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Saini M, Upadhyay N, Dhiman K, Manjhi SK, Kattuparambil AA, Ghoshal A, Arya R, Dey SK, Sharma A, Aduri R, Thelma BK, Ashish F, Kundu S. ARL15, a GTPase implicated in rheumatoid arthritis, potentially repositions its truncated N-terminus as a function of guanine nucleotide binding. Int J Biol Macromol 2024; 254:127898. [PMID: 37939768 DOI: 10.1016/j.ijbiomac.2023.127898] [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: 04/21/2023] [Revised: 10/21/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
The ADP ribosylation factor like protein 15 (ARL15) gene encodes for an uncharacterized GTPase associated with rheumatoid arthritis (RA) and other metabolic disorders. Investigation of the structural and functional attributes of ARL15 is important to position the protein as a potential drug target. Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. The equilibrium dissociation constant (Kd) of GTP binding with ARL15 was estimated to be about eight-fold higher than that of GDP. Small Angle X-ray Scattering (SAXS) data indicated that in solution, the apo state of monomeric ARL15 adopts a shape characterized by a globe of maximum linear dimension (Dmax) of 6.1 nm, and upon binding to GTP or GDP, the vector distribution profile changes to peak-n-tail shoulder with Dmax extended to 7.6 and 7.7 nm, respectively. Structure restoration using a sequence-based template and experimental SAXS data provided the first visual insight revealing that the folded N-terminal in the unbound state of the protein may toggle open upon binding to guanine nucleotides. The conformational dynamics observed in the N-terminal region offer a scope to develop drugs that target this unique GTPase, potentially providing treatments for a range of metabolic disorders.
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Affiliation(s)
- Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Neelam Upadhyay
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Kanika Dhiman
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Satish Kumar Manjhi
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - Aman Achutan Kattuparambil
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - Antara Ghoshal
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Sanjay Kumar Dey
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Raviprasad Aduri
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Fnu Ashish
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India.
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Pandey S, Dinesh S, Rawat CS, Thelma BK. The Spectrum of Non-Parkinsonian Tremor: A Registry at a Tertiary Care Teaching Institute. Tremor Other Hyperkinet Mov (N Y) 2023; 13:48. [PMID: 38145280 PMCID: PMC10742104 DOI: 10.5334/tohm.828] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/09/2023] [Indexed: 12/26/2023] Open
Abstract
Background Tremors other than those associated with Parkinson's disease (non-parkinsonian tremor) are commonly observed in clinical settings. However, their frequency and clinical characteristics have rarely been reported. Objectives To classify non-parkinsonian tremors based on the consensus statement on the classification of tremors, from the task force of the International Parkinson and Movement Disorder Society published in 2018. Methods A prospective registry at a tertiary care teaching institute. Results A total of 475 patients with non-parkinsonian tremors were recruited for the study. 67.57% (n = 321) of our patients were male and a family history of tremor was present in 20.84% (n = 99) of patients. Dystonic tremor (DT) was the most common non-parkinsonian tremor (33.26%). 27.78% of patients fulfilled the new classification criteria for essential tremor, with 13.47% classified as pure ET (ET) and 14.31% exhibiting neurological soft signs, leading to the classification of ET plus (ETP). Patients with ETP had more family history (57.35%) [vs DT (26.48%, p = 0.00004) and ET (10.93%, p = 0.00003], longer duration of disease [mean ± standard deviation (SD) = 9.53 ± 8.64 years] [vs DT (5.60 ± 5.93, p = 0.0003) and ET (6.38 ± 5.97, p = 0.01) years], and more severe tremor as measured by the essential tremor rating assessment scale total score [mean ± SD = 27.42 ± 11.70] [vs DT (23.50 ± 8.62, p = 0.007) and ET (22.12 ± 8.19, p = 0.007)] compared with patients with DT and ET. Conclusions DT was the most common cause of non-parkinsonian tremor in our registry followed by essential tremor syndrome. ETP was more common than ET.
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Affiliation(s)
- Sanjay Pandey
- Department of Neurology, Govind Ballabh Pant Institute of Postgraduate medical education and Research, New Delhi, India
- Department of Neurology and Stroke Medicine, Amrita Hospital, Mata Amritanandamayi Marg Sector 88, Faridabad, Delhi National Capital Region, India
| | - Shreya Dinesh
- Department of Neurology, Govind Ballabh Pant Institute of Postgraduate medical education and Research, New Delhi, India
- Department of Microbiology and Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Chandra Shekhar Rawat
- Department of Neurology, Govind Ballabh Pant Institute of Postgraduate medical education and Research, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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Mukhopadhyay A, Deshpande SN, Bhatia T, Thelma BK. Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case-control association study. Eur Arch Psychiatry Clin Neurosci 2023; 273:1677-1691. [PMID: 37009928 DOI: 10.1007/s00406-023-01596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Genetic etiology of schizophrenia is poorly understood despite large genome-wide association data. Long non-coding RNAs (lncRNAs) with a probable regulatory role are emerging as important players in neuro-psychiatric disorders including schizophrenia. Prioritising important lncRNAs and analyses of their holistic interaction with their target genes may provide insights into disease biology/etiology. Of the 3843 lncRNA SNPs reported in schizophrenia GWASs extracted using lincSNP 2.0, we prioritised n = 247 based on association strength, minor allele frequency and regulatory potential and mapped them to lncRNAs. lncRNAs were then prioritised based on their expression in brain using lncRBase, epigenetic role using 3D SNP and functional relevance to schizophrenia etiology. 18 SNPs were finally tested for association with schizophrenia (n = 930) and its endophenotypes-tardive dyskinesia (n = 176) and cognition (n = 565) using a case-control approach. Associated SNPs were characterised by ChIP seq, eQTL, and transcription factor binding site (TFBS) data using FeatSNP. Of the eight SNPs significantly associated, rs2072806 in lncRNA hsaLB_IO39983 with regulatory effect on BTN3A2 was associated with schizophrenia (p = 0.006); rs2710323 in hsaLB_IO_2331 with role in dysregulation of ITIH1 with tardive dyskinesia (p < 0.05); and four SNPs with significant cognition score reduction (p < 0.05) in cases. Two of these with two additional variants in eQTL were observed among controls (p < 0.05), acting likely as enhancer SNPs and/or altering TFBS of eQTL mapped downstream genes. This study highlights important lncRNAs in schizophrenia and provides a proof of concept of novel interactions of lncRNAs with protein-coding genes to elicit alterations in immune/inflammatory pathways of schizophrenia.
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Affiliation(s)
- Anirban Mukhopadhyay
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Smita N Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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Punchaichira TJ, Kukshal P, Bhatia T, Deshpande SN, Thelma BK. Effect of rs1108580 of DBH and rs1006737 of CACNA1C on Cognition and Tardive Dyskinesia in a North Indian Schizophrenia Cohort. Mol Neurobiol 2023; 60:6826-6839. [PMID: 37493923 DOI: 10.1007/s12035-023-03496-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Genetic perturbations in dopamine neurotransmission and calcium signaling pathways are implicated in the etiology of schizophrenia. We aimed to test the association of a functional splice variant each in Dopamine β-Hydroxylase (DBH; rs1108580) and Calcium voltage-gated channel subunit alpha1 C (CACNA1C; rs1006737) genes in these pathways with schizophrenia (506 cases, 443 controls); Abnormal Involuntary Movement Scale (AIMS) scores in subjects assessed for tardive dyskinesia (76 TD-positive, 95 TD-negative) and Penn Computerized Neurocognitive Battery (PennCNB) scores (334 cases, 234 controls). The effect of smoking status and SNP genotypes on AIMS scores were assessed using ANOVA; health status and SNP genotypes on three performance functions of PennCNB cognitive domains were assessed by ANCOVA with age and sex as covariates. Association with Positive and Negative Syndrome Scale (PANSS) scores in the TD cohort and cognitive scores in healthy controls of the cognition cohort were tested by linear regression. None of the markers were associated with schizophrenia. Smoking status [F(2, 139) = 10.6; p = 5 × 10-5], rs1006737 [F(2, 139) = 7.1; p = 0.001], TD status*smoking [F(2, 139) = 8.0; p = 5.0 × 10-4] and smoking status*rs1006737 [F(4, 139) = 2.7; p = 0.03] had an effect on AIMS score. Furthermore, rs1006737 was associated with orofacial [F(2, 139) = 4.6; p = 0.01] and limb-truncal TD [(F(2, 139) = 3.8; p = 0.02]. Main effect of rs1108580 on working memoryprocessing speed [F(2, 544) = 3.8; p = 0.03] and rs1006737 on spatial abilityefficiency [F(1, 550) = 9.4; p = 0.02] was identified. Health status*rs1006737 interaction had an effect on spatial memoryprocessing speed [F(1, 550) = 6.9; p = 0.01]. Allelic/genotypic association (p = 0.01/0.03) of rs1006737 with disorganized/concrete factor and allelic association of rs1108580 (p = 0.04) with a depressive factor of PANSS was observed in the TD-negative subcohort. Allelic association of rs1006737 with sensorimotor dexterityaccuracy (p = 0.03), attentionefficiency (p = 0.05), and spatial abilityefficiency (p = 0.02); allelic association of rs1108580 with face memoryaccuracy (p = 0.05) and emotionefficiency (p = 0.05); and allelic/genotypic association with emotionaccuracy (p = 0.003/0.009) were observed in healthy controls of the cognition cohort. These association findings may have direct implications for personalized medicine and cognitive remediation.
