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Roychowdhury S, Joshi D, Singh VK, Faruq M, Das P. Genetic and in silico analysis of Indian sporadic young onset patient with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:589-599. [PMID: 38450645 DOI: 10.1080/21678421.2024.2324896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is an old onset devastating neurodegenerative disorder. Young-onset ALS cases especially sporadic ones who are between 25 and 45 years are rarely affected by the disease. Despite the identification of numerous candidate genes associated with ALS, the etiology of the disease remains elusive due to extreme genetic and phenotypic variability. The advent of affordable whole exome sequencing (WES) has opened new avenues for unraveling the disease's pathophysiology better. METHODS AND RESULTS We aimed to determine the genetic basis of an Indian-origin, young onset sporadic ALS patient with very rapid deterioration of the disease course without any cognitive decline who was screened for mutations in major ALS candidate genes by WES. Variants detected were reconfirmed by Sanger sequencing. The clinicopathological features were investigated and two heterozygous missense variants were identified: R452W, not previously associated with ALS, present in one of the four conserved C terminal domains in ANXA11 and R208W in SIGMAR1, respectively. Both of these variants were predicted to be damaging by pathogenicity prediction tools and various in silico methods. CONCLUSION Our study revealed two potentially pathogenic variants in two ALS candidate genes. The genetic makeup of ALS patients from India has been the subject of a few prior studies, but none of them examined ANXA11 and SIGMAR1 genes so far. These results establish the framework for additional research into the pathogenic processes behind these variations that result in sporadic ALS disease and further our understanding of the genetic makeup of Indian ALS patients.
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Affiliation(s)
- Saileyee Roychowdhury
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vinay Kumar Singh
- School of Biotechnology, Centre for Bioinformatics, Institute of Science, Banaras Hindu University, Varanasi, India, and
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, India
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De T, Sharma P, Upilli B, Vivekanand A, Bari S, Sonakar AK, Srivastava AK, Faruq M. Spinocerebellar ataxia type 27B (SCA27B) in India: insights from a large cohort study suggest ancient origin. Neurogenetics 2024:10.1007/s10048-024-00770-y. [PMID: 38976084 DOI: 10.1007/s10048-024-00770-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND The ethnic diversity of India provides a unique opportunity to study the history of the origin of mutations of genetic disorders. Spinocerebellar ataxia type 27B (SCA27B), a recently identified dominantly inherited cerebellar disorder is caused by GAA-repeat expansions in intron 1 of Fibroblast Growth Factor 14 (FGF14). Predominantly reported in the European population, we aimed to screen this mutation and study the founder haplotype of SCA27B in Indian ataxia patients. METHODS We have undertaken screening of GAA repeats in a large Indian cohort of ~ 1400 uncharacterised ataxia patients and kindreds and long-read sequencing-based GAA repeat length assessment. High throughput genotyping-based haplotype analysis was also performed. We utilized ~ 1000 Indian genomes to study the GAA at-risk expansion alleles. FINDINGS We report a high frequency of 1.83% (n = 23) of SCA27B in the uncharacterized Indian ataxia cohort. We observed several biallelic GAA expansion mutations (n = 5) with younger disease onset. We observed a risk haplotype (AATCCGTGG) flanking the FGF14-GAA locus over a 74 kb region in linkage disequilibrium. We further studied the frequency of this risk haplotype across diverse geographical population groups. The highest prevalence of the risk haplotype was observed in the European population (29.9%) followed by Indians (21.5%). The observed risk haplotype has existed through ~ 1100 generations (~ 22,000 years), assuming a correlated genealogy. INTERPRETATION This study provides valuable insights into SCA27B and its Upper Paleolithic origin in the Indian subcontinent. The high occurrence of biallelic expansion is probably relevant to the endogamous nature of the Indian population.
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Affiliation(s)
- Tiyasha De
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
| | - Pooja Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Bharathram Upilli
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - A Vivekanand
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Shreya Bari
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
| | - Akhilesh Kumar Sonakar
- Neurology Department, Neuroscience Centre, All India Institute of Medical Sciences, Ansari Nagar, 110029, India
| | - Achal Kumar Srivastava
- Neurology Department, Neuroscience Centre, All India Institute of Medical Sciences, Ansari Nagar, 110029, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India.
