM, Maier M, Chia CY, Lay K, Ali NA, Larson A, Al Mutairi F, Al-Sannaa NA, Faqeih EA, Alfadhel M, Cheema HA, Dupont J, Bézieau S, Isidor B, Low DY, Wang Y, Tan G, Lai PS, Piloquet H, Joubert M, Kayserili H, Kripps KA, Nahas SA, Wartchow EP, Warren M, Bhavani GS, Dasouki M, Sandoval R, Carvalho E, Ramos L, Porta G, Wu B, Lashkari HP, AlSaleem B, BaAbbad RM, Abreu Ferrão AN, Karageorgou V, Ordonez-Herrera N, Khan S, Bauer P, Cogne B, Bertoli-Avella AM, Vincent M, Girisha KM, Reversade B. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis. Nat Genet 2022; 54:1214-1226. [PMID: 35864190 PMCID: PMC7615854 DOI: 10.1038/s41588-022-01120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Cirrhosis is usually a late-onset and life-threatening disease characterized by fibrotic scarring and inflammation that disrupts liver architecture and function. While it is typically the result of alcoholism or hepatitis viral infection in adults, its etiology in infants is much less understood. In this study, we report 14 children from ten unrelated families presenting with a syndromic form of pediatric liver cirrhosis. By genome/exome sequencing, we found recessive variants in FOCAD segregating with the disease. Zebrafish lacking focad phenocopied the human disease, revealing a signature of altered messenger RNA (mRNA) degradation processes in the liver. Using patient's primary cells and CRISPR-Cas9-mediated inactivation in human hepatic cell lines, we found that FOCAD deficiency compromises the SKI mRNA surveillance pathway by reducing the levels of the RNA helicase SKIC2 and its cofactor SKIC3. FOCAD knockout hepatocytes exhibited lowered albumin expression and signs of persistent injury accompanied by CCL2 overproduction. Our results reveal the importance of FOCAD in maintaining liver homeostasis and disclose a possible therapeutic intervention point via inhibition of the CCL2/CCR2 signaling axis.
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Affiliation(s)
- Ricardo Moreno Traspas
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze Shin Teoh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pui-Mun Wong
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Michael Maier
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Crystal Y Chia
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kenneth Lay
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Nur Ain Ali
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Austin Larson
- Section of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Fuad Al Mutairi
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Medical Genomic Research, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Huma Arshad Cheema
- Division of Pediatric Gastroenterology-Hepatology and Nutrition, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Juliette Dupont
- Department of Pediatrics, Genetic Services, Lisbon North University Hospital Center, Lisbon, Portugal
| | - Stéphane Bézieau
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Bertrand Isidor
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Dorrain Yanwen Low
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Grace Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hugues Piloquet
- Gastropediatrics Department, Nantes University Hospital Center, Nantes, France
| | - Madeleine Joubert
- Anatomopathology Department, Nantes University Hospital Center, Nantes, France
| | - Hulya Kayserili
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey
| | - Kimberly A Kripps
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric P Wartchow
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Majed Dasouki
- Department of Pediatric Genetics, AdventHealth Medical Group, Orlando, FL, USA
| | - Renata Sandoval
- Department of Oncogenetics, Hospital Sírio-Libanês, Brasília, Brazil
| | - Elisa Carvalho
- Department of Pediatric Gastroenterology and Hepatology, Hospital da Criança de Brasília José Alencar, UniCEUB, Brasília, Brazil
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo, Brazil
| | - Gilda Porta
- Department of Pediatric Hepatology, Transplant Unit, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College, Mangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Badr AlSaleem
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Raeda M BaAbbad
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | | | | | | | - Benjamin Cogne
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | | | - Marie Vincent
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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14
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Girisha KM, Jacob P, SriLakshmi Bhavani G, Shah H, Mortier GR. Report of three patients, including monozygotic twins and review of clinical and mutation profiles. Eur J Med Genet 2022; 65:104521. [PMID: 35568358 DOI: 10.1016/j.ejmg.2022.104521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
Steel syndrome (MIM# 615155) is an autosomal recessive skeletal disorder, characterized by dislocations of the hips and radial heads, carpal coalition, short stature, facial dysmorphism, and scoliosis. Until date 47 patients have been reported. However, disease causing variants have been identified only in twenty Puerto Rican and nine non-Puerto Rican families. Here we report two monozygotic twins and a boy from two families with novel missense variants, c.295G > A p.(Ala99 Thr), c.3056C > A p.(Pro1019His) and c.2521G > A p.(Gly841Arg) in COL27A1. We describe for the first time, cleft palate and delayed carpal bone ossification as features of Steel syndrome. We reviewed clinical features in all mutation-proven Steel syndrome patients. Short stature and dislocation/subluxation of hip joint are consistently observed. Other features include dislocated radial heads, scoliosis, lordosis, carpal coalition, facial dysmorphism, hearing loss, bilateral fifth finger clinodactyly, knee deformities and developmental delay. Seven missense variants and eight null variants are reported in COL27A1 until date. We also looked into the genotype-phenotype correlation in Puerto Rican and non-Puerto Rican patients.
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Affiliation(s)
- Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Hitesh Shah
- Department of Orthopaedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Geert R Mortier
- Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium.