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Affiliation(s)
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
- Sri Sathya Sai Sanjeevani International Centre for Child Heart Care & Research, Palwal, Haryana, 121102, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, Baba Kharak Singh Marg, Connaught Place, New Delhi, 110001, India
| | - Smita Neelkanth Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, Baba Kharak Singh Marg, Connaught Place, New Delhi, 110001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Sandhu G, Agrawal P, Bose S, Thelma BK. Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis. J Biomol Struct Dyn 2023:1-19. [PMID: 37378542 DOI: 10.1080/07391102.2023.2229449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
Standard force field-based simulations to accomplish structure-based evaluations of lead molecules is a powerful tool. Combining protein fragmentation into tractable sub-systems with continuum solvation method is envisaged to enable quantum mechanics-based electronic structure calculations of macromolecules in their realistic environment. This along with incorporation of many-body polarization effect in molecular dynamics simulations may augment an accurate description of electrostatics of protein-inhibitor systems for effective drug design. Rheumatoid arthritis (RA) is a complex autoimmune disorder plagued by the ceiling effect of current targeted therapies, encouraging identification of new druggable targets and corresponding drug design to tackle the refractory form of disease. In this study, polarization-inclusive force field approach has been used to model protein solvation and ligand binding for 'Mitogen-activated protein kinase' (MAP3K8), a regulatory node of notable pharmacological relevance in RA synovial biology. For MAP3K8 inhibitors belonging to different scaffold series, the calculations illustrated differential electrostatic contribution to their relative binding affinities and successfully explained examples from available structure-activity relationship studies. Results from this study exemplified i) the advantage of this approach in reliably ranking inhibitors having close nanomolar range activities for the same target; and ii) its prospective application in lead molecule identification aiding drug discovery efforts in RA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurvisha Sandhu
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
| | - Praveen Agrawal
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - Surojit Bose
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
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Yadav N, Thelma BK. Deletion induced splicing in RIC3 drives nicotinic acetylcholine receptor regulation with implications for endoplasmic reticulum stress in human astrocytes. Glia 2023; 71:1217-1232. [PMID: 36602087 DOI: 10.1002/glia.24333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/25/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023]
Abstract
Nicotinic acetylcholine receptor (nAChR) dysregulation in astrocytes is reported in neurodegenerative disorders. Modulation of nAChRs through agonists confers protection to astrocytes from stress but regulation of chaperones involved in proteostasis with pathological implications is unclear. Resistance to inhibitors of cholinesterase 3 (RIC3), a potential chaperone of nAChRs is poorly studied in humans. We characterized RIC3 in astrocytes derived from an isogenic wild-type and Cas9 edited "del" human iPSC line harboring a 25 bp homozygous deletion in exon2. Altered RIC3 transcript ratio due to deletion induced splicing and an unexpected gain of α7nAChR expression were observed in "del" astrocytes. Transcriptome analysis showed higher expression of neurotransmitter/G-protein coupled receptors mediated by cAMP and calcium/calmodulin-dependent kinase signaling with increased cytokines/glutamate secretion. Functional implications examined using tunicamycin induced ER stress in wild-type astrocyte stress model showed cell cycle arrest, RIC3 upregulation, reduction in α7nAChR membrane levels but increased α4nAChR membrane expression. Conversely, tunicamycin-treated "del" astrocytes showed a comparatively higher α4nAChR membrane expression and upsurged cAMP signaling. Furthermore, reduced expression of stress markers CHOP, phospho-PERK and lowered XBP1 splicing in western blot and qPCR, validated by proteome-based pathway analysis indicated lowered disease severity. Findings indicate (i) a complex RNA regulatory mechanism via exonic deletion induced splicing; (ii) RIC-3 as a disordered protein having contrasting effects on co-expressed nAChR subtypes under basal/stress conditions; and (iii) RIC3 as a potential drug target against ER stress in astrocytes for neurodegenerative/nicotine-related brain disorders. Cellular rescue mechanism through deletion induced exon skipping may encourage ASO-based therapies for tauopathies.
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Affiliation(s)
- Navneesh Yadav
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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Sharma N, Banerjee P, Sood A, Midha V, Thelma BK, Senapati S. Celiac disease-associated loci show considerable genetic overlap with neuropsychiatric diseases but with limited transethnic applicability. J Genet 2023; 102. [PMID: 36814110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Clinical and public health research has revealed the co-occurrence of several neuropsychiatric diseases among patients with celiac disease (CD). The significant presence of CD-specific autoantibodies in patients with neuropsychiatric diseases and vice versa are often reported. To explain the genetic basis of such frequent disease co-occurrence and investigate the underlying common pathways/processes, we performed an extensive cross-disease association study followed by supporting in silico functional validation of the leads. Genomewide association study (GWAS) data for CD and eight commonly co-occurring neuropsychiatric diseases from Caucasian populations were analysed, and the shared loci were determined.We performed Immunochip-based fine mapping of these overlapping association signals in an independent European CD data and tested their cross-ethnic transferability using CD association data from the genetically distinct north Indian population. This study identified 12 shared loci between the two diseases with genomewide significance (P = 5e-8). Of these five loci, namely NFIA, KIA1109, NOTCH4-TSBP1-PBX2, HLA-DQA1 and CSK replicated in an independent Dutch cohort representing European ancestry. Three of these loci, namely NFIA, NOTCH4-TSBP1-PBX2 and HLA-DQA1 that are common between CD, anxiety, migraine and schizophrenia respectively withstood locus transferability test in north Indians. Tissue-specific eQTL analysis of SNPs from transferable loci revealed expression QTL effects in brain tissue besides the small intestine and whole blood. Pathway analysis and evidence of epigenetic regulation highlighted the potential contribution of these SNPs to disease pathology. The replicable and transferable association of genetic variants from MHC locus and their functional implications suggest the process of antigen presentation and adaptive/innate immune response regulated by non-HLA genes in the locus may dominate the shared pathogenesis of CD and neuropsychiatric diseases. Functional validation of the shared candidate genes is warranted to unravel the molecular mechanism for the co-occurrence of CD and specific neuropsychiatric diseases.
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Affiliation(s)
- Nidhi Sharma
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda 151 401, India.
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Bhattacharyya U, Deswal P, Polipalli SK, Sharma D, Kaur M, Kapoor S, Thelma BK. Mutation spectrum and enzyme profiling of G6PD deficiency in neonates of north India: a prospective study. J Genet 2023; 102:40. [PMID: 37674284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common X-linked disorder with well-established clinical and allelic heterogeneity and ethnic disparity. With ~390,000 annual births with G6PD deficiency in India, it emerges as the most predictable and preventable inbornmetabolic error. Disease prevalence and mutation spectrum have been reasonably reported fromcentral, western and southern parts of India and are mostly retrospective studies.Although prevalence data fromnorth India is available, there is paucity of data on the mutation spectrum and genotype-phenotype correlation (GxP). Thus, we aimed at establishing the clinical and mutation profiles for G6PD, as a part of a large prospective newborn screening study conducted between 2014 and 2016 across hospitals in Delhi, India. G6PD activity levels were measured at 24-48 h of life for ~200,000 neonates using Victor 2D and/or Genomic Screening Processor followed by confirmatory spectrophotometric analysis usingRBClysates of the respective neonates based on clinical symptoms.Asubset of 570 enzyme deficient neonates were screened formutations by polymerase chain reaction-restriction fragment length polymorphismand/or Sanger sequencing.Mediterraneanwas the most common mutation (n=318; 55.8%) with the lowest enzyme activity and most severe phenotype, followed by G6PD Orissa (n=187;32.8%); Kerala-Kalyan (n=25); Jammu (n=24);Mahidol (n=14); Chattam(n=1) andNilgiri/Coimbra (n=1).Of the 163 intramural neonates followed up, 68 developed clinical jaundice. However, no correlation was observed between jaundice and enzyme level. Notable outcome of this first ever prospective screening approach for G6PD deficiency in neonates may help in prediction of disease severity and appropriate timely management.
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Affiliation(s)
- Upasana Bhattacharyya
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021,
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Juyal G, Pandey A, Garcia SL, Negi S, Gupta R, Kumar U, Bhat B, Juyal RC, Thelma BK. Stratification of rheumatoid arthritis cohort using Ayurveda based deep phenotyping approach identifies novel genes in a GWAS. J Ayurveda Integr Med 2022; 13:100578. [PMID: 35793592 PMCID: PMC9259475 DOI: 10.1016/j.jaim.2022.100578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Background and aim Genome wide association studies have scaled up both in terms of sample size and range of complex disorders investigated, but these have explained relatively little phenotypic variance. Of the several reasons, phenotypic heterogeneity seems to be a likely contributor for missing out genetic associations of large effects. Ayurveda, the traditional Indian system of medicine is one such tool which adopts a holistic deep phenotyping approach and classifies individuals based on their body constitution/prakriti. We hypothesized that Ayurveda based phenotypic stratification of healthy and diseased individuals will allow us to achieve much desired homogeneous cohorts which would facilitate detection of genetic association of large effects. In this proof of concept study, we performed a genome wide association testing of clinically diagnosed rheumatoid arthritis patients and healthy controls, who were re-phenotyped into Vata, Pitta and Kapha predominant prakriti sub-groups. Experimental procedure Genotypes of rheumatoid arthritis cases (Vata = 49; Pitta = 117; Kapha = 78) and controls (Vata = 33; Pitta = 175; Kapha = 85) were retrieved from the total genotype data, used in a recent genome-wide association study performed in our laboratory. A total of 528461 SNPs were included after quality control. Prakriti-wise genome-wide association analysis was employed. Results and conclusion This study identified (i) prakriti-specific novel disease risk genes of high effect sizes; (ii) putative candidates of novel therapeutic potential; and (iii) a good correlation between genetic findings and clinical knowledge in Ayurveda. Adopting Ayurveda based deep phenotyping may facilitate explaining hitherto undiscovered heritability in complex traits and may propel much needed progress in personalized medicine.
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Affiliation(s)
- Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Anuj Pandey
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Sara L Garcia
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sapna Negi
- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India
| | - Ramneek Gupta
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Bheema Bhat
- Department of Ayurveda, Holy Family Hospital, New Delhi 110025, India
| | - Ramesh C Juyal
- National Institute of Immunology, New Delhi 110067, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India.
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Bhattacharyya U, Bhatia T, Deshpande SN, Thelma BK. Association of g-quadruplex variants with schizophrenia symptoms. Schizophr Res 2022; 243:361-363. [PMID: 34187734 PMCID: PMC10132944 DOI: 10.1016/j.schres.2021.06.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023]
Affiliation(s)
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi, India
| | | | - B K Thelma
- University of Delhi South Campus, New Delhi, India.
