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Mahadevan J, Sud R, Nadella RK, Vani P, Subramaniam AG, Paul P, Ganapathy A, Mannan AU, Chandru V, Viswanath B, Purushottam M, Jain S. Targeted Sequencing Detects Variants That May Contribute to the Risk of Neuropsychiatric Disorders. Indian J Psychol Med 2022; 44:516-522. [PMID: 36157006 PMCID: PMC9460021 DOI: 10.1177/0253717621993672] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jayant Mahadevan
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Reeteka Sud
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Ravi Kumar Nadella
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pulaparambil Vani
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Anand G Subramaniam
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pradip Paul
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Aparna Ganapathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, Karnataka, India
| | - Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, Karnataka, India
| | - Vijay Chandru
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, Karnataka, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India.,Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Sanjeev Jain
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India.,Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
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Dhar S, Mannan AU, Singh JJ, Dhar S, Pradhan S. Lynch syndrome: An unusal case of familial cancer unearthed. INDIAN J PATHOL MICR 2022; 65:465-467. [PMID: 35435397 DOI: 10.4103/ijpm.ijpm_809_19] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
Lynch syndrome or hereditary nonpolyposis colorectal cancer (HNPCC) is a type of inherited cancer syndrome with a genetic predisposition to different types of cancer. There is an increased predisposition to cancers in the endometrium, colon, stomach, ovary, uterus, skin, kidney, and brain in patients of Lynch syndrome. We are reporting a 48-year-old male who presented with a pea-sized growth in his left arm which was found to be sebaceoma on histopathology. On further detailed history, examination, and genetic study, it was proved to be a familial case of Lynch syndrome. The case is being reported to stress the importance of knowledge about clinical manifestation, associated neoplasms, and molecular genetic profile of Lynch syndrome which will enable physicians and pathologists to provide highly targeted surveillance and management for patients with high cancer risk.
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Affiliation(s)
- Subhra Dhar
- Consultant Pathologist, Kolkata Reference Lab, SRL Ltd, Kolkata, West Bengal, India
| | - Ashraf U Mannan
- Basic Research Scientist, Department of Clinical Genetics and Genomics, Strand Life Science Private Limited, Bangaluru, Karnataka, India
| | - J Jaya Singh
- Basic Research Scientist, Strand Life Science Private Limited, Bangaluru, Karnataka, India
| | - Sandipan Dhar
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, India
| | - Swetalina Pradhan
- Department of Dermatology, All India Institute of Medical Sciences, Patna, Bihar, India
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Chandrasekharan SV, Nair SS, Ganapathy A, Mannan AU, Sundaram S. Charcot-Marie-Tooth disease type 2S: identical novel missense mutation of IGHMBP2 gene in two unrelated families. Neurol Sci 2021; 43:719-722. [PMID: 34668123 DOI: 10.1007/s10072-021-05668-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Soumya V Chandrasekharan
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | - Sruthi S Nair
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | | | | | - Soumya Sundaram
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India.
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Katragadda S, Hall TO, Bettadapura R, Dalton JC, Ganapathy A, Ghana P, Hariharan R, Janakiraman A, Kotha KBVSSP, Manjunath A, Mannan AU, Ms N, Saraf S, Tzeng KTH, Veeramachaneni V. Determining Cost-Optimal Next-Generation Sequencing Panels for Rare Disease and Pharmacogenomics Testing. Clin Chem 2021; 67:1122-1132. [PMID: 34120169 DOI: 10.1093/clinchem/hvab059] [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: 12/28/2020] [Accepted: 03/25/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Multi-gene panel sequencing using next-generation sequencing (NGS) methods is a key tool for genomic medicine. However, with an estimated 140 000 genomic tests available, current system inefficiencies result in high genetic-testing costs. Reduced testing costs are needed to expand the availability of genomic medicine. One solution to improve efficiency and lower costs is to calculate the most cost-effective set of panels for a typical pattern of test requests. METHODS We compiled rare diseases, associated genes, point prevalence, and test-order frequencies from a representative laboratory. We then modeled the costs of the relevant steps in the NGS process in detail. Using a simulated annealing-based optimization procedure, we determined panel sets that were more cost-optimal than whole exome sequencing (WES) or clinical exome sequencing (CES). Finally, we repeated this methodology to cost-optimize pharmacogenomics (PGx) testing. RESULTS For rare disease testing, we show that an optimal choice of 4-6 panels, uniquely covering genes that comprise 95% of the total prevalence of monogenic diseases, saves $257-304 per sample compared with WES, and $66-135 per sample compared with CES. For PGx, we show that the optimal multipanel solution saves $6-7 (27%-40%) over a single panel covering all relevant gene-drug associations. CONCLUSIONS Laboratories can reduce costs using the proposed method to obtain and run a cost-optimal set of panels for specific test requests. In addition, payers can use this method to inform reimbursement policy.
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Kuthiroly S, Yesodharan D, Radhakrishnan N, Ganapathy A, Mannan AU, Hoffmann MM, Nampoothiri S. Lipoprotein Lipase Deficiency. Indian J Pediatr 2021; 88:147-153. [PMID: 32472350 DOI: 10.1007/s12098-020-03305-z] [Citation(s) in RCA: 6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/13/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To analyse the clinical and molecular spectrum of Lipoprotein Lipase (LPL) deficiency and to highlight the effect of a cost-effective indigenous diet for management of this disorder. METHODS This is a single-centre retrospective study. Fifteen patients from 14 kindreds with severe hypertriglyceridemia (more than 1000 mg/dl) were evaluated for a period of 12.5 y at Amrita Institute of Medical Sciences, Kerala, India. RESULTS Thirteen of 15 patients were referred after incidental detection of lipemic plasma, 1/15 had chylothorax in the neonatal period and 1/15 had pancreatitis. The mean age of presentation was 7 mo (ranging from 2 d to 4 y), and 20% of the patients had a positive history of consanguinity. Hepatomegaly (15/15), splenomegaly (9/15) and lipemia retinalis (14/15) were common findings. Lipemia retinalis was a useful non-invasive diagnostic tool. All the patients were subjected to diet modification and followed up at regular intervals. Fourteen of 15 complied with the diet, resulting in a dramatic improvement in the fasting lipid profile; only 1/15 developed pancreatitis. Genetic screening analysis was offered to 14/15 patients (1/15 was lost to follow-up); six different variants were identified, of which two were novel variants. CONCLUSIONS Lipemic serum, chylothorax and recurrent pancreatitis in children should raise the suspicion of Lipoprotein Lipase deficiency. Early diagnosis and prompt initiation of a stringent fat-restricted diet are the keys to success for the management of LPL deficiency and prevention of pancreatitis.
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Affiliation(s)
- Shwetha Kuthiroly
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Aims Ponekkara PO, Cochin, Kerala, 682041, India
| | - Dhanya Yesodharan
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Aims Ponekkara PO, Cochin, Kerala, 682041, India
| | - Natasha Radhakrishnan
- Department of Ophthalmology, Amrita Institute of Medical Sciences & Research Centre, Aims Ponekkara PO, Cochin, Kerala, 682041, India
| | - Aparna Ganapathy
- Strand Life Sciences, Hebbal PO, Bangalore, Karnataka, 560024, India
| | - Ashraf U Mannan
- Strand Life Sciences, Hebbal PO, Bangalore, Karnataka, 560024, India
| | - Michael M Hoffmann
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Centre & Faculty of Medicine - University of Freiburg, Freiburg im Breisgau, Germany
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Aims Ponekkara PO, Cochin, Kerala, 682041, India.