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15
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Holling T, Bhavani GS, von Elsner L, Shah H, Kausthubham N, Bhattacharyya SS, Shukla A, Mortier GR, Schinke T, Danyukova T, Pohl S, Kutsche K, Girisha KM. A homozygous hypomorphic BNIP1 variant causes an increase in autophagosomes and reduced autophagic flux and results in a spondylo-epiphyseal dysplasia. Hum Mutat 2022; 43:625-642. [PMID: 35266227 DOI: 10.1002/humu.24368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 01/18/2023]
Abstract
BNIP1 (BCL2 interacting protein 1) is a soluble N-ethylmaleimide-sensitive factor-attachment protein receptor involved in ER membrane fusion. We identified the homozygous BNIP1 intronic variant c.84+3A>T in the apparently unrelated patients 1 and 2 with disproportionate short stature. Radiographs showed abnormalities affecting both the axial and appendicular skeleton and spondylo-epiphyseal dysplasia. We detected ~80% aberrantly spliced BNIP1 pre-mRNAs, reduced BNIP1 mRNA level to ~80%, and BNIP1 protein level reduction by ~50% in patient 1 compared to control fibroblasts. The BNIP1 ortholog in drosophila, Sec. 20, regulates autophagy and lysosomal degradation. We assessed lysosome positioning and identified a decrease in lysosomes in the perinuclear region and an increase in the cell periphery in patient 1 cells. Immunofluorescence microscopy and immunoblotting demonstrated an increase in LC3B-positive structures and LC3B-II levels, respectively, in patient 1 fibroblasts under steady-state condition. Treatment of serum-starved fibroblasts with or without bafilomycin A1 identified significantly decreased autophagic flux in patient 1 cells. Our data suggest a block at the terminal stage of autolysosome formation and/or clearance in patient fibroblasts. BNIP1 together with RAB33B and VPS16, disease genes for Smith-McCort dysplasia 2 and a multisystem disorder with short stature, respectively, highlight the importance of autophagy in skeletal development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hitesh Shah
- Department of Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | | | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Geert R Mortier
- Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatyana Danyukova
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Pohl
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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16
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Lashkari HP, Madkaikar M, Dalvi A, Gupta M, Bustamante J, Sharma M, Rawat A, Bhatia P, Bhat KG, Rao S, Kamath N, Moideen F, Latour S, Winter S, Bhavani GS, Girisha KM. Clinical and Genetic Spectrum of Inborn Errors of Immunity in a Tertiary Care Center in Southern India. Indian J Pediatr 2022; 89:233-242. [PMID: 34826056 PMCID: PMC8857151 DOI: 10.1007/s12098-021-03936-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To study the incidence, clinical manifestations, and genetic spectrum of primary immunodeficiency diseases (PID)/inborn errors of immunity (IEI) in a tertiary care hospital in Southern India. METHODS A retrospective analysis of all patients with a clinical suspicion of PID/IEI seen at a tertiary care hospital was performed. All patients had at least one or more warning signs of PID. Serum immunoglobulin levels and other targeted investigations were performed as warranted by the clinical presentation. All families with suspected PID were counseled and offered genetic testing. RESULTS A total of 225 children were evaluated for PID during the study period of 6 y. Fifty-six of them did not meet the European Society of Immunodeficiencies (ESID) criteria (working definition of clinical diagnosis) and were excluded. An IEI was found in 30/49 (61.2%) patients. The most frequent reason for referral was recurrent/unusual or serious infections (28%), or cytopenia (16%). Group IV diseases of immune dysregulation was the most common category (19%), followed by group III predominant antibody deficiencies in 23/163 (14%), as per the International Union of Immunological Societies (IUIS) classification. CONCLUSIONS This study highlights the heterogeneity of the present cohort, the underuse of genetic tests, and efforts to provide optimal care for children with possible IEI in this center.
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Affiliation(s)
- Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, 575001, India.