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Bhattacharyya U, Deshpande SN, Bhatia T, Thelma BK. Revisiting Schizophrenia from an Evolutionary Perspective: An Association Study of Recent Evolutionary Markers and Schizophrenia. Schizophr Bull 2021; 47:827-836. [PMID: 33350444 PMCID: PMC8759809 DOI: 10.1093/schbul/sbaa179] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The persistence of schizophrenia in human populations at a high prevalence and with a large heritability estimate despite reduced fertility and increased mortality rate is a Darwinian paradox. This may be likely if the genomic components that predispose to schizophrenia are also advantageous for the acquisition of important human traits, such as language and cognition. Accordingly, an emerging group of genomic markers of recent evolution in humans, namely human accelerated regions (HARs), since our divergence from chimpanzees, are gaining importance for neurodevelopmental disorders, such as schizophrenia. We hypothesize that variants within HARs may affect the expression of genes under their control, thus contributing to disease etiology. A total of 49 HAR single nucleotide polymorphisms (SNPs) were prioritized from the complete repertoire of HARs (n = 2737) based on their functional relevance and prevalence in the South Asian population. Test of association using 2 independent schizophrenia case-control cohorts of north Indian ethnicity (discovery: n = 930; replication: n = 1104) revealed 3 SNPs (rs3800926, rs3801844, and rs764453) from chromosome 7 and rs77047799 from chromosome 3 to be significantly associated (combined analysis: Bonferroni corrected P < .002-.000004). Of note, these SNPs were found to alter the expression of neurodevelopmental genes such as SLC25A13, MAD1L1, and ULK4; a few from the HOX gene family; and a few genes that are implicated in mitochondrial function. These SNPs may most likely alter binding sites of transcription factors, including TFCP2, MAFK, SREBF2, E2F1, and/or methylation signatures around these genes. These findings reiterate a neurodevelopmental basis of schizophrenia and also open up a promising avenue to investigate HAR-mediated mitochondrial dysfunction in schizophrenia etiology.
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Affiliation(s)
| | | | | | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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12
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Kumar S, Abbas MM, Govindappa ST, Muthane UB, Behari M, Pandey S, Juyal RC, Thelma BK. Compound heterozygous variants in Wiskott-Aldrich syndrome like (WASL) gene segregating in a family with early onset Parkinson's disease. Parkinsonism Relat Disord 2021; 84:61-67. [PMID: 33571872 DOI: 10.1016/j.parkreldis.2021.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Knowledge of genetic determinants in Parkinson's disease is still limited. Familial forms of the disease continue to provide a rich resource to capture the genetic spectrum in disease pathogenesis, and this approach is exploited in this study. METHODS Informative members from a three-generation family of Indian ethnicity manifesting a likely autosomal recessive mode of inheritance of Parkinson's disease were used for whole exome sequencing. Variant data analysis and in vitro functional characterisation of variant(s) segregating with the phenotype were carried out in HEK-293 and SH-SY5Y cells using gene constructs of interest. RESULTS Two compound heterozygous variants, a rare missense (c.1139C > T:p.P380L) and a novel splice variant (c.1456 + 2 delTAGA, intron10) in Wiskott-Aldrich syndrome like gene (WASL, 7q31), both predicted to be deleterious were shared among the proband and two affected siblings. WASL, a gene not previously linked to a human Mendelian disorder is known to regulate actin polymerisation via Arp2/3 complex. Based on exon trapping assay using pSPL3 vector in HEK-293 cells, the splice variant showed skipping of exon10. Characterisation of the missense variant in SH-SY5Y cells demonstrated: i) significant alterations in neurite length and number; ii) decreased reactive oxygen species tolerance in mutation carrying cells on Tetrabutylphosphonium hydroxide induction and iii) increase in alpha-synuclein protein. Screening for WASL variants in two independent PD cohorts identified four individuals with heterozygous but none with biallelic variants. CONCLUSION WASL, with demonstrated functional relevance in neurons may be yet another strong candidate gene for autosomal recessive PD encouraging assessment of its contribution across populations.
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Affiliation(s)
- Sumeet Kumar
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Masoom M Abbas
- Parkinson's and Aging Research Foundation, Bangalore, India
| | | | - Uday B Muthane
- Parkinson's and Aging Research Foundation, Bangalore, India
| | - Madhuri Behari
- All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Pandey
- Department of Neurology, Govind Ballabh Pant Postgraduate Institute of Medical Education and Research, New Delhi, India
| | | | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India.
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13
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Degenhardt F, Mayr G, Wendorff M, Boucher G, Ellinghaus E, Ellinghaus D, ElAbd H, Rosati E, Hübenthal M, Juzenas S, Abedian S, Vahedi H, Thelma BK, Yang SK, Ye BD, Cheon JH, Datta LW, Daryani NE, Ellul P, Esaki M, Fuyuno Y, McGovern DPB, Haritunians T, Hong M, Juyal G, Jung ES, Kubo M, Kugathasan S, Lenz TL, Leslie S, Malekzadeh R, Midha V, Motyer A, Ng SC, Okou DT, Raychaudhuri S, Schembri J, Schreiber S, Song K, Sood A, Takahashi A, Torres EA, Umeno J, Alizadeh BZ, Weersma RK, Wong SH, Yamazaki K, Karlsen TH, Rioux JD, Brant SR, Franke A. Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations. Hum Mol Genet 2021; 30:356-369. [PMID: 33555323 PMCID: PMC8098114 DOI: 10.1093/hmg/ddab017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabrielle Boucher
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Dermatology, Venerology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Homayon Vahedi
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi 110021, India
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Lisa Wu Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Naser Ebrahim Daryani
- Department of Gastroenterology, Emam Hospital, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Pierre Ellul
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuta Fuyuno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Myhunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 351-0198, Japan
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Pediatric Institute, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Stephen Leslie
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Vandana Midha
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Allan Motyer
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - David T Okou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Centre for Genetics and Genomics Versus Arthritis, Division of Musculosceletal and Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - John Schembri
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Ajit Sood
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Atsushi Takahashi
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, Riken, Yokohama, 230-0045, Japan
| | - Esther A Torres
- Department of Medicine, University of Puerto Rico Center for IBD, University of Puerto Rico School of Medicine, Rio Piedras, San Juan, PR 00936-5067, USA
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700 AB Groningen, The Netherlands
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway.,Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, 0372 Oslo, Norway
| | - John D Rioux
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Medicine, Rutgers Robert Wood Johnson School of Medicine and Department of Genetics, Rutgers University Brunswick and Piscataway, NJ 08903-0019, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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Pandey AK, Saxena A, Dey SK, Kanjilal M, Kumar U, Thelma BK. Correlation between an intronic SNP genotype and ARL15 level in rheumatoid arthritis. J Genet 2021; 100:26. [PMID: 34187973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
ADP ribosylation factor like protein 15 (ARL15) was identified as a novel susceptibility gene for rheumatoid arthritis (RA) based on a genomewide association study in a north Indian cohort. Mechanism of its action and functional relevance in RA biology remain largely unknown. In this study, we aimed to establish (i) ARL15 protein level in sera samples of RA patients; and (ii) its correlation, if any, with the RA associated ARL15 intronic single-nucleotide polymorphism (SNP) rs255758 (A>C). DNA, RNA and sera were isolated from blood samples of 117 RA patients and 25 age-matched healthy controls recruited at All India Institute of Medical Sciences, New Delhi with institutional ethical committee clearance. SNP rs255758 (A>C) was genotyped by Sanger sequencing; ARL15 RNA and protein levels were estimated by quantitative polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively; and genotype-phenotype correlation established using Mann-Whitney nonparametric test. Very low level of ARL15 expression in human blood was confirmed at both RNA and protein levels. Genotype-wise distribution showed increased levels (P = 0.05) of ARL15 protein in RA patients with the homozygous variant (CC) as compared to AA + AC genotypes of rs255758. This first-ever correlation between higher ARL15 protein levels and the intronic susceptibility genotype (CC; rs255758) in RA patients may be of diagnostic and therapeutic relevance encouraging additional investigations.
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Affiliation(s)
- Anuj Kumar Pandey
- Department of Genetics, University of Delhi South Campus, New Delhi 110 021, India.
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15
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Bhagavatula S, Banerjee P, Sood A, Midha V, Thelma BK, Senapati S. Multiple allelic associations from genes involved in energy metabolism were identified in celiac disease. J Biosci 2021; 46:61. [PMID: 34168104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Energy metabolism is a critical factor that influences disease pathogenesis. Recent high-throughput genomic studies have enabled us to look into disease biology with greater details. Celiac disease (CD) is an inflammatory autoimmune disease where ~60 non-HLA genes were identified which in conjunction with HLA genes explain ~55% of the disease heritability. In this study we aimed to identify susceptibility energy metabolism genes and investigate their role in CD. We re-analysed published Immunochip genotyping data, which were originally analysed for CD association studies in north Indian and Dutch population. 269 energy metabolism genes were tested. Meta-analysis was done for the identified SNPs. To validate the functional implications of identified markers and/or genes, in silico functional annotation was performed. Six SNPs were identified in north Indians, of which three markers from two loci were replicated in Dutch. rs2071592 (PMeta=5.01e-75) and rs2251824 (PMeta=1.87e-14) from ATP6V1G2-NFKBIL1-DDX39B locus and rs4947331 (PMeta= 9.85e-13) from NEU1 locus were found significantly associated. Identified genes are key regulators of cellular energy metabolism and associated with several immune mediated diseases. In silico functional annotation showed significant biological relevance of these novel markers and genes. FDI approved therapeutics against ATP6V1G2 and NEU1 are currently in use to treat chronic and inflammatory diseases. This study identified two pathogenic loci, originally involved in energy metabolism. Extensive investigation showed their synergistic role in CD pathogenesis by promoting immune mediated enteric inflammation. Proposed CD pathogenesis model in this study needs to be tested through tissue-on-chip and in vivo methods to ensure its translational application.