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Nadaf SN, Chakor RT, Kothari KV, Mannan AU. Synaptic Nuclear Envelope Protein 1 (SYNE 1) Ataxia with Amyotrophic Lateral Sclerosis-like Presentation: A Novel Synaptic Nuclear Envelope Protein 1 (SYNE 1) Gene Deletion Mutation from India. Ann Indian Acad Neurol 2020; 23:539-541. [PMID: 33223674 PMCID: PMC7657298 DOI: 10.4103/aian.aian_448_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/29/2018] [Accepted: 12/12/2018] [Indexed: 11/09/2022] Open
Abstract
A 24-year-old female presented with wasting and weakness of both hands and fasciculations over the chin since 12 years, followed by imbalance while walking and speech changes since 10 years. Her 12-year-old sister also had a similar clinical presentation. There were fasciculations over the chin, tongue, hands, back, thighs with wasting and weakness in tongue, and C7, C8, T1 segments in both upper limbs along with bipyramidal signs. There was limb and gait ataxia. Magnetic resonance imaging brain showed pancerebellar atrophy, and electromyography was suggestive of anterior horn cell involvement in bulbar, cervical, thoracic, and lumbar segments. Next-generation sequencing identified a novel likely pathogenic deletion mutation: chr6:152527389_152527399del, c.22711_22721del, and p.Ala7571ArgfsTer4 in exon 125 of synaptic nuclear envelope protein 1 (SYNE1) gene. This mutation leads to frameshift and premature termination of the protein 'Nesprin 1'. Amyotrophic lateral sclerosis-like presentation followed by cerebellar ataxia have been described with SYNE1 ataxia. This unique phenotype and novel deletion mutation of SYNE1 gene is the first case reported from India.
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Affiliation(s)
| | - Rahul T Chakor
- Department of Neurology, TNMC, Nair Hospital, Mumbai, Maharashtra, India
| | - Kaumil V Kothari
- Department of Neurology, TNMC, Nair Hospital, Mumbai, Maharashtra, India
| | - Ashraf U Mannan
- Department of Clinical Genomics, Strand Life Sciences, Bengaluru, Karnataka, India
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Yesodharan D, Krishnan V, Nair IR, Ganapathy A, Mannan AU, Nampoothiri S. Lethal Cenani Lenz syndrome in two consecutive pregnancies: Further extension of phenotype from Maldives. Am J Med Genet A 2020; 185:620-624. [PMID: 33179409 DOI: 10.1002/ajmg.a.61971] [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: 09/03/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 11/07/2022]
Abstract
Cenani Lenz syndrome is a rare autosomal recessive disorder associated with variable degree of limb malformations, dysmorphism, and renal agenesis. It is caused due to pathogenic variants in the LRP4 gene, which plays an important role in limb and renal development. Mutations in the APC gene have also been occasionally associated with CLS. The phenotypic spectrum ranges from mild to very severe perinatal lethal type depending on the type of variant. We report a pathogenic variant, c.2710 del T (p.Trp904GlyfsTer5) in theLRP4 gene, in a fetus with lethal Cenani Lenz syndrome with antenatal presentation of tetraphocomelia and symmetrical involvement of hands and feet.
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Affiliation(s)
- Dhanya Yesodharan
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, India
| | - Vivek Krishnan
- Department of Perinatology, Amrita Institute of Medical Sciences and Research Center, Cochin, India
| | - Indu R Nair
- Department of Pathology, Amrita Institute of Medical Sciences and Research Center, Cochin, India
| | | | | | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, India
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Malhotra H, Kowtal P, Mehra N, Pramank R, Sarin R, Rajkumar T, Gupta S, Bapna A, Bhattacharyya GS, Gupta S, Maheshwari A, Mannan AU, Reddy Kundur R, Sekhon R, Singhal M, Smruti B, SP S, Suryavanshi M, Verma A. Genetic Counseling, Testing, and Management of HBOC in India: An Expert Consensus Document from Indian Society of Medical and Pediatric Oncology. JCO Glob Oncol 2020; 6:991-1008. [PMID: 32628584 PMCID: PMC7392772 DOI: 10.1200/jgo.19.00381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Hereditary breast and ovarian cancer (HBOC) syndrome is primarily characterized by mutations in the BRCA1/2 genes. There are several barriers to the implementation of genetic testing and counseling in India that may affect clinical decisions. These consensus recommendations were therefore convened as a collaborative effort to improve testing and management of HBOC in India. DESIGN Recommendations were developed by a multidisciplinary group of experts from the Indian Society of Medical and Pediatric Oncology and some invited experts on the basis of graded evidence from the literature and using a formal Delphi process to help reach consensus. PubMed and Google Scholar databases were searched to source relevant articles. RESULTS This consensus statement provides practical insight into identifying patients who should undergo genetic counseling and testing on the basis of assessments of family and ancestry and personal history of HBOC. It discusses the need and significance of genetic counselors and medical professionals who have the necessary expertise in genetic counseling and testing. Recommendations elucidate requirements of pretest counseling, including discussions on genetic variants of uncertain significance and risk reduction options. The group of experts recommended single-site mutation testing in families with a known mutation and next-generation sequencing coupled with multiplex ligation probe amplification for the detection of large genomic rearrangements for unknown mutations. Recommendations for surgical and lifestyle-related risk reduction approaches and management using poly (ADP-ribose) polymerase inhibitors are also detailed. CONCLUSION With rapid strides being made in the field of genetic testing/counseling in India, more oncologists are expected to include genetic testing/counseling as part of their clinical practice. These consensus recommendations are anticipated to help homogenize genetic testing and management of HBOC in India for improved patient care.