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Suroliya V, Uppili B, Kumar M, Jha V, Srivastava AK, Faruq M. Identifying unstable CNG repeat loci in the human genome: a heuristic approach and implications for neurological disorders. Hum Genome Var 2024; 11:25. [PMID: 38871700 DOI: 10.1038/s41439-024-00281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
Tandem nucleotide repeat (TNR) expansions, particularly the CNG nucleotide configuration, are associated with a variety of neurodegenerative disorders. In this study, we aimed to identify novel unstable CNG repeat loci associated with the neurogenetic disorder spinocerebellar ataxia (SCA). Using a computational approach, 15,069 CNG repeat loci in the coding and noncoding regions of the human genome were identified. Based on the feature selection criteria (repeat length >10 and functional location of repeats), we selected 52 repeats for further analysis and evaluated the repeat length variability in 100 control subjects. A subset of 19 CNG loci observed to be highly variable in control subjects was selected for subsequent analysis in 100 individuals with SCA. The genes with these highly variable repeats also exhibited higher gene expression levels in the brain according to the tissue expression dataset (GTEx). No pathogenic expansion events were identified in patient samples, which is a limitation given the size of the patient group examined; however, these loci contain potential risk alleles for expandability. Recent studies have implicated GLS, RAI1, GIPC1, MED15, EP400, MEF2A, and CNKSR2 in neurological diseases, with GLS, GIPC1, MED15, RAI1, and MEF2A sharing the same repeat loci reported in this study. This finding validates the approach of evaluating repeat loci in different populations and their possible implications for human pathologies.
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Affiliation(s)
- Varun Suroliya
- Department of Neurology, All India Institute of Medical Sciences, Ansari Nagar, Delhi, 110020, India
| | - Bharathram Uppili
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy for Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Manish Kumar
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy for Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Vineet Jha
- Persistent LABS, Persistent Systems Ltd., Pune, Maharashtra, India
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, Ansari Nagar, Delhi, 110020, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
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Kumar M, Sahni S, A V, Kumar D, Kushwah N, Goel D, Kapoor H, Srivastava AK, Faruq M. Molecular clues unveiling spinocerebellar ataxia type-12 pathogenesis. iScience 2024; 27:109768. [PMID: 38711441 PMCID: PMC11070597 DOI: 10.1016/j.isci.2024.109768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/31/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Spinocerebellar Ataxia type-12 (SCA12) is a neurodegenerative disease caused by tandem CAG repeat expansion in the 5'-UTR/non-coding region of PPP2R2B. Molecular pathology of SCA12 has not been studied in the context of CAG repeats, and no appropriate models exist. We found in human SCA12-iPSC-derived neuronal lineage that expanded CAG in PPP2R2B transcript forms nuclear RNA foci and were found to sequester variety of proteins. Further, the ectopic expression of transcript containing varying length of CAG repeats exhibits non-canonical repeat-associated non-AUG (RAN) translation in multiple frames in HEK293T cells, which was further validated in patient-derived neural stem cells using specific antibodies. mRNA sequencing of the SCA12 and control neurons have shown a network of crucial transcription factors affecting neural fate, in addition to alteration of various signaling pathways involved in neurodevelopment. Altogether, this study identifies the molecular signatures of SCA12 disorder using patient-derived neuronal cell lines.
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Affiliation(s)
- Manish Kumar
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR -IGIB), Mall Road, Delhi 110007, India
- CSIR-HRDC Campus, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shweta Sahni
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR -IGIB), Mall Road, Delhi 110007, India
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vivekanand A
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR -IGIB), Mall Road, Delhi 110007, India
- CSIR-HRDC Campus, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Deepak Kumar
- Division of Genomics and Molecular Medicine, CSIR - Institute of Genomics and Integrative Biology (IGIB), New Delhi 110007, India
- Department of Zoology, University of Allahabad, Prayagraj, Uttar Pradesh 211002, India
| | - Neetu Kushwah
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR -IGIB), Mall Road, Delhi 110007, India
| | - Divya Goel
- Department of Pharmacology, School of Pharmaceutical Education & Research (SPER), Jamia Hamdard, New Delhi 110062, India
| | - Himanshi Kapoor
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR -IGIB), Mall Road, Delhi 110007, India
| | - Achal K. Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR -IGIB), Mall Road, Delhi 110007, India
- CSIR-HRDC Campus, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
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Zahra S, Kapoor H, Ahmad I, Kamai A, Srivastava AK, Faruq M. Generation of an Induced pluripotent stem cell (iPSC) line (IGIBi011-A) from a Spinocerebellar ataxia type 12 gait dominant patient. Stem Cell Res 2024; 76:103319. [PMID: 38340452 DOI: 10.1016/j.scr.2024.103319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/30/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The PPP2R2B gene, expressed highly in the brain, harbours trinucleotide CAG repeats in the 5'UTR region, in the range of 7-42 repeats. Individuals carrying CAG repeats greater than 43 have been associated to manifest a neurodegenerative disease condition termed as Spinocerebellar Ataxia type 12 (SCA12). An iPSC line from an adult male diagnosed with SCA12 presenting symptoms of gait (Gait Dominance) was generated. It showed pluripotency and trilineage markers without any chromosomal abnormality. This line can be utilized as an essential resource in enhancing our understanding of the molecular pathogenic mechanisms underlying SCA12 by facilitating generation of various neuronal cell types.