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Affiliation(s)
- Sandilya Bhagavatula
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
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Sharma A, Saini M, Kundu S, Thelma BK. Computational insight into the three-dimensional structure of ADP ribosylation factor like protein 15, a novel susceptibility gene for rheumatoid arthritis. J Biomol Struct Dyn 2020; 40:4626-4641. [PMID: 33356902 DOI: 10.1080/07391102.2020.1860826] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/22/2022]
Abstract
The ARL15 gene (ADP ribosylation factor like protein 15) encodes for an uncharacterized small GTP-binding protein. Its exact role in human physiology remains unknown, but a number of genetic association studies have recognised different variants in this gene to be statistically associated with numerous traits and complex diseases. We have previously reported a novel association of ARL15 with rheumatoid arthritis (RA) based on a genome-wide association study in a north Indian cohort. Subsequent investigations have provided leads for its involvement in RA pathophysiology, especially its potential as a novel therapeutic target. However, the absence of an experimentally determined tertiary structure for ARL15 significantly hinders the understanding of its biochemical and physiological functions, as well as development of potential lead molecules. We, therefore, aimed to derive a high quality, refined model of the three dimensional structure of human ARL15 protein using two different computational protein structure prediction methods - template-based threading and ab initio modelling. The best model each from among the five each derived from both the approaches was selected based on stringent quality assessment and refinement. Molecular dynamics simulations over long timescales revealed the ab initio model to be relatively more stable, and it marginally outperformed the template-based model in the quality assessment as well. A putative GTP-binding site was also predicted using homology for the ARL15 protein, where potential competitive inhibitors can be targeted. This high quality predicted model may provide insights to the biological role(s) of ARL15 and inform and guide further experimental, structural and biochemical characterization efforts.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Sharma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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18
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Kumar S, Yadav N, Pandey S, Muthane UB, Govindappa ST, Abbas MM, Behari M, Thelma BK. Novel and reported variants in Parkinson's disease genes confer high disease burden among Indians. Parkinsonism Relat Disord 2020; 78:46-52. [PMID: 32707456 DOI: 10.1016/j.parkreldis.2020.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 01/31/2020] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Genetic heterogeneity in Parkinson's disease (PD) has been unambiguously reported across different populations. Assuming a higher genetic load, we tested variant burden in PD genes to an early onset PD cohort from India. METHODS Whole exome sequencing was performed in 250 PD patients recruited following MDS-UPDRS criteria. The number of rare variants in the 20 known PD genes per exome were used to calculate average rare variant burden with the 616 non-PD exomes available in-house as a comparison group. SKAT-O test was used for gene level analysis. RESULTS 80 patients harboured rare variants in 20 PD genes, of which six had known pathogenic variants accounting for 2.4% of the cohort. Of 80 patients, 12 had homozygous and nine had likely compound heterozygous variants in recessive PD genes and 59 had heterozygous variants in only dominant PD genes. Of the 16 novel variants of as yet unknown significance identified, four homozygous across ATP13A2, PRKN, SYNJ1 and PARK7; and 12 heterozygous among LRRK2, VPS35, EIF4G1 and CHCHD2 were observed. SKAT-O test suggested a higher burden in GBA (punadjusted = 0.002). Aggregate rare variant analysis including 75 more individuals with only heterozygous variants in recessive PD genes (excluding GBA), with an average of 0.85 protein-altering rare variants per PD patient exome versus 0.51 in the non-PD group, revealed a significant enrichment (p < 0.0001). CONCLUSION This first study in an early onset PD cohort among Indians identified 16 novel variants in known genes and also provides evidence for a high genetic burden in this ethnically distinct population.
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Affiliation(s)
- Sumeet Kumar
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Navneesh Yadav
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Sanjay Pandey
- Govind Ballabh Pant Postgraduate Institute of Medical Education and Research, New Delhi, India
| | - Uday B Muthane
- Parkinson's and Aging Research Foundation, Bengaluru, India
| | | | - Masoom M Abbas
- Parkinson's and Aging Research Foundation, Bengaluru, India
| | - Madhuri Behari
- All India Institute of Medical Sciences, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India.
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Garg R, Sait H, Jindal A, Juneja M, Gupta S, Thelma BK, Kapoor S. Factors Associated with Transient Neonatal Hyperthyrotropinemia. Indian J Pediatr 2020; 87:482-483. [PMID: 31705380 DOI: 10.1007/s12098-019-03095-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/30/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Ritika Garg
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Haseena Sait
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Ankur Jindal
- Division of Genetics & Metabolism, Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Monica Juneja
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Sangeeta Gupta
- Department of Obstretics & Gynecology, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - B K Thelma
- Department of Genetics, UDSC, New Delhi, India
| | - Seema Kapoor
- Division of Genetics & Metabolism, Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India.
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20
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Punchaichira TJ, Mukhopadhyay A, Kukshal P, Bhatia T, Deshpande SN, Thelma BK. Association of regulatory variants of dopamine β-hydroxylase with cognition and tardive dyskinesia in schizophrenia subjects. J Psychopharmacol 2020; 34:358-369. [PMID: 31913053 PMCID: PMC7150076 DOI: 10.1177/0269881119895539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Dopamine-β-hydroxylase (DBH, EC 1.14.17.1), which converts dopamine to norepinephrine, is a candidate gene in neuropsychiatric diseases. AIM To assess the effect of regulatory variants in DBH on schizophrenia and its endophenotypes -cognition and tardive dyskinesia. METHODS We tested association of functional variants 19bp Ins/Del, rs1989787 and rs1611115 in DBH with i) schizophrenia (1236 cases, 1136 controls), ii) tardive dyskinesia (83 positive, 162 negative) and iii) performance functions of cognition (357 cases, 306 controls) estimated by the Penn Computerized Neurocognitive Battery. RESULTS A modest haplotypic (Ins-C; 19bp Ins/Del - rs1989787 C>T; p=0.04) association was observed with schizophrenia. We observed ~39% reduction in activity of 19bp Del allele on luciferase assay. Analysis of covariance revealed interactions of tardive dyskinesia status and: i) 19bp Ins/Del (genotypic, p=0.04) and ii) rs1989787 and rs1611115 (combined genotypic, p=0.004) on Abnormal Involuntary Movement Scale total score. Association of rs1611115 with positive and negative syndrome scale (PANSS) total score (p=0.05) and allelic/genotypic association with lower positive (p=0.03/0.04), general psychopathology (p=0.01/0.01) PANSS scales in tardive dyskinesia-positive; and allelic/genotypic (p=0.02/0.05) with higher score of depressive factors in tardive dyskinesia-negative subgroups were observed. Analysis of covariance with continuous variable of cognition showed interaction of health status with: i) rs1989787 on accuracy and efficiency (p=0.03) of abstraction and mental flexibility; ii) rs1611115 on accuracy of working memory and emotion (p=0.05); iii) 19bp Ins/Del on processing speed of emotion (p=0.03). Allelic/genotypic association of rs1989787 with spatial ability (p=0.02-0.05) among healthy controls; association of rs1611115 with Global Assessment Scale scores in the past month (p=0.05) among schizophrenia subjects of cognition cohort was also observed. CONCLUSIONS With modest genotype-phenotype correlations available for DBH variants, personalized treatment regimens based on DBH activity for ameliorating tardive dyskinesia and cognitive symptoms may be plausible.
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Affiliation(s)
| | | | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research–Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Smita N Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research–Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - BK Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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21
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Degenhardt F, Wendorff M, Wittig M, Ellinghaus E, Datta LW, Schembri J, Ng SC, Rosati E, Hübenthal M, Ellinghaus D, Jung ES, Lieb W, Abedian S, Malekzadeh R, Cheon JH, Ellul P, Sood A, Midha V, Thelma BK, Wong SH, Schreiber S, Yamazaki K, Kubo M, Boucher G, Rioux JD, Lenz TL, Brant SR, Franke A. Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles. Hum Mol Genet 2020; 28:2078-2092. [PMID: 30590525 PMCID: PMC6548229 DOI: 10.1093/hmg/ddy443] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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] [Received: 08/09/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/16/2022] Open
Abstract
Genotype imputation of the human leukocyte antigen (HLA) region is a cost-effective means to infer classical HLA alleles from inexpensive and dense SNP array data. In the research setting, imputation helps avoid costs for wet lab-based HLA typing and thus renders association analyses of the HLA in large cohorts feasible. Yet, most HLA imputation reference panels target Caucasian ethnicities and multi-ethnic panels are scarce. We compiled a high-quality multi-ethnic reference panel based on genotypes measured with Illumina’s Immunochip genotyping array and HLA types established using a high-resolution next generation sequencing approach. Our reference panel includes more than 1,300 samples from Germany, Malta, China, India, Iran, Japan and Korea and samples of African American ancestry for all classical HLA class I and II alleles including HLA-DRB3/4/5. Applying extensive cross-validation, we benchmarked the imputation using the HLA imputation tool HIBAG, our multi-ethnic reference and an independent, previously published data set compiled of subpopulations of the 1000 Genomes project. We achieved average imputation accuracies higher than 0.924 for the commonly studied HLA-A, -B, -C, -DQB1 and -DRB1 genes across all ethnicities. We investigated allele-specific imputation challenges in regard to geographic origin of the samples using sensitivity and specificity measurements as well as allele frequencies and identified HLA alleles that are challenging to impute for each of the populations separately. In conclusion, our new multi-ethnic reference data set allows for high resolution HLA imputation of genotypes at all classical HLA class I and II genes including the HLA-DRB3/4/5 loci based on diverse ancestry populations.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lisa W Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John Schembri
- Division of Gastroenterology, Mater Dei Hospital, Msida MSD, Malta
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Wolfgang Lieb
- Biobank PopGen and Institute of Epidemiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, RB Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Pierre Ellul
- Division of Gastroenterology, Mater Dei Hospital, Msida MSD, Malta
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Vandana Midha
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India.,Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Japan.,Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - John D Rioux
- Montreal Heart Institute, Research Center, Montréal, Québec, Canada.,Université de Montréal Department of Medicine, Montréal, Québec, Canada
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Steven R Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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22
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Vats P, Dabas A, Jain V, Seth A, Yadav S, Kabra M, Gupta N, Singh P, Sharma R, Kumar R, Polipalli SK, Batra P, Thelma BK, Kapoor S. Newborn Screening and Diagnosis of Infants with Congenital Adrenal Hyperplasia. Indian Pediatr 2020; 57:49-55. [PMID: 31937698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Congenital adrenal hyperplasia (CAH) is an autosomal recessive endocrine disorder which can manifest after birth with ambiguous genitalia and salt-wasting crisis. However, genital ambiguity is not seen in male babies and may be mild in female babies, leading to a missed diagnosis of classical CAH at birth. In this review, we provide a standard operating protocol for routine newborn screening for CAH in Indian settings. A standardization of first tier screening tests with a single consistent set of cut-off values stratified by gestational age is also suggested. The protocol also recommends a two-tier protocol of initial immunoassay/time resolved fluoroimmunoassay followed by liquid chromatography tandem mass spectrometry for confirmation of screen positive babies, wherever feasible. Routine molecular and genetic testing is not essential for establishing the diagnosis in all screen positive babies, but has significant utility in prenatal diagnosis and genetic counseling for future pregnancy.