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Affiliation(s)
- Hemant Malhotra
- Department of Medical Oncology, Sri Ram Cancer Center, Mahatma Gandhi Medical College Hospital, Jaipur, India
| | - Pradnya Kowtal
- Sarin Laboratory and OIC Sanger Sequencing Facility, Advanced Centre for Treatment Research, and Education in Cancer, Navi Mumbai, India
| | - Nikita Mehra
- Department of Medical Oncology, Cancer Institute (WIA), Chennai, India
| | - Raja Pramank
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajiv Sarin
- Radiation Oncology, Cancer Genetics Unit, Tata Memorial Centre and PI Sarin Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | | | - Sudeep Gupta
- Tata Memorial Centre Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Ajay Bapna
- Department of Medical Oncology, Bhagwan Mahavir Cancer Hospital Research Center, Jaipur, India
| | | | - Sabhyata Gupta
- Department of Gynae Oncology, Medanta-The Medicity, Gurgaon, India
| | - Amita Maheshwari
- Department of Gynecologic Oncology, Tata Memorial Centre, Mumbai, India
| | - Ashraf U. Mannan
- Clinical Diagnostics, Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Rupinder Sekhon
- Gynae Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - B.K. Smruti
- Bombay Hospital and Medical Research Centre, Mumbai, India
| | - Somashekhar SP
- Manipal Comprehensive Cancer Center, Manipal Hospital, Bengaluru, India
| | - Moushumi Suryavanshi
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Amit Verma
- Molecular Oncology and Cancer Genetics, Max Hospital, New Delhi, India
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Radha Rama Devi A, Ganapathy A, Mannan AU, Sabharanjak S, Naushad SM. 1q42.12q42.2 Deletion in a Child with Midline Defects and Hypoplasia of the Corpus Callosum. Mol Syndromol 2019; 10:161-166. [PMID: 31191205 DOI: 10.1159/000496079] [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] [Accepted: 11/27/2018] [Indexed: 11/19/2022] Open
Abstract
Chromosome 1q42.12q42.2 deletions are documented as "disease causing" and show overlapping phenotypes depending on the genes involved in the deletion. In this report, we detected a 5.8-Mb deletion encompassing the chromosome 1q42.12q42.2 region in a 4-year-old boy with hypoplastic corpus callosum, epilepsy, developmental delay, microcephaly, cataract, cleft palate, and skeletal changes. The deletion was de novo. Genotype-phenotype correlations suggest that the major features of 1q42.12q42.2 microdeletion were attributed to the genes with a high probability of loss-of-function intolerance score in this deletion, namely LBR, ENAH, ACBD3, LIN9, ITPKB, CDC42BPA, ARF1, TAF5L, GALNT2, SPRTN, and EGLN1 along with GNPAT.
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Affiliation(s)
| | - Aparna Ganapathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Shefali Sabharanjak
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Shaik M Naushad
- Sandor Speciality Diagnostics Pvt Ltd, Strand Life Sciences, Bangalore, Hyderabad, India
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Ganapathy A, Mishra A, Soni MR, Kumar P, Sadagopan M, Kanthi AV, Patric IRP, George S, Sridharan A, Thyagarajan TC, Aswathy SL, Vidya HK, Chinnappa SM, Nayanala S, Prakash MB, Raghavendrachar VG, Parulekar M, Gowda VK, Nampoothiri S, Menon RN, Pachat D, Udani V, Naik N, Kamate M, Devi ARR, Mohammed Kunju PA, Nair M, Hegde AU, Kumar MP, Sundaram S, Tilak P, Puri RD, Shah K, Sheth J, Hasan Q, Sheth F, Agrawal P, Katragadda S, Veeramachaneni V, Chandru V, Hariharan R, Mannan AU. Multi-gene testing in neurological disorders showed an improved diagnostic yield: data from over 1000 Indian patients. J Neurol 2019; 266:1919-1926. [PMID: 31069529 DOI: 10.1007/s00415-019-09358-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 01/21/2019] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Neurological disorders are clinically heterogeneous group of disorders and are major causes of disability and death. Several of these disorders are caused due to genetic aberration. A precise and confirmatory diagnosis in the patients in a timely manner is essential for appropriate therapeutic and management strategies. Due to the complexity of the clinical presentations across various neurological disorders, arriving at an accurate diagnosis remains a challenge. METHODS We sequenced 1012 unrelated patients from India with suspected neurological disorders, using TruSight One panel. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS We were able to detect mutations in 197 genes in 405 (40%) cases and 178 mutations were novel. The highest diagnostic rate was observed among patients with muscular dystrophy (64%) followed by leukodystrophy and ataxia (43%, each). In our cohort, 26% of the patients who received definitive diagnosis were primarily referred with complex neurological phenotypes with no suggestive diagnosis. In terms of mutations types, 62.8% were truncating and in addition, 13.4% were structural variants, which are also likely to cause loss of function. CONCLUSION In our study, we observed an improved performance of multi-gene panel testing, with an overall diagnostic yield of 40%. Furthermore, we show that NGS (next-generation sequencing)-based testing is comprehensive and can detect all types of variants including structural variants. It can be considered as a single-platform genetic test for neurological disorders that can provide a swift and definitive diagnosis in a cost-effective manner.
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Affiliation(s)
- Aparna Ganapathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Avshesh Mishra
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Megha Rani Soni
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Priyanka Kumar
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Mukunth Sadagopan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Anil Vittal Kanthi
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Irene Rosetta Pia Patric
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Sobha George
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Aparajit Sridharan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - T C Thyagarajan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - S L Aswathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - H K Vidya
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Swathi M Chinnappa
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Swetha Nayanala
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Manasa B Prakash
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Vijayashree G Raghavendrachar
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Minothi Parulekar
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | | | | | - Ramshekhar N Menon
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | | | - Vrajesh Udani
- P. D. Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - Neeta Naik
- EN1 Neuro Services Pvt. Ltd., Mumbai, India
| | | | | | | | | | | | | | - Soumya Sundaram
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Preetha Tilak
- St. Johns Medical College Hospital, Bangalore, India
| | | | - Krati Shah
- ONE-Centre for Rheumatology and Genetics, Vadodara, India
| | - Jayesh Sheth
- FRIGE'S Institute of Human Genetics, Ahmedabad, India
| | | | - Frenny Sheth
- FRIGE'S Institute of Human Genetics, Ahmedabad, India
| | - Pooja Agrawal
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Shanmukh Katragadda
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Vamsi Veeramachaneni
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Vijay Chandru
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India.,Indian Institute of Science, Bangalore, India
| | - Ramesh Hariharan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India.,Indian Institute of Science, Bangalore, India
| | - Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India.
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Bhattacharya S, Khadilkar SV, Nalini A, Ganapathy A, Mannan AU, Majumder PP, Bhattacharya A. Mutation Spectrum of GNE Myopathy in the Indian Sub-Continent. J Neuromuscul Dis 2018; 5:85-92. [PMID: 29480215 DOI: 10.3233/jnd-170270] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND GNE myopathy is an adult onset recessive genetic disorder that affects distal muscles sparing the quadriceps. GNE gene mutations have been identified in GNE myopathy patients all over the world. Homozygosity is a common feature in GNE myopathy patients worldwide. OBJECTIVES The major objective of this study was to investigate the mutation spectrum of GNE myopathy in India in relation to the population diversity in the country. MATERIALS AND METHODS We have collated GNE mutation data of Indian GNE myopathy patients from published literature and from recently identified patients. We also used data of people of Indian subcontinent from 1000 genomes database, South Asian Genome database and Strand Life Science database to determine frequency of GNE mutations in the general population. RESULTS A total of 67 GNE myopathy patients were studied, of whom 21% were homozygous for GNE variants, while the rest were compound heterozygous. Thirty-five different mutations in the GNE gene were recorded, of which 5 have not been reported earlier. The most frequent mutation was p.Val727Met (65%) found mainly in the heterozygous form. Another mutation, p.Ile618Thr was also common (16%) but was found mainly in patients from Rajasthan, while p.Val727Met was more widely distributed. The latter was also seen at a high frequency in general population of Indian subcontinent in all the databases. It was also present in Thailand but was absent in general population elsewhere in the world. CONCLUSION p.Val727Met is likely to be a founder mutation of Indian subcontinent.