| | - Manisha Madkaikar
- ICMR-National Institute of Immunohematology, KEM Hospital, Parel, Mumbai, Maharashtra, India
| | - Aparna Dalvi
- ICMR-National Institute of Immunohematology, KEM Hospital, Parel, Mumbai, Maharashtra, India
| | - Maya Gupta
- ICMR-National Institute of Immunohematology, KEM Hospital, Parel, Mumbai, Maharashtra, India
| | - Jacinta Bustamante
- Génétique Humaine Des Maladies Infectieuses/Human Genetics of Infectious Diseases, INSERM UMR 1163, Université de Paris, Institut Imagine, Paris, France
| | - Madhubala Sharma
- Pediatric Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Center, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Amit Rawat
- Pediatric Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Center, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Prateek Bhatia
- Pediatric Hematology & Pediatric Molecular Hematology Laboratory, Pediatric Hematology-Oncology Unit, Department of Pediatrics, Advanced Pediatrics Center, PGIMER, Chandigarh, India
| | - Kamalakshi G Bhat
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, 575001, India
| | - Sadashiva Rao
- Department of Pediatric Surgery, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nutan Kamath
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, 575001, India
| | - Faheem Moideen
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, 575001, India
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Sarah Winter
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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17
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Verheyen S, Blatterer J, Speicher MR, Bhavani GS, Boons GJ, Ilse MB, Andrae D, Sproß J, Vaz FM, Kircher SG, Posch-Pertl L, Baumgartner D, Lübke T, Shah H, Al Kaissi A, Girisha KM, Plecko B. Novel subtype of mucopolysaccharidosis caused by arylsulfatase K (ARSK) deficiency. J Med Genet 2021; 59:957-964. [PMID: 34916232 PMCID: PMC9554054 DOI: 10.1136/jmedgenet-2021-108061] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/31/2021] [Indexed: 11/07/2022]
Abstract
Background Mucopolysaccharidoses (MPS) are monogenic metabolic disorders that significantly affect the skeleton. Eleven enzyme defects in the lysosomal degradation of glycosaminoglycans (GAGs) have been assigned to the known MPS subtypes (I–IX). Arylsulfatase K (ARSK) is a recently characterised lysosomal hydrolase involved in GAG degradation that removes the 2-O-sulfate group from 2-sulfoglucuronate. Knockout of Arsk in mice was consistent with mild storage pathology, but no human phenotype has yet been described. Methods In this study, we report four affected individuals of two unrelated consanguineous families with homozygous variants c.250C>T, p.(Arg84Cys) and c.560T>A, p.(Leu187Ter) in ARSK, respectively. Functional consequences of the two ARSK variants were assessed by mutation-specific ARSK constructs derived by site-directed mutagenesis, which were ectopically expressed in HT1080 cells. Urinary GAG excretion was analysed by dimethylene blue and electrophoresis, as well as liquid chromatography/mass spectrometry (LC-MS)/MS analysis. Results The phenotypes of the affected individuals include MPS features, such as short stature, coarse facial features and dysostosis multiplex. Reverse phenotyping in two of the four individuals revealed additional cardiac and ophthalmological abnormalities. Mild elevation of dermatan sulfate was detected in the two subjects investigated by LC-MS/MS. Human HT1080 cells expressing the ARSK-Leu187Ter construct exhibited absent protein levels by western blot, and cells with the ARSK-Arg84Cys construct showed markedly reduced enzyme activity in an ARSK-specific enzymatic assay against 2-O-sulfoglucuronate-containing disaccharides as analysed by C18-reversed-phase chromatography followed by MS. Conclusion Our work provides a detailed clinical and molecular characterisation of a novel subtype of mucopolysaccharidosis, which we suggest to designate subtype X.
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Affiliation(s)
- Sarah Verheyen
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Jasmin Blatterer
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Michael R Speicher
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Mai-Britt Ilse
- Department of Chemistry, Biochemistry, Bielefeld University, Bielefeld, Germany
| | - Dominik Andrae
- Department of Chemistry, Biochemistry, Bielefeld University, Bielefeld, Germany
| | - Jens Sproß
- Faculty of Chemistry, Industrial Organic Chemistry and Biotechnology - Mass Spectrometry, Bielefeld University, Bielefeld, Germany
| | - Frédéric Maxime Vaz
- Laboratory Genetic Metabolic Disease, Amsterdam UMC, University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Core Facility Metabolomics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands, Amsterdam UMC Locatie Meibergdreef, Amsterdam, North Holland, The Netherlands
| | - Susanne G Kircher
- Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | - Laura Posch-Pertl
- Department of Ophthalmology, Medical University of Graz, Graz, Austria
| | - Daniela Baumgartner
- Department of Pediatrics and Adolescent Medicine; Division of Pediatric Cardiology, Medical University of Graz, Graz, Austria
| | - Torben Lübke
- Department of Chemistry, Biochemistry, Bielefeld University, Bielefeld, Germany
| | - Hitesh Shah
- Department of Orthopedics, Kasturba Medical College Manipal, Manipal, India
| | - Ali Al Kaissi
- Pediatric Department, Speising Orthopaedic Hospital, Vienna, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Barbara Plecko
- Department of Pediatrics, Division of General Pediatrics, Medical University of Graz, Graz, Austria
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18
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Chaudhary AK, Gholse A, Nagarajaram HA, Dalal AB, Gupta N, Dutta AK, Danda S, Gupta R, Sankar HV, Bhavani GS, Girisha KM, Phadke SR, Ranganath P, Bashyam MD. Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India. Am J Med Genet A 2021; 188:788-805. [PMID: 34863015 DOI: 10.1002/ajmg.a.62579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED) is a rare genetic disorder caused by mutational inactivation of a developmental pathway responsible for generation of tissues of ectodermal origin. The X-linked form accounts for the majority of HED cases and is caused by Ectodysplasin (EDA) pathogenic variants. We performed a combined analysis of 29 X-linked hypohidrotic ectodermal dysplasia (XLHED) families (including 12 from our previous studies). In addition to the classical triad of symptoms including loss (or reduction) of ectodermal structures, such as hair, teeth, and sweat glands, we detected additional HED-related clinical features including facial dysmorphism and hyperpigmentation in several patients. Interestingly, global developmental delay was identified as an unusual clinical symptom in many patients. More importantly, we identified 22 causal pathogenic variants that included 15 missense, four small in-dels, and one nonsense, splice site, and large deletion each. Interestingly, we detected 12 unique (India-specific) pathogenic variants. Of the 29 XLHED families analyzed, 11 (38%) harbored pathogenic variant localized to the furin cleavage site. A comparison with HGMD revealed significant differences in the frequency of missense pathogenic variants; involvement of specific exons and/or protein domains and transition/transversion ratios. A significantly higher proportion of missense pathogenic variants (33%) localized to the EDA furin cleavage when compared to HGMD (7%), of which p.R155C, p.R156C, and p.R156H were detected in three families each. Therefore, the first comprehensive analysis of XLHED from India has revealed several unique features including unusual clinical symptoms and high frequency of furin cleavage site pathogenic variants.