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Affiliation(s)
- Pallavi Vats
- Department of Pediatrics, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Aashima Dabas
- Department of Pediatrics, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Vandana Jain
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Anju Seth
- Department of Pediatrics, Lady Hardinge Medical College and Kalawati Saran Children's Hospital, New Delhi, India
| | - Sangeeta Yadav
- Department of Pediatrics, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Preeti Singh
- Department of Pediatrics, Lady Hardinge Medical College and Kalawati Saran Children's Hospital, New Delhi, India
| | - Rajni Sharma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ravindra Kumar
- Department of Pediatrics, Hindu Rao Hospital, New Delhi, India
| | - Sunil K Polipalli
- Department of Pediatrics, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Prerna Batra
- Department of Pediatrics, University College of Medical Sciences, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi, New Delhi, India
| | - Seema Kapoor
- Department of Pediatrics, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India. Correspondence to: Dr Seema Kapoor, Director Professor, Department of Pediatrics, Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India.
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23
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Banerjee P, Bhagavatula S, Sood A, Midha V, Thelma BK, Senapati S. Association study identified biologically relevant receptor genes with synergistic functions in celiac disease. Sci Rep 2019; 9:13811. [PMID: 31554915 PMCID: PMC6761106 DOI: 10.1038/s41598-019-50120-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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] [Received: 05/14/2019] [Accepted: 09/02/2019] [Indexed: 11/10/2022] Open
Abstract
Receptors are essential mediators of cellular physiology, which facilitate molecular and cellular cross-talk with the environment. Nearly 20% of the all known celiac disease (CD) genes are receptors by function. We hypothesized that novel biologically relevant susceptibility receptor genes act in synergy in CD pathogenesis. We attempted to identify novel receptor genes in CD by re-analyzing published Illumina Immunochip dense genotype data for a north Indian and a European (Dutch) cohort. North Indian dataset was screened for 269 known receptor genes. Association statistics for SNPs were considered with minor allele frequency >15% and association P ≤ 0.005 to attend desired study power. Identified markers were tested for cross-ethnic replication in a European CD dataset. Markers were analyzed in-silico to explain their functional significance in CD. Six novel SNPs from MOG (rs29231, p = 1.21e-11), GABBR1 (rs3025643, p = 1.60e-7), OR2H2 (rs1233388, p = 0.0002), ABCF1 (rs9262119, p = 0.0005), ADRA1A (rs10102024, p = 0.003), and ACVR2A (rs7560426, p = 0.004) were identified in north Indians, of which three genes namely, GABBR1 (rs3025643, p = 5.38e-8), OR2H2 (rs1233388, p = 3.29e-5) and ABCF1 (rs9262119, p = 0.0002) were replicated in Dutch. Tissue specific functional annotation, potential epigenetic regulation, co-expression, protein-protein interaction and pathway enrichment analyses indicated differential expression and synergistic function of key genes that could alter cellular homeostasis, ubiquitination mediated phagosome pathway and cellular protein processing to contribute for CD. At present multiple therapeutic compounds/drugs are available targeting GABBR1 and ADRA1A, which could be tested for their effectiveness against CD in controlled drug trials.
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Affiliation(s)
- Pratibha Banerjee
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Sandilya Bhagavatula
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College & Hospital, Ludhiana, Punjab, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College & Hospital, Ludhiana, Punjab, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sabyasachi Senapati
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India.
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24
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Pandey S, Tomar LR, Kumar S, Dinesh S, Thelma BK. Expanding the canvas of PRKN mutations in familial and early-onset Parkinson disease. Parkinsonism Relat Disord 2019; 66:216-219. [PMID: 31409571 DOI: 10.1016/j.parkreldis.2019.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/14/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Mutations in PRKN (PARK2) are commonly encountered in early-onset Parkinson disease (PD). OBJECTIVES To screen for PRKN mutations in a clinically well-characterized cohort of early-onset PD patients with a family history (FEOPD; ≤50 years at onset) or sporadic (SEOPD; ≤50 years at onset) and late-onset familial patients (FLOPD; >50 years at onset). METHODS A total of 97 patients including 52 SEOPD and 45 familial PD (FEOPD: 23; FLOPD: 22) were screened for variants in PRKN by PCR- Sanger sequencing. PRKN dosage and variants in known PD genes were screened by qPCR and whole-exome sequencing in a subset of samples. RESULTS A total of 25 (25.77%) patients (SEOPD: 12, FEOPD: 6, and FLOPD: 7) were positive for PRKN variants. Of these, two patients manifested homozygous variants; while one patient was carrying three PRKN variants and two patients were carrying two PRKN variants. But, we could not examine their parents or relatives and their genotypes remain unknown. The remaining 20 (80%) patients were carrying heterozygous variants only. 32% of these variants were in exon 2, including a novel truncating homozygous variant (c.97C > T:p.Arg33Ter) in a SEOPD patient. CONCLUSION In our cohort, a novel homozygous variant (c.97C > T:p.Arg33Ter) in a patient with hyperhidrosis expands the spectrum of PRKN associated mutations. Furthermore, ~80% of the PRKN variants being heterozygous in this study cohort, implies the utility of the cohort for identification of additional novel/known causative PD gene(s).
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Affiliation(s)
- Sanjay Pandey
- Department of Neurology, Govind Ballabh Pant Postgraduate institute of medical education and research, New Delhi, 110002, India.
| | - Laxmikant Ramkumarsingh Tomar
- Department of Neurology, Govind Ballabh Pant Postgraduate institute of medical education and research, New Delhi, 110002, India
| | - Sumeet Kumar
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Shreya Dinesh
- Department of Neurology, Govind Ballabh Pant Postgraduate institute of medical education and research, New Delhi, 110002, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
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25
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John J, Kukshal P, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare variant based evidence for oligogenic contribution of neurodevelopmental pathway genes to schizophrenia. Schizophr Res 2019; 210:296-298. [PMID: 30612842 PMCID: PMC7018639 DOI: 10.1016/j.schres.2018.12.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/23/2018] [Accepted: 12/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St., Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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26
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Sait H, Kapoor S, Jindal A, Garg R, Belwal RS, Yadav S, Gupta S, Thelma BK. Association Between Neonatal Thyroid Stimulating Hormone Status and Maternal Urinary Iodine Status. Indian Pediatr 2019; 56:472-475. [PMID: 31278226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND Maternal urinary iodine concentration (MUIC) and percentage of neonates with Thyroid stimulating hormone (TSH) >5 mIU/L are amongst the parameters suggested for assessing adequate iodine status. OBJECTIVE To assess the correlation between MUIC and neonatal TSH levels. STUDY DESIGN Cross-sectional. SETTINGS Tertiary care center in Delhi, India, between November 2015 to November 2016. PARTICIPANTS Postnatal mother-neonate dyads. METHODS TSH levels assessed among neonatal samples were stratified as below and above 5 mIU/L. MUIC was measured in 544 mothers, 400 mother-neonate dyads with neonatal TSH levels >5 mIU/L (cases) and 144 mother-neonate newborn mother dyads with neonatal TSH <5 mIU/L (controls). RESULTS Results: The percentage of mothers with iodine insufficiency (9.8% vs 5.6%) as well as iodine excess (54.3% vs 41.7%) were significant higher in cases than controls. Mean TSH was also higher (P=0.0002) in both the iodine deficient and iodine excess group. There was no correlation between neonatal TSH values and MUIC. CONCLUSION Lack of correlation between neonatal TSH and MUIC is due to iodine excess together with iodine deficiency.
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Affiliation(s)
- Haseena Sait
- Department of Pediarics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Seema Kapoor
- Department of Pediarics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India. Correspondence to: Dr Seema Kapoor, Director Professor, Division of Genetics and Metabolism, Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India.
| | - Ankur Jindal
- Department of Pediarics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Ritika Garg
- Department of Pediarics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | | | - Sangita Yadav
- Department of Pediarics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Sangeeta Gupta
- Department of Obstretics and Gynecology, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi - South Campus, New Delhi, India
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27
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Sharma A, Thelma BK. Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors. J Mol Model 2019; 25:179. [PMID: 31172362 DOI: 10.1007/s00894-019-4047-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a known drug target for B cell malignancies and autoimmune diseases like rheumatoid arthritis. Consequently, efforts to develop BTK inhibitors have gained momentum in the last decade, resulting in a number of potential inhibitory molecules. However, to date, there are only two FDA approved drugs for B cell malignancies (Ibrutinib and Acalabrutinib), thus continued efforts are warranted. A large number of molecular scaffolds with potential BTK inhibitory activity are already available from these studies, and therefore we employed a ligand-based approach towards computer-aided drug design to develop a pharmacophore model for BTK inhibitors. Using over 400 molecules with known half maximal inhibitory concentrations (IC50) for BTK, a four-point pharmacophore hypothesis was derived, with two aromatic rings (R), one hydrogen bond acceptor (A) and one hydrogen bond donor (D). Screening of two small-molecule databases against this pharmacophore returned 620 hits with matching chemical features. Docking these against the ATP-binding site of the BTK kinase domain through a virtual screening workflow yielded 30 hits from which ultimately two natural compounds (two best scoring poses for each) were prioritized. Molecular dynamics simulations of these four docked complexes confirmed the stability of protein-ligand binding over a 200 ns time period, and thus their suitability for lead molecule development with further optimization and experimental testing. Of note, the pharmacophore model developed in this study would also be further useful for de novo drug design and virtual screening efforts on a larger scale. Graphical abstract Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors.
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Affiliation(s)
- Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India.