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Affiliation(s)
- Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,World Without GNE Myopathy (India), New Delhi, India
| | - Satish V Khadilkar
- Department of Neurology, Grant Government Medical College and J.J. Hospital, Byculla, Mumbai, Maharashtra, India
| | - Atchayaram Nalini
- Departments of Neurology and Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
| | | | | | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,World Without GNE Myopathy (India), New Delhi, India
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Rangaraju A, Krishnan S, Aparna G, Sankaran S, Mannan AU, Rao BH. Genetic variants in post myocardial infarction patients presenting with electrical storm of unstable ventricular tachycardia. Indian Pacing Electrophysiol J 2018; 18:91-94. [PMID: 29396286 PMCID: PMC5986548 DOI: 10.1016/j.ipej.2018.01.003] [Citation(s) in RCA: 2] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/21/2017] [Accepted: 01/25/2018] [Indexed: 11/25/2022] Open
Abstract
Electrical storm (ES) is a life threatening clinical situation. Though a few clinical pointers exist, the occurrence of ES in a patient with remote myocardial infarction (MI) is generally unpredictable. Genetic markers for this entity have not been studied. In the present study, we carried out genetic screening in patients with remote myocardial infarction presenting with ES by next generation sequencing and identified 25 rare variants in 19 genes predominantly in RYR2, SCN5A, KCNJ11, KCNE1 and KCNH2, CACNA1B, CACNA1C, CACNA1D and desmosomal genes - DSP and DSG2 that could potentially be implicated in electrical storm. These genes have been previously reported to be associated with inherited syndromes of Sudden Cardiac Death. The present study suggests that the genetic architecture in patients with remote MI and ES of unstable ventricular tachycardia may be similar to that of Ion channelopathies. Identification of these variants may identify post MI patients who are predisposed to develop electrical storm and help in risk stratification.
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Affiliation(s)
- Advithi Rangaraju
- KIMS Foundation and Research Centre, Minister Road, Secunderabad, Telangana, India
| | | | - G Aparna
- STRAND Life Sciences, Bangalore, India
| | - Satish Sankaran
- Division of Pacing & Electrophysiology, Krishna Institute of Medical Sciences, Minister Road, Secunderabad, Telangana, India
| | | | - B Hygriv Rao
- Division of Pacing & Electrophysiology, Krishna Institute of Medical Sciences, Minister Road, Secunderabad, Telangana, India; Arrhythmia Research & Training Society (ARTS), Hyderabad, India.
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Chatterjee M, Chinder P, Mannan AU, Sheela M, Mukherjee U, Choudhury S, Lo C, Singh S, Singh J, Hazarika D, Prabhudesai S, Gupta V, Kunigal SS, Swamy SK, Agrawal V, Kumar A, Ghosh M. Genotype-Phenotype Analysis in an Indian Family Affected with Li-Fraumeni Syndrome-Role of Genetic Counselling. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2016.11886284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manjima Chatterjee
- Triesta Sciences, HCG, Bangalore, Karnataka, India
- School of Bio Sciences and Technology, VIT University, Vellore 632 014, Tamil Nadu, India
| | - Pramod Chinder
- Health Care Global Enterprises Limited, Bangalore 560027 Karnataka, India
| | - Ashraf U. Mannan
- Strand Centre for Genomics and Personalized Medicine, Bangalore 600 024 Karnataka, India
| | - M.L. Sheela
- Triesta Sciences, HCG, Bangalore, Karnataka, India
| | - Upasana Mukherjee
- Triesta Sciences, HCG, Bangalore, Karnataka, India
- School of Bio Sciences and Technology, VIT University, Vellore 632 014, Tamil Nadu, India
| | | | - Caroline Lo
- Triesta Sciences, HCG, Bangalore, Karnataka, India
| | - Suhasini Singh
- Strand Centre for Genomics and Personalized Medicine, Bangalore 600 024 Karnataka, India
| | - Jaya Singh
- Strand Centre for Genomics and Personalized Medicine, Bangalore 600 024 Karnataka, India
| | | | | | - Vaijayanti Gupta
- Strand Centre for Genomics and Personalized Medicine, Bangalore 600 024 Karnataka, India
| | | | - Shiva Kumar Swamy
- Health Care Global Enterprises Limited, Bangalore 560027 Karnataka, India
| | - Vijay Agrawal
- Health Care Global Enterprises Limited, Bangalore 560027 Karnataka, India
| | - Ajai Kumar
- Health Care Global Enterprises Limited, Bangalore 560027 Karnataka, India
| | - Mithua Ghosh
- Triesta Sciences, HCG, Bangalore, Karnataka, India
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Singh J, Mishra A, Pandian AJ, Mallipatna AC, Khetan V, Sripriya S, Kapoor S, Agarwal S, Sankaran S, Katragadda S, Veeramachaneni V, Hariharan R, Subramanian K, Mannan AU. Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort. Mol Vis 2016; 22:1036-47. [PMID: 27582626 PMCID: PMC4985049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/14/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Retinoblastoma (Rb) is the most common primary intraocular cancer of childhood and one of the major causes of blindness in children. India has the highest number of patients with Rb in the world. Mutations in the RB1 gene are the primary cause of Rb, and heterogeneous mutations are distributed throughout the entire length of the gene. Therefore, genetic testing requires screening of the entire gene, which by conventional sequencing is time consuming and expensive. METHODS In this study, we screened the RB1 gene in the DNA isolated from blood or saliva samples of 50 unrelated patients with Rb using the TruSight Cancer panel. Next-generation sequencing (NGS) was done on the Illumina MiSeq platform. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS We were able to detect germline pathogenic mutations in 66% (33/50) of the cases, 12 of which were novel. We were able to detect all types of mutations, including missense, nonsense, splice site, indel, and structural variants. When we considered bilateral Rb cases only, the mutation detection rate increased to 100% (22/22). In unilateral Rb cases, the mutation detection rate was 30% (6/20). CONCLUSIONS Our study suggests that NGS-based approaches increase the sensitivity of mutation detection in the RB1 gene, making it fast and cost-effective compared to the conventional tests performed in a reflex-testing mode.
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Affiliation(s)
- Jaya Singh
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Avshesh Mishra
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Ashwin C. Mallipatna
- Department of Pediatric Ophthalmology and Strabismology, Narayana Nethralaya, Bangalore, India
| | - Vikas Khetan
- Department of Vitreo Retina, Sankara Nethralaya, Chennai, India
| | - S. Sripriya
- Sankara Nethralaya ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India
| | - Suman Kapoor
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Smita Agarwal
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Satish Sankaran
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Shanmukh Katragadda
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Vamsi Veeramachaneni
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Ramesh Hariharan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India,Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India
| | | | - Ashraf U. Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
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Sundaramurthy S, Swaminathan M, Sen P, Arokiasamy T, Deshpande S, John N, Gadkari RA, Mannan AU, Soumittra N. Homozygosity mapping guided next generation sequencing to identify the causative genetic variation in inherited retinal degenerative diseases. J Hum Genet 2016; 61:951-958. [DOI: 10.1038/jhg.2016.83] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 11/09/2022]
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Ghosh M, ML S, Upasana M, Chodhury S, Mannan AU, Southekal S, Manjima C, Patil S, Murugan K, Mahesh B, Nayak R, Sridhar PSS, Rao N, Krishnamoorthy N, Gupta V, Satheesh CT, Subramanian K, Ajaikumar BS. Abstract P6-06-06: Comprehensive analysis of BRCA (BRCAm) and other germline mutations (GRm) with a clinicopathological association in breast cancer: An Indian study. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-06-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: BRCAm and other GRm testing using next generation sequencing (NGS) in early diagnosed and/or metastatic breast cancer (BC) helps in the identification of both unambiguously defined deleterious mutations and sequence variants of unknown clinical significance (VUS). The early detection of these mutations in the proband and the family members help in risk stratification and instituting effective monitoring, surveillance and disease management strategies.