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Affiliation(s)
- Ajay Kumar Chaudhary
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Aishwarya Gholse
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ashwin Bhikaji Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Atanu Kumar Dutta
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Rekha Gupta
- Department of Medical Genetics, Mahatma Gandhi Medical College and Hospital, Jaipur, India
| | - Hariharan V Sankar
- Department of Pediatrics, SAT Hospital, Medical College, Trivandrum, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Shubha Rao Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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19
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Guo L, Iida A, Bhavani GS, Gowrishankar K, Wang Z, Xue JY, Wang J, Miyake N, Matsumoto N, Hasegawa T, Iizuka Y, Matsuda M, Nakashima T, Takechi M, Iseki S, Yambe S, Nishimura G, Koseki H, Shukunami C, Girisha KM, Ikegawa S. Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling. Nat Commun 2021; 12:2046. [PMID: 33824347 PMCID: PMC8024261 DOI: 10.1038/s41467-021-22340-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/02/2021] [Indexed: 01/08/2023] Open
Abstract
Bone formation represents a heritable trait regulated by many signals and complex mechanisms. Its abnormalities manifest themselves in various diseases, including sclerosing bone disorder (SBD). Exploration of genes that cause SBD has significantly improved our understanding of the mechanisms that regulate bone formation. Here, we discover a previously unknown type of SBD in four independent families caused by bi-allelic loss-of-function pathogenic variants in TMEM53, which encodes a nuclear envelope transmembrane protein. Tmem53-/- mice recapitulate the human skeletal phenotypes. Analyses of the molecular pathophysiology using the primary cells from the Tmem53-/- mice and the TMEM53 knock-out cell lines indicates that TMEM53 inhibits BMP signaling in osteoblast lineage cells by blocking cytoplasm-nucleus translocation of BMP2-activated Smad proteins. Pathogenic variants in the patients impair the TMEM53-mediated blocking effect, thus leading to overactivated BMP signaling that promotes bone formation and contributes to the SBD phenotype. Our results establish a previously unreported SBD entity (craniotubular dysplasia, Ikegawa type) and contribute to a better understanding of the regulation of BMP signaling and bone formation.
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Affiliation(s)
- Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.
| | - Aritoshi Iida
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | | | - Zheng Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Medical Genetics, Institute of Basic Medical Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jing-Yi Xue
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Juan Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Ultrasound, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takanori Hasegawa
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yusuke Iizuka
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Matsuda
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomoki Nakashima
- Department of Cell Signaling, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Takechi
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sachiko Iseki
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shinsei Yambe
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Gen Nishimura
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chisa Shukunami
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.
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20
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Patil SJ, Karthik GA, Bhavani GS, Bhat V, Matalia J, Shah J, Shukla A, Girisha KM. Bosley-Salih-Alorainy syndrome in patients from India. Am J Med Genet A 2020; 182:2699-2703. [PMID: 32864817 DOI: 10.1002/ajmg.a.61809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 02/05/2020] [Accepted: 07/20/2020] [Indexed: 11/07/2022]
Abstract
Bi-allelic HOXA1 pathogenic variants clinically manifest as two distinct syndromes, Bosley-Salih-Alorainy syndrome (BSAS) and Athabascan brainstem dysgenesis syndrome, mainly reported in two different populations from Saudi Arabia and southwest North America, respectively. Here we report two siblings of Indian origin with BSAS phenotype caused by a novel homozygous exon 2 HOXA1 pathogenic variants.
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Affiliation(s)
- Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | | | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Venkatraman Bhat
- Department of Radiology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Jyoti Matalia
- Department of Pediatric Ophthalmology & Strabismology, Narayana Nethralaya, Bangalore, India
| | - Jhanvi Shah
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
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21
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Uttarilli A, Shah H, Bhavani GS, Upadhyai P, Shukla A, Girisha KM. Phenotyping and genotyping of skeletal dysplasias: Evolution of a center and a decade of experience in India. Bone 2019; 120:204-211. [PMID: 30408610 DOI: 10.1016/j.bone.2018.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/16/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022]
Abstract
Genetic heterogeneity, high burden and the paucity of genetic testing for rare diseases challenge genomic healthcare for these disorders in India. Here we report our experience over the past decade, of establishing the genomic evaluation of skeletal dysplasia at a tertiary university hospital in India. Research or clinical genomic testing was carried out by Sanger sequencing and next-generation sequencing. Close national and international collaborations aided phenotyping and genotyping. We report 508 families (557 affected individuals) with the definitive molecular diagnosis of skeletal dysplasia. Dysostoses multiplex (n = 196), genetic inflammatory/rheumatoid-like osteoarthropathies (n = 114) and osteogenesis imperfecta and decreased bone density (n = 58) were the most common diagnoses. We enumerate the processes, clinical diagnoses and causal variants in the cohort with 48 novel variants in 21 genes. We summarize scientific contributions of the center to the description of clinical and mutation profiles and discovery of new phenotypes and genetic etiology. Our study illustrates the establishment and application of genomic testing tools for genetic disorders of skeleton in a large cohort. We believe this could be a model to emulate for other developing genetic centers.