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28
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Verma P, Kapoor S, Kalaivani M, Vats P, Yadav S, Jain V, Thelma BK. An Optimal Capillary Screen Cut-off of Thyroid Stimulating Hormone for Diagnosing Congenital Hypothyroidism: Data from a Pilot Newborn Screening Program in Delhi. Indian Pediatr 2019; 56:281-286. [PMID: 31064895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To determine an appropriate cut-off of capillary Thyroid stimulating hormone (TSH) for congenital hypothyroidism. STUDY DESIGN Cross-sectional. PARTICIPANTS 174,000 neonates born in different hospitals of Delhi, India, from November 2014 to October 2016. MAIN OUTCOME MEASURES Correlation between initial and repeat capillary TSH level and subsequent venous free thyroxine (fT4) level. RESULTS 102 newborns with initial/ repeat capillary TSH level of ≥20 mIU/L (n=174) were confirmed to have congenital hypothyroidism at mean (SD) age of 5 (4) days. A good correlation between capillary TSH level and confirmatory venous fT4 level and postnatal age of sampling was obtained (r -0.6, -0.4). The area under the ROC curve (AUC) was 0.81 (95%CI 0.75 to 0.88), indicating referral capillary TSH level of 20 mIU/L to be a good predictor of subsequent high venous TSH level. CONCLUSIONS A cut off of ≥20 mIU/L for capillary TSH screening beyond 24 hours of life is optimal in the Indian setting for deciding further recall and workup, keeping a balance between sensitivity and recall rate.
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Affiliation(s)
- Prashant Verma
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Seema Kapoor
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India. Correspondence to: Dr Seema Kapoor, Director-Professor, Department of Pediatrics, Maulana Azad Medical College, New Delhi, India.
| | - Mani Kalaivani
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Pallavi Vats
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Sangeeta Yadav
- Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Vandana Jain
- Department of Pediatric Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi (South Campus), New Delhi, India
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29
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John J, Kukshal P, Sharma A, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare variants in Protein tyrosine phosphatase, receptor type A (PTPRA) in schizophrenia: Evidence from a family based study. Schizophr Res 2019; 206:75-81. [PMID: 30594456 PMCID: PMC7321970 DOI: 10.1016/j.schres.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/25/2018] [Accepted: 12/08/2018] [Indexed: 12/23/2022]
Abstract
The contribution of both common and rare risk variants to the genetic architecture of schizophrenia (SZ) has been documented in genome-wide association studies, whole exome and whole genome sequencing approaches. As SZ is highly heritable and segregates in families, highly penetrant rare variants are more likely to be identified through analyses of multiply affected families. Further, much of the gene mapping studies in SZ have utilized individuals of Caucasian ancestry. Analysis of other ethnic groups may be informative. In this study, we aimed at identification of rare, penetrant risk variants utilizing whole exome sequencing (WES) in a three-generation Indian family with multiple members affected. Filtered data from WES, combined with in silico analyses revealed a novel heterozygous missense variant (NM_080841:c.1730C>G:p.T577R; exon18) in Protein tyrosine phosphatase, receptor type A (PTPRA 20p13). The variant was located in an evolutionarily conserved position and predicted to be damaging. Screening for variants in this gene in the WES data of an independent SZ cohort (n = 350) of matched ethnicity, identified five additional rare missense variants with MAF < 0.003, which were also predicted to be damaging. In conclusion, the rare missense variants in PTPRA identified in this study could confer risk for SZ. This has also derived support from concordant data from prior linkage and association, as well as animal studies which indicated a role for PTPRA in glutamate function.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St, Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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30
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John J, Sharma A, Kukshal P, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare Variants in Tissue Inhibitor of Metalloproteinase 2 as a Risk Factor for Schizophrenia: Evidence From Familial and Cohort Analysis. Schizophr Bull 2019; 45:256-263. [PMID: 29385606 PMCID: PMC6293225 DOI: 10.1093/schbul/sbx196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Indexed: 01/14/2023]
Abstract
Candidate gene and genome-wide association study based common risk variant identification is being complemented by whole exome sequencing (WES)/whole genome sequencing based rare variant discovery in elucidation of genetic landscape of schizophrenia (SZ), a common neuropsychiatric disorder. WES findings of de novo mutations in case-parent trios have further implied genetic etiology, but do not explain the high genetic risk in general populations. Conversely, WES in multiplex families may be an insightful strategy for the identification of highly penetrant rare variants in SZ and possibly enhance our understanding of disease biology. In this study, we analyzed a 5-generation Indian family with multiple members affected with SZ by WES. We identified a rare heterozygous missense variant (NM_003255: c.506C>T; p.Pro169Leu; MAF = 0.0001) in Tissue Inhibitor of Metalloproteinase 2 (TIMP2, 17q25.3) segregating with all 6 affected individuals but not with unaffected members. Linkage analysis indicated a maximum logarithm of the odds score of 1.8, θ = 0 at this locus. The variant was predicted to be damaging by various in silico tools and also disrupt the structural integrity by molecular dynamics simulations. WES based screening of an independent SZ cohort (n = 370) identified 4 additional rare missense variants (p.Leu20Met, p.Ala26Ser, p.Lys48Arg and p. Ile217Leu) and a splice variant rs540397728 (NM_003255:c.232-5T>C), also predicted to be damaging, increasing the likelihood of contribution of this gene to SZ risk. Extensive biochemical and knockout mouse studies suggesting involvement of TIMP2 in neurodevelopmental and behavioral deficits, together with genetic evidence for TIMP2 conferring SZ risk from this study may have possible implications for new therapeutics.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi, India
| | - Vishwajit L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh PA
| | | | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India,To whom correspondence should be addressed; Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India; tel: +91-11-24118201, fax: +91-11-24112761, e-mail:
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Abstract
Inborn errors of metabolism (IEM) are a heterogeneous group of genetic disorders that cause significant neonatal and infant mortality. Expanded newborn screening which detects these disorders at birth is the standard preventive strategy in most countries. Prospective studies to evaluate the impact of these in the Indian population are lacking. The imminent need to address this lacuna warrants a review of available pan India data, as well as efforts for a carefully conducted prospective assessment of the burden of IEM. Published data on IEM in the Indian population comprising universal prospective screening and screening in selected subgroups (patients admitted to pediatric/neonatal ICUs, patients with developmental delay/mental retardation) was collected through a systematic search. The primary focus was to get an estimate of the disease burden in the Indian population. A true prevalence of IEM in India is not available. The systematic review identifies and stratifies the various situations where IEM are found. Data collected by universal screening of the low risk population is essential to identify the true prevalence of IEM in India.
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Affiliation(s)
- Seema Kapoor
- Division of Genetics and Metabolism, Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India.
| | - B K Thelma
- Department of Genetics, University of Delhi, South Campus, New Delhi, India.
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Juyal G, Sood A, Midha V, Thelma BK. Genetics of ulcerative colitis: putting into perspective the incremental gains from Indian studies. J Genet 2018; 97:1493-1507. [PMID: 30555100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ulcerative colitis (UC), one of the two clinical subtypes of inflammatory bowel disease is perceived as a potential 'sleeping giant' in the Indian subcontinent. Clinical manifestation is overall believed to be the same across ethnic groups but overwhelming genetics from large European and fewer non-European studies have revealed shared as well as unique disease susceptibly signaturesbetween them, pointing to population specific differences at genomic and environmental levels. A systematic recount of the four major eras in UC genetics spanning earliest linkage analysis, cherry picked candidate gene association studies, unbiased genomewide association studies, their logical extension in trans-ethnic setting (Immunochip study), lastly whole exome sequencing efforts forrare variant burden; and lessons learnt thereof in context of genetically distinct Indian population was attempted in this review. Genetic heterogeneity manifesting at allelic/locus level across these approaches has been the consistent finding through the range of pan India studies. On the other hand, these salient findings also highlight the limitations of even the best of these genetic leadsfor prognostic/clinical application. The imminent need, therefore, for the UC research community to adopt newer approaches/tools with improved study design to (i) gain better insight into genetic/mechanistic basis of disease; (ii) identify biomarkers of immediate translational value; and (iii) develop new/alternate therapeutic options is emphasized at the end.
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Affiliation(s)
- Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India. ,
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Punchaichira TJ, Deshpande SN, Thelma BK. Determination of Dopamine-β-hydroxylase Activity in Human Serum Using UHPLC-PDA Detection. Neurochem Res 2018; 43:2324-2332. [PMID: 30357655 DOI: 10.1007/s11064-018-2653-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/13/2018] [Accepted: 09/28/2018] [Indexed: 01/13/2023]
Abstract
Dopamine-β-hydroxylase (DBH, EC 1.14.17.1) is an enzyme with implications in various neuropsychiatric and cardiovascular diseases and is a known drug target. There is a dearth of cost effective and fast method for estimation of activity of this enzyme. A sensitive UHPLC based method for the estimation of DBH activity in human sera samples based on separation of substrate tyramine from the product octopamine in 3 min is described here. In this newly developed protocol, a Solid Phase Extraction (SPE) sample purification step prior to LC separation, selectively removes interferences from the reaction cocktail with almost no additional burden on analyte recovery. The response was found to be linear with an r2 = 0.999. The coefficient of variation for assay precision was < 10% and recovery > 90%. As a proof of concept, DBH activity in sera from healthy human volunteers (n = 60) and schizophrenia subjects (n = 60) were successfully determined using this method. There was a significant decrease in sera DBH activity in subjects affected by schizophrenia (p < 0.05) as compared to healthy volunteers. This novel assay employing SPE to separate octopamine and tyramine from the cocktail matrix may have implications for categorising subjects into various risk groups for Schizophrenia, Parkinson's disease as well as in high throughput screening of inhibitors.