Methods: Out of total 200 patients diagnosed with BC (April 2013-15) 77 unrelated individuals were consented to be profiled by NGS on MiSeq platform using TruSight Cancer panel (consisting of 94 genes including 13 genes highly associated with risk of inherited breast and/or ovarian cancer) in an IRB-approved prospective study in a CLIA compliant laboratory. Paired end sequencing was done with an average coverage of > 450X. Data was processed using STRAND software and interpreted using "Strand Omics" platform. The paired tumor samples were analysed for pathological stage, histological type and hormonal status.
Results: GRm were detected in 61 cases (79%). Among all mutations detected, BRCA1/2 were found in 51% (31% in BRCA1, 20% in BRCA2) of cases. BRCA1 was found to be co-mutated with BRCA2 in 2 cases. Out of 37 deleterious mutations in BRCA1/2 genes only 10 were reported to be pathogenic (6 in BRCA1 and 4 in BRCA2) and rest were VUS. Mutation frequencies were higher among high grade IDC with HER2-ve tumors including TNBC (53%, p<0.05) with an early onset of the disease. TNBC with BRCAm were found to have no/incomplete pCR on conventional TAC regimen , subsequently started with platinum therapy and the outcome being monitored. Interestingly, 4 BRCA1 mutations including 3 non-sense and 1 frameshift mutation were found in two unrelated individuals suggesting them to be founder mutations in Indian population. The other GRm frequency (alone/ co-mutated with BRCA) was also found to be significantly high (49%) and include BRIP1, CHEK2, ERCC2, CDH1, SDHB, APC, MSH6, TP53, PALB2 and RAD51C. Stratification based on age of diagnosis(dx) showed a detection rate significantly higher in the age group of 25-50 yrs (74%) as compared to the 50-75 yrs (26%). Also a strong association of GRm status with the family history(Hx) of BC in 1st or 2nd degree relatives was indicated.
Table 1: Correlation of GRm with Dx and HxGenen%Age at dx(yrs)Family Hx (Yes=Y, No=N,Unknown=UK)BRCA1193125-50 (n=23) 50-75(n=8)Y(n=13) N(n=3) UK(n=3)BRCA2122025-50(n=21) 50-75(n=9)Y(n=8) N(n=2) UK(n=2)PALB211.7>50YCHEK258.825-50 (n=4) 50-75(n=1)YATM610.525-50 (n=4) 50-75(n=2)Y(n=5) N(n=1)RAD5111.7<50Y
Conclusions: Our study in a small cohort clearly highlighted the significance of germline testing and classifying the variant in larger cohort of BC patients with a strong family Hx of cancer particularly in BRCA1/2 positive families , and in women <50yrs for early detection and risk assessment. The study also indicates BRCAm to be an important contributor to the etiology of high grade HER2-/ TNBC in Indian patients. Expanded testing of this subtype is warranted to impact management of the disease with PARP inhibitors and/or platinum therapy.
Citation Format: Ghosh M, ML S, Upasana M, Chodhury S, Mannan AU, Southekal S, Manjima C, Patil S, Murugan K, Mahesh B, Nayak R, Sridhar PSS, Rao N, Krishnamoorthy N, Gupta V, Satheesh CT, Subramanian K, Ajaikumar BS. Comprehensive analysis of BRCA (BRCAm) and other germline mutations (GRm) with a clinicopathological association in breast cancer: An Indian study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-06-06.
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Affiliation(s)
- M Ghosh
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - S ML
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - M Upasana
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - S Chodhury
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - AU Mannan
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - S Southekal
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - C Manjima
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - S Patil
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - K Murugan
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - B Mahesh
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - R Nayak
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - PSS Sridhar
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - N Rao
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - N Krishnamoorthy
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - V Gupta
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - CT Satheesh
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - K Subramanian
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
| | - BS Ajaikumar
- Triesta Sciences , Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Health Care Global Enterprises Ltd., Bangalore, Karnataka, India; Strand Center for Genomics and Personalized Medicine, Bangalore, Karnataka, India
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Gupta V, Mannan AU, Agrawal P, Sen M, Sankaran S, Vitthal V, Pathak V, Swetha N, Vishwanath D, Deshpande G, Kumari K, Gadkari R, Singh J, Lakshmikeshava R, Manek P, B.P. M, Awasthy D, Yousuff M, Kapoor S, Subramanian K. Targeted sequencing to confirm clinical diagnosis of Li-Fraumeni syndrome. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e22052] [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: 11/20/2022] Open
Affiliation(s)
- Vaijayanti Gupta
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Pooja Agrawal
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Manimala Sen
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Satish Sankaran
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Vikram Vitthal
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Vaibhavi Pathak
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - N.S.N Swetha
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Divya Vishwanath
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Gouri Deshpande
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Kiran Kumari
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Rupali Gadkari
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Jaya Singh
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | | | - Payal Manek
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Manasa B.P.
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Disha Awasthy
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Mohammed Yousuff
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Suman Kapoor
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
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Mannan AU, Singh J, Gadkari R, Lakshmikeshava R, Manek P, Ramalingam R, B.P. M, Kapoor S, Yadhav J, Sankaran S, Katragadda S, Veeramachaneni V, Ramamoorthy P, Hariharan R, Subramanian K. Screening of an Indian cohort with breast and/or ovarian cancer by a next-generation sequencing-based panel to detect a high frequency of mutations. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e12505] [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: 11/20/2022] Open
Affiliation(s)
- Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Jaya Singh
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Rupali Gadkari
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | | | - Payal Manek
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Ravi Ramalingam
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Manasa B.P.
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Suman Kapoor
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Jamuna Yadhav
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | - Satish Sankaran
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
| | | | | | | | - Ramesh Hariharan
- Strand Center for Genomics and Personalized Medicine, Bangalore, India
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Tantra M, Hammer C, Kästner A, Dahm L, Begemann M, Bodda C, Hammerschmidt K, Giegling I, Stepniak B, Castillo Venzor A, Konte B, Erbaba B, Hartmann A, Tarami A, Schulz-Schaeffer W, Rujescu D, Mannan AU, Ehrenreich H. Mild expression differences of MECP2 influencing aggressive social behavior. EMBO Mol Med 2014; 6:662-84. [PMID: 24648499 PMCID: PMC4023888 DOI: 10.1002/emmm.201303744] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The X-chromosomal MECP2/Mecp2 gene encodes methyl-CpG-binding protein 2, a transcriptional activator and repressor regulating many other genes. We discovered in male FVB/N mice that mild (∼50%) transgenic overexpression of Mecp2 enhances aggression. Surprisingly, when the same transgene was expressed in C57BL/6N mice, transgenics showed reduced aggression and social interaction. This suggests that Mecp2 modulates aggressive social behavior. To test this hypothesis in humans, we performed a phenotype-based genetic association study (PGAS) in >1000 schizophrenic individuals. We found MECP2 SNPs rs2239464 (G/A) and rs2734647 (C/T; 3′UTR) associated with aggression, with the G and C carriers, respectively, being more aggressive. This finding was replicated in an independent schizophrenia cohort. Allele-specific MECP2mRNA expression differs in peripheral blood mononuclear cells by ∼50% (rs2734647: C > T). Notably, the brain-expressed, species-conserved miR-511 binds to MECP2 3′UTR only in T carriers, thereby suppressing gene expression. To conclude, subtle MECP2/Mecp2 expression alterations impact aggression. While the mouse data provides evidence of an interaction between genetic background and mild Mecp2 overexpression, the human data convey means by which genetic variation affects MECP2 expression and behavior.