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Affiliation(s)
- Anusha Uttarilli
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Pediatric Orthopedics Services, Department of Orthopedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
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22
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Girisha KM, von Elsner L, Neethukrishna K, Muranjan M, Shukla A, Bhavani GS, Nishimura G, Kutsche K, Mortier G. The homozygous variant c.797G>A/p.(Cys266Tyr) in PISD is associated with a Spondyloepimetaphyseal dysplasia with large epiphyses and disturbed mitochondrial function. Hum Mutat 2018; 40:299-309. [PMID: 30488656 DOI: 10.1002/humu.23693] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/16/2018] [Accepted: 11/24/2018] [Indexed: 02/06/2023]
Abstract
Spondyloepimetaphyseal dysplasias (SEMD) are a group of genetically heterogeneous skeletal disorders characterized by abnormal vertebral bodies and epimetaphyseal abnormalities. We investigated two families with a new SEMD type with one proband each. They showed mild facial dysmorphism, flat vertebral bodies (platyspondyly), large epiphyses, metaphyseal dysplasia, and hallux valgus as common clinical features. By trio-exome sequencing, the homozygous missense variant c.797G>A/p.(Cys266Tyr) in PISD was found in both affected individuals. Based on exome data analyses for homozygous regions, the two patients shared a single homozygous block on chromosome 22 including PISD, indicating their remote consanguinity. PISD encodes phosphatidylserine (PS) decarboxylase that is localized in the inner mitochondrial membrane and catalyzes the decarboxylation of PS to phosphatidylethanolamine (PE) in mammalian cells. PE occurs at high abundance in mitochondrial membranes. Patient-derived fibroblasts showed fragmented mitochondrial morphology. Treatment of patient cells with MG-132 or staurosporine to induce activation of the intrinsic apoptosis pathway revealed significantly decreased cell viability with increased caspase-3 and caspase-7 activation. Remarkably, ethanolamine (Etn) supplementation largely restored cell viability and enhanced apoptosis in MG-132-stressed patient cells. Our data demonstrate that the biallelic hypomorphic PISD variant p.(Cys266Tyr) is associated with a novel SEMD form, which may be treatable with Etn administration.
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Affiliation(s)
- Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Mamta Muranjan
- Department of Clinical Genetics, Seth GS Medical College and KEM Hospital, Mumbai, India.,Consultant in Clinical Genetics, P.D. Hinduja National Hospital & MRC, Mumbai, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Gen Nishimura
- Department of Pediatric Imaging, Tokyo Metropolitan Children's Medical Center, Fuchu, Japan
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Geert Mortier
- Centre of Medical Genetics, University of Antwerp & University Hospital Antwerp, Antwerp, Belgium
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23
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Mrosk J, Bhavani GS, Shah H, Hecht J, Krüger U, Shukla A, Kornak U, Girisha KM. Diagnostic strategies and genotype-phenotype correlation in a large Indian cohort of osteogenesis imperfecta. Bone 2018; 110:368-377. [PMID: 29499418 DOI: 10.1016/j.bone.2018.02.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 12/31/2022]
Abstract
Osteogenesis Imperfecta (OI) is a clinically and genetically heterogeneous disorder. Although differential diagnosis is greatly facilitated by next generation sequencing, its availability can vary considerably. In this study, we compared targeted gene panel or exome sequencing with clinical scoring and grouping in a cohort of 50 OI index patients recruited by a single Indian clinical center in an unselected fashion. In 48 patients we observed a total of 24 novel mutations and 24 known OI mutations, of which several were recurrent. In one patient neither gene panel nor exome sequencing revealed any significant mutation and another patient harbored a class III COL1A1 intronic variant. The percentage of autosomal recessive forms due to mutations in BMP1, FKBP10, LEPRE1, SERPINF1, and WNT1 was unusually high (48%). Grouping according to phenotypic and radiographic features revealed four individuals with Bruck syndrome due to FKBP10 mutations, three patients with hypertrophic callus caused by IFITM5 mutations, and twenty with pronounced bone bowing, of which eight carried WNT1 mutations. There was a clear correlation between genotype and phenotype severity: IFITM5=LEPRE1>WNT1>SERPINF1>COL1A1 (qualitative)>BMP1>FKBP10>COL1A2 (qualitative)>COL1A1 (quantitative)>COL1A2 (quantitative). In one patient we found heterozygous variants in COL1A1 and COL1A2 inherited from parents without an obvious bone phenotype indicating that both variants might contribute to the phenotype. Our findings demonstrate the clinical utility of gene panel testing for OI, but in cases with contractures, hypertrophic callus formation, or - to some extent - extensive bowing single gene analysis might still be more cost-effective.