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Affiliation(s)
| | - Smita Neelkanth Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, Baba Kharak Singh Marg, Connaught Place, New Delhi, 110001, India
| | - B K Thelma
- Department of Genetics, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018; 97:625-648. [PMID: 30027900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neurodegenerative diseases constitute a large proportion of disorders in elderly, majority being sporadic in occurrence with ∼5-10% familial. A strong genetic component underlies the Mendelian forms but nongenetic factors together with genetic vulnerability contributes to the complex sporadic forms. Several gene discoveries in the familial forms have provided novel insights into the pathogenesis of neurodegeneration with implications for treatment. Conversely, findings from genetic dissection of the sporadic forms, despite large genomewide association studies and more recently whole exome and whole genome sequencing, have been limited. This review provides a concise account of the genetics that we know, the pathways that they implicate, the challenges that are faced and the prospects that are envisaged for the sporadic, complex forms of neurodegenerative diseases, taking four most common conditions, namely Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington disease as examples. Poor replication across studies, inability to establish genotype-phenotype correlations and the overall failure to predict risk and/or prevent disease in this group poses a continuing challenge. Among others, clinical heterogeneity emerges as the most important impediment warranting newer approaches. Advanced computational and system biology tools to analyse the big data are being generated and the alternate strategy such as subgrouping of case-control cohorts based on deep phenotyping using the principles of Ayurveda to overcome current limitation of phenotype heterogeneity seem to hold promise. However, at this point, with advances in discovery genomics and functional analysis of putative determinants with translation potential for the complex forms being minimal, stem cell therapies are being attempted as potential interventions. In this context, the possibility to generate patient derived induced pluripotent stem cells, mutant/gene/genome correction through CRISPR/Cas9 technology and repopulating the specific brain regions with corrected neurons, which may fulfil the dream of personalized medicine have been mentioned briefly. Understanding disease pathways/biology using this technology, with implications for development of novel therapeutics are optimistic expectations in the near future.
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Affiliation(s)
- Sumeet Kumar
- Department of Genetics, University of Delhi South Campus, New Delhi 110 021, India.
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Kashyap S, Kumar U, Pandey AK, Kanjilal M, Chattopadhyay P, Yadav C, Thelma BK. Functional characterisation of ADP ribosylation factor-like protein 15 in rheumatoid arthritis synovial fibroblasts. Clin Exp Rheumatol 2018; 36:581-588. [PMID: 29465355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/30/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVES ARL15 is a novel susceptibility gene identified in a recent GWAS in a north Indian rheumatoid arthritis (RA) cohort. However, the role of ARL15 or ARF family genes in RA aetiology remains unknown. Therefore, we aimed to i) establish the expression of ARL15 in rheumatoid arthritis synovial fibroblasts (RASF) and ii) its functional characterisation by assessing its effects on major inflammatory cytokines and interacting partners using a knockdown approach. METHODS RASF were cultured from synovial tissue obtained from RA patients (n=5) and osteoarthritis (OA) patients (n=3) serving as controls. Expression of ARL15, ARF1 and ARF6 in RASF was checked by semi-quantitative PCR and western blots; and altered expression of ARL15, if any, by induction of RASF with TNF using real-time PCR. The effect of ARL15 on the expression of adiponectin, adiponectin receptor I, IL6 and GAPDH and on cell mobility by invasion and migration assays were assessed by siRNA mediated gene knockdown. RESULTS Expression of ARL15, ARF1 and ARF6 was confirmed in RASF and OASF samples but ARL15 expression remained unaltered on TNF induction. Notably, ARL15 knockdown resulted in downregulation of IL6 and GAPDH, upregulation of adiponectin and adiponectin receptor I genes; and significant reduction in migration and invasion of RASF. Genemania showed significant interactions of ARL15 with genes responsible for insulin resistance and phospholipase D. CONCLUSIONS This first report on ARL15 expression in RASF and its likely role in inflammation and metabolic syndromes through a TNF independent pathway, encourages hypothesis-free studies to identify additional pathways underlying RA disease biology.
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Affiliation(s)
- Sujit Kashyap
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Anuj Kumar Pandey
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Maumita Kanjilal
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Chandrashekhar Yadav
- Departmentof Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India.
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Sood A, Midha V, Makharia G, Thelma BK, Halli SS, Mehta V, Mahajan R, Narang V, Sood K, Kaur K. A simple phenotypic classification for celiac disease. Intest Res 2018; 16:288-292. [PMID: 29743842 PMCID: PMC5934602 DOI: 10.5217/ir.2018.16.2.288] [Citation(s) in RCA: 3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/01/2018] [Accepted: 01/03/2018] [Indexed: 12/13/2022] Open
Abstract
Background/Aims Celiac disease is a global health problem. The presentation of celiac disease has unfolded over years and it is now known that it can manifest at different ages, has varied presentations, and is prone to develop complications, if not managed properly. Although the Oslo definitions provide consensus on the various terminologies used in literature, there is no phenotypic classification providing a composite diagnosis for the disease. Methods Various variables identified for phenotypic classification included age at diagnosis, age at onset of symptoms, clinical presentation, family history and complications. These were applied to the existing registry of 1,664 patients at Dayanand Medical College and Hospital, Ludhiana, India. In addition, age was evaluated as below 15 and below 18 years. Cross tabulations were used for the verification of the classification using the existing data. Expert opinion was sought from both international and national experts of varying fields. Results After empirical verification, age at diagnosis was considered appropriate in between A1 (<18) and A2 (≥18). The disease presentation has been classified into 3 types–P1 (classical), P2 (non-classical) and P3 (asymptomatic). Complications were considered as absent (C0) or present (C1). A single phenotypic classification based on these 3 characteristics, namely age at the diagnosis, clinical presentation, and intestinal complications (APC classification) was derived. Conclusions APC classification (age at diagnosis, presentation, complications) is a simple disease explanatory classification for patients with celiac disease aimed at providing a composite diagnosis.
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Affiliation(s)
- Ajit Sood
- Department of Gastroenterology, Dayanand Medical College, Ludhiana, India
| | - Vandana Midha
- Department of Internal Medicine, Dayanand Medical College, Ludhiana, India
| | - Govind Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Shivalingappa S Halli
- Department of Community Health Sciences, Faculty of Medicine, University of Manitoba, Winnipeg, Canada
| | - Varun Mehta
- Department of Gastroenterology, Dayanand Medical College, Ludhiana, India
| | - Ramit Mahajan
- Department of Gastroenterology, Dayanand Medical College, Ludhiana, India
| | - Vikram Narang
- Department of Pathology, Dayanand Medical College, Ludhiana, India
| | - Kriti Sood
- Department of Pathology, Dayanand Medical College, Ludhiana, India
| | - Kirandeep Kaur
- Department of Pharmacology, Dayanand Medical College, Ludhiana, India
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Singh A, Beniwal RP, Kukshal P, Bhatia T, Thelma BK, Deshpande SN. A preliminary study of association of genetic variants with early response to olanzapine in schizophrenia. Indian J Psychiatry 2018; 60:10-16. [PMID: 29736057 PMCID: PMC5914236 DOI: 10.4103/psychiatry.indianjpsychiatry_104_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Treatment response can be predicted in schizophrenia by DNA information in the drug metabolism pathways. This study aimed to examine clinical characteristics and genetic determinant (s) of early response to olanzapine treatment in schizophrenia using specified drug metabolizing genes. MATERIALS AND METHODS Consenting participants (n = 33) suffering from schizophrenia were diagnosed on Diagnostic Interview for Genetic Studies. Oral olanzapine was administered in an incremental dose up to 10 mg (2 weeks) and 20 mg (6 weeks). All participants were tested on Positive and Negative Syndrome Scale, Clinical Global Impressions, and Global Assessment of Functioning at 0, 2, and 6 weeks. Side effects were also evaluated. After 2 weeks, 11 (33.33%) fulfilled criteria for early response, whereas 17 (51.52%) responded at 6 weeks. We investigated the contribution of clinical factors and five polymorphisms (rs2740574, rs2470890, rs762551, rs3892097, and rs1065852) in predicting response to olanzapine at 2 and 6 weeks of treatment with a standard dose. RESULTS Severity of positive symptoms at baseline was associated with response at 2 weeks (P = 0.01) while higher scores on Scale for the Assessment of Negative Symptoms (SANS) at baseline was associated with response at both 2 (P = 0.04) and 6 weeks (P = 0.03). None of the five single nucleotide polymorphisms (SNPs) selected were significantly associated with response to olanzapine. CONCLUSIONS Olanzapine is an effective and safe drug. Positive and Negative Syndrome Scale positive score and SANS score were variably associated with response at 2 and/or 6 weeks. Replicate studies with bigger sample size are warranted for conclusive results in the Indian population for genetic association.