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Affiliation(s)
- Martesa Tantra
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
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Bodda C, Tantra M, Mollajew R, Arunachalam JP, Laccone FA, Can K, Rosenberger A, Mironov SL, Ehrenreich H, Mannan AU. Mild Overexpression of Mecp2 in Mice Causes a Higher Susceptibility toward Seizures. The American Journal of Pathology 2013; 183:195-210. [DOI: 10.1016/j.ajpath.2013.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/31/2013] [Accepted: 03/14/2013] [Indexed: 10/26/2022]
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Pantakani DVK, Czyzewska MM, Sikorska A, Bodda C, Mannan AU. Oligomerization of ZFYVE27 (Protrudin) is necessary to promote neurite extension. PLoS One 2011; 6:e29584. [PMID: 22216323 PMCID: PMC3247280 DOI: 10.1371/journal.pone.0029584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 12/01/2011] [Indexed: 11/20/2022] Open
Abstract
ZFYVE27 (Protrudin) was originally identified as an interacting partner of spastin, which is most frequently mutated in hereditary spastic paraplegia. ZFYVE27 is a novel member of FYVE family, which is implicated in the formation of neurite extensions by promoting directional membrane trafficking in neurons. Now, through a yeast two-hybrid screen, we have identified that ZFYVE27 interacts with itself and the core interaction region resides within the third hydrophobic region (HR3) of the protein. We confirmed the ZFYVE27's self-interaction in the mammalian cells by co-immunoprecipitation and co-localization studies. To decipher the oligomeric nature of ZFYVE27, we performed sucrose gradient centrifugation and showed that ZFYVE27 oligomerizes into dimer/tetramer forms. Sub-cellular fractionation and Triton X-114 membrane phase separation analysis indicated that ZFYVE27 is a peripheral membrane protein. Furthermore, ZFYVE27 also binds to phosphatidylinositol 3-phosphate lipid moiety. Interestingly, cells expressing ZFYVE27ΔHR3 failed to produce protrusions instead caused swelling of cell soma. When ZFYVE27ΔHR3 was co-expressed with wild-type ZFYVE27 (ZFYVE27WT), it exerted a dominant negative effect on ZFYVE27WT as the cells co-expressing both proteins were also unable to induce protrusions and showed cytoplasmic swelling. Altogether, it is evident that a functionally active form of oligomer is crucial for ZFYVE27 ability to promote neurite extensions.
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Affiliation(s)
| | - Marta M. Czyzewska
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Anna Sikorska
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Chiranjeevi Bodda
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Ashraf U. Mannan
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
- * E-mail:
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Klimpe S, Zibat A, Zechner U, Wellek B, Shoukier M, Sauter SM, Pantakani DVK, Mannan AU. Evaluating the effect of spastin splice mutations by quantitative allele-specific expression assay. Eur J Neurol 2011; 18:99-105. [PMID: 20491894 DOI: 10.1111/j.1468-1331.2010.03079.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND mutations in the SPG4/SPAST gene are the most common cause for hereditary spastic paraplegia (HSP). The splice-site mutations make a significant contribution to HSP and account for 17.4% of all types of mutations and 30.8% of point mutations in the SPAST gene. However, only few studies with limited molecular approach were conducted to investigate and decipher the role of SPAST splice-site mutations in HSP. METHODS a reverse transcriptase-polymerase chain reaction (RT-PCR) analysis and quantitative allele-specific expression assay were performed. RESULTS we have characterized the consequence of two novel splice-site mutations (c.1493 + 1G>A and c.1414-1G>A) in the SPAST gene in two different families with pure HSP. The RT-PCR analysis revealed that both spastin mutations are indeed splice-site mutations and cause skipping of exon 12. Furthermore, RT-PCR data suggested that these splice-site mutations may cause leaky splicing. By means of a quantitative allele-specific expression assay, we could confirm that both splice-site mutations cause leaky splicing, as the relative expression of the exon 12-skipped transcript was reduced (21.1 ± 3.6 compared to expected 50%). CONCLUSIONS our finding supports a "threshold-effect-model" for functional spastin in HSP. A higher level (78.8 ± 3.9%) of functional spastin than the expected ratio of 50% owing to leaky splicing might cause late age at onset of HSP. Remarkably, we could show that a quantitative allele-specific expression assay is a simple and effective tool to evaluate the role of most types of spastin splice-site mutations in HSP.
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Affiliation(s)
- S Klimpe
- Department of Neurology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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Abstract
An autosomal recessive form of hereditary spastic paraplegia (AR-HSP) is primarily caused by mutations in the SPG7 gene, which codes for paraplegin, a subunit of the hetero-oligomeric m-AAA protease in mitochondria. In the current study, sequencing of the SPG7 gene in the genomic DNA of 25 unrelated HSP individuals/families led to the identification of two HSP patients with compound heterozygous mutations (p.G349S/p.W583C and p.A510V/p.N739KfsX741) in the coding sequence of the SPG7 gene. We used a yeast complementation assay to evaluate the functional consequence of novel SPG7 sequence variants detected in the HSP patients. We assessed the proteolytic activity of hetero-oligomeric m-AAA proteases composed of paraplegin variant(s) and proteolytically inactive forms of AFG3L2 (AFG3L2(E575Q) or AFG3L2(K354A)) upon expression in m-AAA protease-deficient yeast cells. We demonstrate that the newly identified paraplegin variants perturb the proteolytic function of hetero-oligomeric m-AAA protease. Moreover, commonly occurring silent polymorphisms such as p.T503A and p.R688Q could be distinguished from mutations (p.G349S, p.W583C, p.A510V, and p.N739KfsX741) in our HSP cohort. The yeast complementation assay thus can serve as a reliable system to distinguish a pathogenic mutation from a silent polymorphism for any novel SPG7 sequence variant, which will facilitate the interpretation of genetic data for SPG7.