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Affiliation(s)
- Julia Mrosk
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Pediatric Orthopedics Services, Department of Orthopedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Jochen Hecht
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ulrike Krüger
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany.
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
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24
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Nakatsuka N, Moorjani P, Rai N, Sarkar B, Tandon A, Patterson N, Bhavani GS, Girisha KM, Mustak MS, Srinivasan S, Kaushik A, Vahab SA, Jagadeesh SM, Satyamoorthy K, Singh L, Reich D, Thangaraj K. The promise of discovering population-specific disease-associated genes in South Asia. Nat Genet 2017; 49:1403-1407. [PMID: 28714977 PMCID: PMC5675555 DOI: 10.1038/ng.3917] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/21/2017] [Indexed: 12/21/2022]
Abstract
The more than 1.5 billion people who live in South Asia are correctly viewed not as a single large population but as many small endogamous groups. We assembled genome-wide data from over 2,800 individuals from over 260 distinct South Asian groups. We identified 81 unique groups, 14 of which had estimated census sizes of more than 1 million, that descend from founder events more extreme than those in Ashkenazi Jews and Finns, both of which have high rates of recessive disease due to founder events. We identified multiple examples of recessive diseases in South Asia that are the result of such founder events. This study highlights an underappreciated opportunity for decreasing disease burden among South Asians through discovery of and testing for recessive disease-associated genes.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
| | - Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Arti Tandon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nick Patterson
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, India
| | | | - Amit Kaushik
- Amity Institute of Biotechnology, Amity University, Noida, India
| | | | | | | | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
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25
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Salian S, Cho TJ, Phadke SR, Gowrishankar K, Bhavani GS, Shukla A, Jagadeesh S, Kim OH, Nishimura G, Girisha KM. Cover Image, Volume 173A, Number 3, March 2017. Am J Med Genet A 2017. [DOI: 10.1002/ajmg.a.38197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Smrithi Salian
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | - Tae-Joon Cho
- Division of Pediatric Orthopedics; Seoul National University Children's Hospital; Seoul Korea
| | - Shubha R. Phadke
- Department of Medical Genetics; Sanjay Gandhi Postgraduate Institute of Medical Sciences; Lucknow India
| | - Kalpana Gowrishankar
- Department of Medical Genetics; Apollo Children's Hospital; Chennai Tamilnadu India
| | | | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | | | - Ok-Hwa Kim
- Department of Radiology; Woorisoa Children's Hospital; Seoul Korea
| | - Gen Nishimura
- Department of Pediatric Imaging; Tokyo Metropolitan Children's Medical Center; Tokyo Japan
| | - Katta M. Girisha
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
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26
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Ranganath P, Matta D, Bhavani GS, Wangnekar S, Jain JMN, Verma IC, Kabra M, Puri RD, Danda S, Gupta N, Girisha KM, Sankar VH, Patil SJ, Devi ARR, Bhat M, Gowrishankar K, Mandal K, Aggarwal S, Tamhankar PM, Tilak P, Phadke SR, Dalal A. Spectrum of mutations in the SMPD1
gene in Asian Indian patients with acid sphingomyelinase deficient Niemann-Pick disease. Am J Med Genet A 2017. [DOI: 10.1002/ajmg.a.38040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Salian S, Cho TJ, Phadke SR, Gowrishankar K, Bhavani GS, Shukla A, Jagadeesh S, Kim OH, Nishimura G, Girisha KM. Additional three patients with Smith-McCort dysplasia due to novel RAB33B mutations. Am J Med Genet A 2017; 173:588-595. [PMID: 28127940 DOI: 10.1002/ajmg.a.38064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/14/2016] [Indexed: 11/06/2022]
Abstract
Smith-McCort dysplasia (SMC OMIM 615222) and Dyggve-Melchior-Clausen dysplasia (DMC OMIM 223800) are allelic skeletal dysplasias caused by homozygous or compound heterozygous mutations in DYM (OMIM 607461). Both disorders share the same skeletal phenotypes characterized by spondylo-epi-metaphyseal dysplasia with distinctive lacy ilia. The difference rests on the presence or absence of intellectual disability, that is, intellectual disability in DMC and normal cognition in SMC. However, genetic heterogeneity was suspected in SMC. Recently, RAB33B (OMIM 605950) has been identified as the second gene for SMC. Nevertheless, only two affected families have been reported so far. Here we present three SMC patients with four novel pathogenic variants in RAB33B, including homozygosity for c.211C>T (p.R71*), homozygosity for c.365T>C (p.F122S), and compound heterozygosity for c.48delCGGGGCAG (p.G17Vfs*58) and c.490C>T (p.Q164*). We also summarize the clinical, radiological, and mutation profile of RAB33B after literature mining. This report ascertains the pathogenic relationship between RAB33B and SMC. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Smrithi Salian
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Tae-Joon Cho
- Division of Pediatric Orthopedics, Seoul National University Children's Hospital, Seoul, Korea
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, Apollo Children's Hospital, Chennai, Tamilnadu, India
| | | | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | | | - Ok-Hwa Kim
- Department of Radiology, Woorisoa Children's Hospital, Seoul, Korea
| | - Gen Nishimura
- Department of Pediatric Imaging, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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28
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Girisha KM, Kortüm F, Shah H, Alawi M, Dalal A, Bhavani GS, Kutsche K. A novel multiple joint dislocation syndrome associated with a homozygous nonsense variant in the EXOC6B gene. Eur J Hum Genet 2016; 24:1206-10. [PMID: 26669664 PMCID: PMC4970677 DOI: 10.1038/ejhg.2015.261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/04/2015] [Accepted: 11/15/2015] [Indexed: 01/12/2023] Open
Abstract
We report two brothers from a consanguineous couple with spondyloepimetaphyseal dysplasia (SEMD), multiple joint dislocations at birth, severe joint laxity, scoliosis, gracile metacarpals and metatarsals, delayed bone age and poorly ossified carpal and tarsal bones, probably representing a yet uncharacterized SEMD with laxity and dislocations. This condition has clinical overlap with autosomal dominantly inherited SEMD with joint laxity, leptodactylic type caused by recurrent missense variants in the kinesin family member 22 gene (KIF22). Single-nucleotide polymorphism array analysis and whole-exome sequencing in the two affected siblings revealed a shared homozygous nonsense variant [c.906T>A/p.(Tyr302*)] in EXOC6B as the most likely cause. EXOC6B encodes a component of the exocyst complex required for tethering secretory vesicles to the plasma membrane. As transport of vesicles from the golgi apparatus to the plasma membrane occurs through kinesin motor proteins along microtubule tracks, the function of EXOC6B is linked to KIF22 suggesting a common pathogenic mechanism in skeletal dysplasias with joint laxity and dislocations.