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Affiliation(s)
- Sana Zahra
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Himanshi Kapoor
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi 110007, India
| | - Istaq Ahmad
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi 110007, India; Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Asangla Kamai
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Achal Kumar Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Division of Investigations of Human Pathology by Application Genomics and Stem Cells (iHPSCs-AG).
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Tyagi N, Uppili B, Sharma P, Parveen S, Saifi S, Jain A, Sonakar A, Ahmed I, Sahni S, Shamim U, Anand A, Suroliya V, Asokachandran V, Srivastava A, Sivasubbu S, Scaria V, Faruq M. Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort. Neurogenetics 2024; 25:13-25. [PMID: 37917284 DOI: 10.1007/s10048-023-00736-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
An intronic bi-allelic pentanucleotide repeat expansion mutation, (AAGGG)400-2000, at AAAAG repeat locus in RFC1 gene, is known as underlying genetic cause in cases with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and late-onset sporadic ataxia. Biallelic positive cases carry a common recessive risk haplotype, "AAGA," spanning RFC1 gene. In this study, our aim is to find prevalence of bi-allelic (AAGGG)exp in Indian ataxia and other neurological disorders and investigate the complexity of RFC1 repeat locus and its potential association with neurodegenerative diseases in Indian population-based cohorts. We carried out repeat number and repeat type estimation using flanking PCR and repeat primed PCR (AAAAG/AAAGG/AAGGG) in four Indian disease cohorts and healthy controls. Haplotype assessment of suspected cases was done by genotyping and confirmed by Sanger sequencing. Blood samples and consent of all the cases and detailed clinical details of positive cases were collected in collaboration with A.I.I.M.S. Furthermore, comprehension of RFC1 repeat locus and risk haplotype analysis in Indian background was performed on the NGS data of Indian healthy controls by ExpansionHunter, ExpansionHunter Denovo, and PHASE analysis, respectively. Genetic screening of RFC1-TNR locus in 1998 uncharacterized cases (SCA12: 87; uncharacterized ataxia: 1818, CMT: 93) and 564 heterogenous controls showed that the frequency of subjects with bi-allelic (AAGGG)exp are 1.15%, < 0.05%, 2.15%, and 0% respectively. Two RFC1 positive sporadic late-onset ataxia cases, one bi-allelic (AAGGG)exp and another, (AAAGG)~700/(AAGGG)exp, had recessive risk haplotype and CANVAS symptoms. Long normal alleles, 15-27, are significantly rare in ataxia cohort. In IndiGen control population (IndiGen; N = 1029), long normal repeat range, 15-27, is significantly associated with A3G3 and some rare repeat motifs, AGAGG, AACGG, AAGAG, and AAGGC. Risk-associated "AAGA" haplotype of the original pathogenic expansion of A2G3 was found associated with the A3G3 representing alleles in background population. Apart from bi-allelic (AAGGG)exp, we report cases with a new pathogenic expansion of (AAAGG)exp/(AAGGG)exp in RFC1 and recessive risk haplotype. We found different repeat motifs at RFC1 TNR locus, like AAAAG, AAAGG, AAAGGG, AAAAGG, AAGAG, AACGG, AAGGC, AGAGG, and AAGGG, in Indian background population except ACAGG and (AAAGG)n/(AAGGG)n. Our findings will help in further understanding the role of long normal repeat size and different repeat motifs, specifically AAAGG, AAAGGG, and other rare repeat motifs, at the RFC1 locus.
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Affiliation(s)
- Nishu Tyagi
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bharathram Uppili
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Sharma
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shaista Parveen
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Sheeba Saifi
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Abhinav Jain
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akhilesh Sonakar
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Istaq Ahmed
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Shweta Sahni
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Uzma Shamim
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Avni Anand
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Varun Suroliya
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Vivekanand Asokachandran
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Achal Srivastava
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Vinod Scaria
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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