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Affiliation(s)
- Florian Bonn
- Institute of Genetics, Center for Molecular Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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Kifayathullah LA, Arunachalam JP, Bodda C, Agbemenyah HY, Laccone FA, Mannan AU. MeCP2 mutant protein is expressed in astrocytes as well as in neurons and localizes in the nucleus. Cytogenet Genome Res 2010; 129:290-7. [PMID: 20625242 DOI: 10.1159/000315906] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2010] [Indexed: 11/19/2022] Open
Abstract
The MECP2 gene, located at Xq28, encodes methyl-CpG-binding protein 2 (MeCP2), which is frequently mutated (up to 90%) in Rett syndrome (RTT). RTT is a progressive neurodevelopmental disorder, which affects primarily girls during early childhood and it is one of the most common causes of mental retardation in females. R270X is one of the most frequent recurrent MECP2 mutations among RTT cohorts. The R270X mutation resides within the TRD-NLS (Transcription Repression Domain-Nuclear Localization Signal) region of MeCP2 and causes a more severe clinical phenotype with increased mortality as compared to other mutations. To evaluate the functional role of the R270X mutation, we generated a transgenic mouse model expressing MeCP2(270_EGFP) (human mutation equivalent) by BAC recombineering. The expression pattern of MeCP2(270_EGFP) was similar to that of endogenous MeCP2. Strikingly, MeCP2(270_EGFP) localizes in the nucleus, contrary to the conjecture that R270X could cause disruption of the NLS. In primary hippocampal cells, we show that MeCP2(270_EGFP) was expressed in astrocytes by colocalization with the astrocyte-specific marker glial fibrillary acidic protein. Our data showing expression of MeCP2(270_EGFP) in transgenic mice astrocytes further reinforce the recent findings concerning the expression of MeCP2 in the glial cells.
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Affiliation(s)
- L A Kifayathullah
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
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25
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Böhm J, Buck A, Borozdin W, Mannan AU, Matysiak-Scholze U, Adham I, Schulz-Schaeffer W, Floss T, Wurst W, Kohlhase J, Barrionuevo F. Sall1, sall2, and sall4 are required for neural tube closure in mice. Am J Pathol 2008; 173:1455-63. [PMID: 18818376 DOI: 10.2353/ajpath.2008.071039] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Four homologs to the Drosophila homeotic gene spalt (sal) exist in both humans and mice (SALL1 to SALL4/Sall1 to Sall4, respectively). Mutations in both SALL1 and SALL4 result in the autosomal-dominant developmental disorders Townes-Brocks and Okihiro syndrome, respectively. In contrast, no human diseases have been associated with SALL2 to date, and Sall2-deficient mice have shown no apparent abnormal phenotype. We generated mice deficient in Sall2 and, contrary to previous reports, 11% of our Sall2-deficient mice showed background-specific neural tube defects, suggesting that Sall2 has a role in neurogenesis. To investigate whether Sall4 may compensate for the absence of Sall2, we generated compound Sall2 knockout/Sall4 genetrap mutant mice. In these mutants, the incidence of neural tube defects was significantly increased. Furthermore, we found a similar phenotype in compound Sall1/4 mutant mice, and in vitro studies showed that SALL1, SALL2, and SALL4 all co-localized in the nucleus. We therefore suggest a fundamental and redundant function of the Sall proteins in murine neurulation, with the heterozygous loss of a particular SALL protein also possibly compensated in humans during development.
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Affiliation(s)
- Johann Böhm
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Freiburg, Germany
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Shoukier M, Neesen J, Sauter SM, Argyriou L, Doerwald N, Pantakani DVK, Mannan AU. Expansion of mutation spectrum, determination of mutation cluster regions and predictive structural classification of SPAST mutations in hereditary spastic paraplegia. Eur J Hum Genet 2008; 17:187-94. [PMID: 18701882 DOI: 10.1038/ejhg.2008.147] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The SPAST gene encoding for spastin plays a central role in the genetically heterogeneous group of diseases termed hereditary spastic paraplegia (HSP). In this study, we attempted to expand and refine the genetic and phenotypic characteristics of SPAST associated HSP by examining a large cohort of HSP patients/families. Screening of 200 unrelated HSP cases for mutations in the SPAST gene led to detection of 57 mutations (28.5%), of which 47 were distinct and 29 were novel mutations. The distribution analysis of known SPAST mutations over the structural domains of spastin led to the identification of several regions where the mutations were clustered. Mainly, the clustering was observed in the AAA (ATPases associated with diverse cellular activities) domain; however, significant clustering was also observed in the MIT (microtubule interacting and trafficking), MTBD (microtubule-binding domain) and an N-terminal region (228-269 residues). Furthermore, we used a previously generated structural model of spastin as a framework to classify the missense mutations in the AAA domain from the HSP patients into different structural/functional groups. Our data also suggest a tentative genotype-phenotype correlation and indicate that the missense mutations could cause an earlier onset of the disease.
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Affiliation(s)
- Moneef Shoukier
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
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27
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Pantakani DVK, Swapna LS, Srinivasan N, Mannan AU. Spastin oligomerizes into a hexamer and the mutant spastin (E442Q) redistribute the wild-type spastin into filamentous microtubule. J Neurochem 2008; 106:613-24. [DOI: 10.1111/j.1471-4159.2008.05414.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Pantakani DVK, Zechner U, Arygriou L, Pauli S, Sauter SM, Mannan AU. Compound heterozygosity in the SPG4 gene causes hereditary spastic paraplegia. Clin Genet 2008; 73:268-72. [DOI: 10.1111/j.1399-0004.2007.00953.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Mannan AU, Krawen P, Sauter SM, Boehm J, Chronowska A, Paulus W, Neesen J, Engel W. ZFYVE27 (SPG33), a novel spastin-binding protein, is mutated in hereditary spastic paraplegia. Am J Hum Genet 2006; 79:351-7. [PMID: 16826525 PMCID: PMC1559503 DOI: 10.1086/504927] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [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: 01/16/2006] [Accepted: 04/05/2006] [Indexed: 01/14/2023] Open
Abstract
Spastin, the most commonly mutated protein in the autosomal dominant form of hereditary spastic paraplegia (AD-HSP) has been suggested to be involved in vesicular cargo trafficking; however, a comprehensive function of spastin has not yet been elucidated. To characterize the molecular function of spastin, we used the yeast two-hybrid approach to identify new interacting partners of spastin. Here, we report ZFYVE27, a novel member of the FYVE-finger family of proteins, as a specific spastin-binding protein, and we validate the interaction by both in vivo coimmunoprecipitation and colocalization experiments in mammalian cells. More importantly, we report a German family with AD-HSP in which ZFYVE27 (SPG33) is mutated; furthermore, we demonstrate that the mutated ZFYVE27 protein shows an aberrant intracellular pattern in its tubular structure and that its interaction with spastin is severely affected. We postulate that this specific mutation in ZFYVE27 affects neuronal intracellular trafficking in the corticospinal tract, which is consistent with the pathology of HSP.
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Affiliation(s)
- Ashraf U Mannan
- Institute of Human Genetics, University of Goettingen, Heinrich-Dueker Weg 12, D-37073, Goettingen, Germany.