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Affiliation(s)
- Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hitesh Shah
- Division of Pediatric Orthopedics, Department of Orthopedics, Kasturba Medical College, Manipal University, Manipal, India
| | - Malik Alawi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Service Facility, Hamburg, Germany
- Center for Bioinformatics, University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz-Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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29
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Ranganath P, Matta D, Bhavani GS, Wangnekar S, Jain JMN, Verma IC, Kabra M, Puri RD, Danda S, Gupta N, Girisha KM, Sankar VH, Patil SJ, Ramadevi AR, Bhat M, Gowrishankar K, Mandal K, Aggarwal S, Tamhankar PM, Tilak P, Phadke SR, Dalal A. Spectrum of SMPD1 mutations in Asian-Indian patients with acid sphingomyelinase (ASM)-deficient Niemann-Pick disease. Am J Med Genet A 2016; 170:2719-30. [PMID: 27338287 DOI: 10.1002/ajmg.a.37817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/13/2016] [Indexed: 01/02/2023]
Abstract
Acid sphingomyelinase (ASM)-deficient Niemann-Pick disease is an autosomal recessive lysosomal storage disorder caused by biallelic mutations in the SMPD1 gene. To date, around 185 mutations have been reported in patients with ASM-deficient NPD world-wide, but the mutation spectrum of this disease in India has not yet been reported. The aim of this study was to ascertain the mutation profile in Indian patients with ASM-deficient NPD. We sequenced SMPD1 in 60 unrelated families affected with ASM-deficient NPD. A total of 45 distinct pathogenic sequence variants were found, of which 14 were known and 31 were novel. The variants included 30 missense, 4 nonsense, and 9 frameshift (7 single base deletions and 2 single base insertions) mutations, 1 indel, and 1 intronic duplication. The pathogenicity of the novel mutations was inferred with the help of the mutation prediction software MutationTaster, SIFT, Polyphen-2, PROVEAN, and HANSA. The effects of the identified sequence variants on the protein structure were studied using the structure modeled with the help of the SWISS-MODEL workspace program. The p. (Arg542*) (c.1624C>T) mutation was the most commonly identified mutation, found in 22% (26 out of 120) of the alleles tested, but haplotype analysis for this mutation did not identify a founder effect for the Indian population. To the best of our knowledge, this is the largest study on mutation analysis of patients with ASM-deficient Niemann-Pick disease reported in literature and also the first study on the SMPD1 gene mutation spectrum in India. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Genetics, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Divya Matta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Savita Wangnekar
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Ishwar C Verma
- Center of Medical Genetics, Sir GangaRam Hospital, New Delhi, India
| | - Madhulika Kabra
- Genetics Unit, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna Dua Puri
- Center of Medical Genetics, Sir GangaRam Hospital, New Delhi, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Neerja Gupta
- Genetics Unit, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Vaikom H Sankar
- Genetic Clinic, Department of Pediatrics, SAT Hospital, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Siddaramappa J Patil
- Clinical Genetics Unit, Mazumdhar Shaw Medical Center, Bengaluru, Karnataka, India
| | | | | | - Kalpana Gowrishankar
- Department of Medical Genetics, CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, Tamil Nadu, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Genetics, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Parag Mohan Tamhankar
- Genetic Research Centre, National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Preetha Tilak
- Division of Human Genetics, St. John's Medical College, Bengaluru, Karnataka, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.
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30
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Girisha KM, Shukla A, Trujillano D, Bhavani GS, Hebbar M, Kadavigere R, Rolfs A. A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Clin Genet 2016; 90:536-539. [PMID: 26880018 DOI: 10.1111/cge.12762] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 11/30/2022]
Abstract
Intraflagellar transport (IFT) is vital for the functioning of primary cilia. Defects in several components of IFT complexes cause a spectrum of ciliopathies with variable involvement of skeleton, brain, eyes, ectoderm and kidneys. We examined a child from a consanguineous family who had short stature, narrow thorax, short hands and feet, postaxial polydactyly of hands, pigmentary retinopathy, small teeth and skeletal dysplasia. The clinical phenotype of the child shows significant overlap with cranioectodermal dysplasia type I (Sensenbrenner syndrome). Whole-exome sequencing revealed a homozygous nonsense variant p.R142* in IFT52 encoding an IFT-B core complex protein as the probable cause of her condition. This is the first report of a human disease associated with IFT52.
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Affiliation(s)
- K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - A Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - D Trujillano
- Department of Bioinformatics, Centogene AG, Rostock, Germany
| | - G S Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - M Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - R Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal University, Manipal, India
| | - A Rolfs
- Department of Bioinformatics, Centogene AG, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
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31
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Bhavani GS, Shah H, Shukla A, Gupta N, Gowrishankar K, Rao AP, Kabra M, Agarwal M, Ranganath P, Ekbote AV, Phadke SR, Kamath A, Dalal A, Girisha KM. Clinical and mutation profile of multicentric osteolysis nodulosis and arthropathy. Am J Med Genet A 2015; 170A:410-417. [DOI: 10.1002/ajmg.a.37447] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/15/2015] [Indexed: 01/17/2023]
Affiliation(s)
| | - Hitesh Shah
- Department of Orthopedics, Pediatric Orthopedics services, Kasturba Medical College; Manipal University; Manipal India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics; All India Institute of Medical Sciences; New Delhi India
| | - Kalpana Gowrishankar
- Department of Medical Genetics; Kanchi Kamakoti Childs Trust Hospital; Chennai Tamilnadu India
| | | | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics; All India Institute of Medical Sciences; New Delhi India
| | - Meenal Agarwal
- Department of Medical Genetics; Sanjay Gandhi Postgraduate Institute of Medical Sciences; Lucknow India
| | - Prajnya Ranganath
- Department of Medical Genetics; Nizam's Institute of Medical Sciences; Hyderabad India
- Division of Diagnostics; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - Alka V. Ekbote
- Department of Clinical Genetics; Christian Medical College and Hospital; Vellore India
| | - Shubha R. Phadke
- Department of Medical Genetics; Sanjay Gandhi Postgraduate Institute of Medical Sciences; Lucknow India
| | - Asha Kamath
- Department of Community Medicine; Kasturba Medical College, Manipal University; Manipal Karnataka India
| | - Ashwin Dalal
- Division of Diagnostics; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
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32
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Bartakke S, Saindane A, Udgirkar V, Shrividya S, Bhavani GS, Girisha KM. Novel Mutation in an Indian Patient with Transcobalamin II Deficiency. Indian J Pediatr 2015; 82:1073-4. [PMID: 25947267 DOI: 10.1007/s12098-015-1770-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Sandip Bartakke
- Department of Clinical Hematology, Aditya Birla Memorial Hospital, Chinchwad, Pune, 411033, India.
| | - Avinash Saindane
- Department of Pediatrics, Aditya Birla Memorial Hospital, Chinchwad, Pune, India
| | | | - S Shrividya
- Department of Pathology, Aditya Birla Memorial Hospital, Chinchwad, Pune, India
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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Bhavani GS, Shah H, Dalal AB, Shukla A, Danda S, Aggarwal S, Phadke SR, Gupta N, Kabra M, Gowrishankar K, Gupta A, Bhat M, Puri RD, Bijarnia-Mahay S, Nampoothiri S, Mohanasundaram KM, Rajeswari S, Kulkarni AM, Kulkarni ML, Ranganath P, Ramadevi AR, Hariharan SV, Girisha KM. Novel and recurrent mutations in WISP3 and an atypical phenotype. Am J Med Genet A 2015; 167A:2481-4. [PMID: 25988854 DOI: 10.1002/ajmg.a.37164] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/03/2015] [Indexed: 12/22/2022]
Affiliation(s)
| | - Hitesh Shah
- Department of Orthopedics, Pediatric Orthopedics Services, Kasturba Medical College, Manipal University, Manipal, India
| | - Ashwin B Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Neerja Gupta
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Science, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Science, New Delhi, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, Kanchi Kamakoti Childs Trust Hospital, Chennai, Tamil Nadu, India
| | - Anju Gupta
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Ratna D Puri
- Centre of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
| | | | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Ponekkara, Cochin, Kerala, India
| | | | - S Rajeswari
- Department of Rheumatology, Madras Medical College, Chennai, India
| | - Akhil M Kulkarni
- Department of Radiodiagnosis, SS Institute of Medical Sciences and Research Centre, Davangere, India
| | - Muralidhar L Kulkarni
- Department of Pediatrics, Jagadguru Jayadeva Murugarajendra Medical College, Davangere, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - A Radha Ramadevi
- Department of Clinical Genetics, Genetics Unit, Rainbow Children Hospital, Hyderabad, India
| | - Sankar V Hariharan
- Department of Pediatrics, Sree Avittom Thirunal Hospital, Government Medical College, Trivandrum, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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