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30
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Mannan AU, Boehm J, Sauter SM, Rauber A, Byrne PC, Neesen J, Engel W. Spastin, the most commonly mutated protein in hereditary spastic paraplegia interacts with Reticulon 1 an endoplasmic reticulum protein. Neurogenetics 2006; 7:93-103. [PMID: 16602018 DOI: 10.1007/s10048-006-0034-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [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: 12/05/2005] [Accepted: 02/14/2006] [Indexed: 12/11/2022]
Abstract
Spastin, an ATPase belonging to the AAA family of proteins is most commonly mutated in autosomal dominant hereditary spastic paraplegias (HSP). Spastin is a multifaceted protein with versatile role in cellular events, principally involved in microtubule dynamics. To gain further insight into the molecular function of spastin, we used the yeast two-hybrid approach to identify novel interacting partners of spastin. Using spastin as bait, we identified reticulon 1 (RTN1) and reticulon 3 (RTN3) as potential spastin interacting proteins. RTN1 and RTN3 belong to the reticulon (RTN) gene family, which are primarily expressed in the endoplasmic reticulum. Moreover, RTN1 is known to play a role in vesicular transport processes. Using in vitro and in vivo immunoprecipitation experiments, we were able to demonstrate that RTN1 interacts specifically with spastin. Intracellular distribution studies using immunostaining and overexpression of epitope-tagged protein revealed an obvious colocalization of spastin and RTN1 in discrete vesicles in the cytoplasm. Spastin mediates its interaction with RTN1 through its N-terminal region containing a microtubule-interacting and trafficking domain. It is interesting to note that the aberrant intracellular distribution of a truncated spastin protein was rescued by coexpression with RTN1, which highlights the physiological significance of this interaction. Our findings strengthen the hypothesis that disruption of intracellular vesicular transport processes could cause HSP. It is interesting to note that RTN1 is localized to 14q23.1 where SPG15 locus was mapped. Therefore, we considered RTN1 as a candidate gene for the SPG15 locus, but our mutational analysis possibly excludes RTN1 as causative gene.
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Affiliation(s)
- Ashraf U Mannan
- Institute of Human Genetics, University of Goettingen, Heinrich-Dueker-Weg 12, Goettingen 37073, Germany.
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Mannan AU, Roussa E, Kraus C, Rickmann M, Maenner J, Nayernia K, Krieglstein K, Reis A, Engel W. Mutation in the gene encoding lysosomal acid phosphatase (Acp2) causes cerebellum and skin malformation in mouse. Neurogenetics 2004; 5:229-38. [PMID: 15503243 DOI: 10.1007/s10048-004-0197-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [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: 09/03/2004] [Accepted: 09/27/2004] [Indexed: 10/26/2022]
Abstract
We report a novel spontaneous mutation named nax in mice, which exhibit delayed hair appearance and ataxia in a homozygote state. Histological analyses of nax brain revealed an overall impairment of the cerebellar cortex. The classical cortical cytoarchitecture was disrupted, the inner granule cell layer was not obvious, the Purkinje cells were not aligned as a Purkinje cell layer, and Bergmann glias did not span the molecular layer. Furthermore, histological analyses of skin showed that the hair follicles were also abnormal. We mapped the nax locus between marker D2Mit158 and D2Mit100 within a region of 800 kb in the middle of chromosome 2 and identified a missense mutation (Gly244Glu) in Acp2, a lysosomal monoesterase. The Glu244 mutation does not affect the stability of the Acp2 transcript, however it renders the enzyme inactive. Ultrastructural analysis of nax cerebellum showed lysosomal storage bodies in nucleated cells, suggesting progressive degeneration as the underlying mechanism. Identification of Acp2 as the gene mutated in nax mice provides a valuable model system for studying the role of Acp2 in cerebellum and skin homeostasis.
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Affiliation(s)
- Ashraf U Mannan
- Institute of Human Genetics, University of Goettingen, Heinrich-Dueker-Weg 12, 37073, Goettingen, Germany
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Abstract
The murine calgizzarin like gene (Cal) encodes for a calcium binding protein, which belongs to the S100 family of EF-hand proteins. It is specifically expressed in Sertoli cells in the testis and its expression is down-regulated by unknown factor(s) from spermatocytes/spermatids. In this paper, we show by transfection of a fusion protein of green fluorescent protein and Cal protein into NIH3T3 cells, that the expression of Cal is restricted only in the cytoplasm of the cell. A differentially regulated cytoplasmic expression of the Cal in Sertoli cells during mouse development suggests that Cal might play an important role during spermatogenesis. In order to elucidate the function of the Cal protein in the spermatogenesis, we disrupted the Cal locus in mouse by homologous recombination. In our knockout mouse, we deleted exon 2 and exon 3 of the Cal gene and replaced them with a neomycin cassette, which resulted in a complete loss of the Cal transcript. Male and female Cal4+/- and Cal4-/- mice from genetic backgrounds C57BL/6J x 129X1/SvJ hybrid and 129X1/SvJ inbred exhibited normal phenotype and were fertile. An intensive phenotypic analysis showed no gross abnormalities in testis morphology. The lack of the Cal protein also does not affect the parameters of sperm, as they are able to fertilize the oocytes in a competent manner, which is comparable to wild-type sperm. Collectively our results demonstrate that Cal is a nonessential protein and it does not play an important role in mouse spermatogenesis or in process of fertilization.
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Affiliation(s)
- Ashraf U Mannan
- Institute of Human Genetics, University of Goettingen, Heinrich-Dueker-Weg 12, Goettingen, Germany
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Mannan AU, Nayernia K, Mueller C, Burfeind P, Adham IM, Engel W. Male mice lacking the Theg (testicular haploid expressed gene) protein undergo normal spermatogenesis and are fertile. Biol Reprod 2003; 69:788-96. [PMID: 12748127 DOI: 10.1095/biolreprod.103.017400] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The testicular haploid expressed gene (Theg) encodes for a novel approximately 42.0-kDa nuclear protein, which is specifically expressed in spermatid cells. Its expression is upregulated by some unknown factor(s) from Sertoli cells. To elucidate the function of Theg protein and its role in spermatogenesis, we disrupted the Theg locus in mouse by homologous recombination. For functional dissection of the domain structure of the Theg protein, two different knockout approaches were undertaken. In the first knockout mouse (Th14), the C-terminal region of the Theg protein (amino acids 137-376) was deleted. Both Th14+/- and Th14-/- mice from genetic backgrounds of C57BL/6J x 129X1/SvJ hybrid and 129X1/SvJ inbred exhibited a normal phenotype and were fertile. The testes of Th14-/- mice were smaller than those of Th14+/- and Th14+/+ mice; however, the testicular morphology and the properties of sperm, including morphology and motility, from Th14-/- mice were similar to those of Th14+/- and Th14+/+ mice. These results demonstrate that the C-terminal region of Theg (amino acids 137-376) does not play an important role in progression of spermatogenesis. In the second knockout mouse (Th15), we deleted the N-terminal domain of the Theg protein, which resulted in complete loss of Theg transcripts. Both Th15+/- and Th15-/- mice from genetic backgrounds C57BL/6J x 129X1/SvJ hybrid, C3H/J congenic, and 129X1/SvJ inbred appeared normal and were fertile, with no gross abnormalities detected in testicular morphology or sperm properties. Our results from both knockout mouse model systems clearly illustrate that Theg is not essential for spermatogenesis in the mouse.
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Affiliation(s)
- Ashraf U Mannan
- Institute of Human Genetics, University of Goettingen, 37073 Goettingen, Germany
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