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Affiliation(s)
- Anmol Singh
- Department of Psychiatry and Drug De-Addiction, Centre of Excellence in Mental Health, PGIMER-Dr RML Hospital, New Delhi, India
| | - Ram Pratap Beniwal
- Department of Psychiatry and Drug De-Addiction, Centre of Excellence in Mental Health, PGIMER-Dr RML Hospital, New Delhi, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry and Drug De-Addiction, Centre of Excellence in Mental Health, PGIMER-Dr RML Hospital, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi, New Delhi, India
| | - Smita N Deshpande
- Department of Psychiatry and Drug De-Addiction, Centre of Excellence in Mental Health, PGIMER-Dr RML Hospital, New Delhi, India
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John J, Kukshal P, Bhatia T, Chowdari KV, Nimgaonkar VL, Deshpande SN, Thelma BK. Possible role of rare variants in Trace amine associated receptor 1 in schizophrenia. Schizophr Res 2017; 189:190-195. [PMID: 28242106 PMCID: PMC5569002 DOI: 10.1016/j.schres.2017.02.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 10/20/2022]
Abstract
Schizophrenia (SZ) is a chronic mental illness with behavioral abnormalities. Recent common variant based genome wide association studies and rare variant detection using next generation sequencing approaches have identified numerous variants that confer risk for SZ, but etiology remains unclear propelling continuing investigations. Using whole exome sequencing, we identified a rare heterozygous variant (c.545G>T; p.Cys182Phe) in Trace amine associated receptor 1 gene (TAAR1 6q23.2) in three affected members in a small SZ family. The variant predicted to be damaging by 15 prediction tools, causes breakage of a conserved disulfide bond in this G-protein-coupled receptor. On screening this intronless gene for additional variant(s) in ~800 sporadic SZ patients, we identified six rare protein altering variants (MAF<0.001) namely p.Ser47Cys, p.Phe51Leu, p.Tyr294Ter, p.Leu295Ser in four unrelated north Indian cases (n=475); p.Ala109Thr and p.Val250Ala in two independent Caucasian/African-American patients (n=310). Five of these variants were also predicted to be damaging. Besides, a rare synonymous variant was observed in SZ patients. These rare variants were absent in north Indian healthy controls (n=410) but significantly enriched in patients (p=0.036). Conversely, three common coding SNPs (rs8192621, rs8192620 and rs8192619) and a promoter SNP (rs60266355) tested for association with SZ in the north Indian cohort were not significant (P>0.05). TAAR1 is a modulator of monoaminergic pathways and interacts with AKT signaling pathways. Substantial animal model based pharmacological and functional data implying its relevance in SZ are also available. However, this is the first report suggestive of the likely contribution of rare variants in this gene to SZ.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - K V Chowdari
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street,Pittsburgh, PA 15213, USA
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street,Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St, Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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Abstract
PURPOSE Familial clustering of common forms of primary strabismus like esotropia (ET) and exotropia (XT) is observed in a proportion of the strabismus cohort. The genetic components of this remain unidentified. Linkage studies have demonstrated susceptibility locus for primary strabismus at the STBMS1 locus on 7p22.1 as well as other loci on 4q28.3 and 7q31.2. Recently next generation sequencing (NGS) technology has emerged as a powerful tool in discovery genomics and a large number of novel disease-causing variants are being reported. In this study, we recruited informative families for subsequent genetic analysis for disease-causing variant identification. METHODS All consecutive families with two or more affected members with primary concomitant horizontal strabismus were prospectively recruited at the ophthalmic outpatients department (OPD) of Lady Hardinge Medical College, New Delhi, from August 2014 to February 2017. Detailed phenotypic evaluation and pedigree documentation was performed. RESULTS Of the 39 recruited families of north Indian origin, 18 families each had affected family members demonstrating either ET or XT. 100% concordance of the phenotype in the affected family members was observed in these families. While vertical transmission was observed in 17/18 families with XT, 7 with ET had affected members across one generation, 2 demonstrated consanguineous pedigree, and 2 comprised identical twin families. In 3 families, a combination of ET and XT was noted. This comprised one family with the ET and XT patients being from 2 separate arms of the family related by marriage, one family where one sibling had XT and the other had ET, and another family where the maternal aunt of the affected proband with ET had XT. CONCLUSIONS Subjects with familial primary concomitant strabismus recruited in this study may provide a valuable resource to unravel the genetic determinants of this condition, which is a common disorder of early childhood with high ophthalmic morbidity.
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Affiliation(s)
- Zia Chaudhuri
- a Lady Hardinge Medical College , University of Delhi , New Delhi , India.,b Department of Genetics , University of Delhi South Campus , New Delhi, India
| | - Jibin John
- b Department of Genetics , University of Delhi South Campus , New Delhi, India
| | - Satinder Aneja
- a Lady Hardinge Medical College , University of Delhi , New Delhi , India
| | - B K Thelma
- b Department of Genetics , University of Delhi South Campus , New Delhi, India
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Punchaichira TJ, Dey SK, Mukhopadhyay A, Kundu S, Thelma BK. Characterization of SNPs in the dopamine-β-hydroxylase gene providing new insights into its structure-function relationship. Neurogenetics 2017; 18:155-168. [PMID: 28707163 DOI: 10.1007/s10048-017-0519-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 11/24/2022]
Abstract
Dopamine-β-hydroxylase (DBH, EC 1.14.17.1), an oxido-reductase that catalyses the conversion of dopamine to norepinephrine, is largely expressed in sympathetic neurons and adrenal medulla. Several regulatory and structural variants in DBH associated with various neuropsychiatric, cardiovascular diseases and a few that may determine enzyme activity have also been identified. Due to paucity of studies on functional characterization of DBH variants, its structure-function relationship is poorly understood. The purpose of the study was to characterize five non-synonymous (ns) variants that were prioritized either based on previous association studies or Sorting Tolerant From Intolerant (SIFT) algorithm. The DBH ORF with wild type (WT) and site-directed mutagenized variants were transfected into HEK293 cells to generate transient and stable lines expressing these variant enzymes. Activity was determined by UPLC-PDA and corresponding quantity by MRMHR on a TripleTOF 5600 MS respectively of spent media from stable cell lines. Homospecific activity computed for the WT and variant proteins showed a marginal decrease in A318S, W544S and R549C variants. In transient cell lines, differential secretion was observed in the case of L317P, W544S and R549C. Secretory defect in L317P was confirmed by localization in ER. R549C exhibited both decreased homospecific activity and differential secretion. Of note, all the variants were seen to be destabilizing based on in silico folding analysis and molecular dynamics (MD) simulation, lending support to our experimental observations. These novel genotype-phenotype correlations in this gene of considerable pharmacological relevance have implications for dopamine-related disorders.
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Affiliation(s)
| | - Sanjay Kumar Dey
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Anirban Mukhopadhyay
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Chowdhury MR, Chauhan S, Dabral A, Thelma BK, Gupta N, Kabra M. Validation of Polymerase Chain Reaction-Based Assay to Detect Actual Number of CGG Repeats in FMR1 Gene in Indian Fragile X Syndrome Patients. J Child Neurol 2017; 32:371-378. [PMID: 28193118 DOI: 10.1177/0883073816683075] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Molecular genetic testing for fragile X (FX) is complicated due to the large variation in the size of CGG expansion. The aim of this study was to apply this new technique using AmplideX FMR1 PCR assay, which is considered a better diagnostic tool for detecting expanded alleles in Indian population. The primary objective was to identify the carrier status of females and to correlate the instability of premutation alleles in females with the repeat sizes. 24 children with FX based on rapid PCR and 29 female relatives of these patients were included. Out of the 29 females screened, those whose child (or children) was affected by FX, were all premutation carriers confirming their role in transmission. The smallest PM allele that expanded into FM in the next generation was 78 repeats and the smallest PM allele detected was 63 repeats, and when transmitted from mother to offspring remained in the premutation range. In 4 families, the repeat size of the allele reduced from PM to normal repeat numbers in their daughters and in 1 case to borderline PM range. Thus, apart from the reduced turnaround time, this PCR based assay offers advantage by its sensitivity to detect CGG repeats in the intermediate region and lower range of premutation alleles. It also provides added information of AGG interruptions, which may have an impact on the counseling of women with intermediate and PM alleles.
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Affiliation(s)
- Madhumita Roy Chowdhury
- 1 Genetics Division, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeepa Chauhan
- 1 Genetics Division, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Anjali Dabral
- 2 Department of Genetics, University of Delhi, South Campus, New Delhi, India
| | - B K Thelma
- 2 Department of Genetics, University of Delhi, South Campus, New Delhi, India
| | - Neerja Gupta
- 1 Genetics Division, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- 1 Genetics Division, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Gogtay NJ, Kapileshwar SR, Shah SU, Bendkhale SR, Ramakrishna S, Sridharan K, Thelma BK, Thatte UM, Kshirsagar NA. Evaluation of cytochrome P4502E1 polymorphisms in healthy adult Western Indians and patients with antituberculous drug-induced hepatotoxicity. Indian J Pharmacol 2017; 48:42-6. [PMID: 26997721 PMCID: PMC4778206 DOI: 10.4103/0253-7613.174519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Objectives: Cytochrome P4502E1 (CYP2E1) is involved in the metabolism of isoniazid and the mediation of its hepatotoxicity. It exhibits genetic polymorphism in humans. This study evaluated the polymorphism of CYP2E1 in adult healthy Western Indians and patients on antituberculous drugs by phenotyping and genotyping. Methods: A 500 mg single dose of chlorzoxazone (CZX) was administered to 136 healthy adult Western Indian participants. Venous blood samples 2 h postdose were analyzed for the levels of CZX and 6-hydroxy CZX, and the metabolic ratio (MR) was calculated to determine the extent of rapid and poor metabolizers using probit plot analysis. Patients on antituberculous drugs who had raised the liver enzymes or clinical symptoms of hepatotoxicity were also recruited. Genotyping for CYP2E1 * 5B allele was performed by polymerase chain reaction – rapid fragment length polymorphism technique. Results: A total of 139 healthy participants were enrolled, of which the final analysis consisted of data from 136 participants for genotyping and 137 for phenotyping. Only 1 participant had reported mild drowsiness 2 h postdose, and no other adverse events were observed. The median (range) MR of population was 0.2 (0.1–4.0), and no polymorphisms were detected using phenotype data. A total of 134/136 (98.5%) had c1/c1 genotype and 1/136 each (0.75%) had c1/c2 and c2/c2 genotypes, respectively. Of the 2/136 participants harboring c2 allele, one had MR of 0.1 (c1/c2) and another had 0.5 (c2/c2). A total of 25 cases of antituberculous drug-induced hepatotoxicity and 50 control patients were recruited, of which finally 22 cases and 49 controls were available for evaluation. All the cases had c1/c1 genotype while 42/49 (85.7%) controls had c1/c1, 6/49 (12.2%) had c1/c2, and 1/49 (2.1%) had c2/c2 genotype and the crude odds ratio was 7.9 (0.4, 145.6). Conclusions: A background prevalence of CYP2E1*B polymorphism and their activity in Western Indian population was observed. The study suggests no association between the CYP2E1 genotyping with antituberculous drug-induced hepatotoxicity.
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Affiliation(s)
- Nithya J Gogtay
- Department of Clinical Pharmacology, King Edward Memorial Hospital and Seth Gordhandas Sunderdas Medical College, Mumbai, Maharashtra, India
| | - Swapnali R Kapileshwar
- Department of Clinical Pharmacology, King Edward Memorial Hospital and Seth Gordhandas Sunderdas Medical College, Mumbai, Maharashtra, India
| | - Sanket U Shah
- Department of Clinical Pharmacology, King Edward Memorial Hospital and Seth Gordhandas Sunderdas Medical College, Mumbai, Maharashtra, India
| | - Shital R Bendkhale
- Department of Clinical Pharmacology, King Edward Memorial Hospital and Seth Gordhandas Sunderdas Medical College, Mumbai, Maharashtra, India
| | - Suresh Ramakrishna
- Department of Clinical Pharmacology, King Edward Memorial Hospital and Seth Gordhandas Sunderdas Medical College, Mumbai, Maharashtra, India
| | - Kannan Sridharan
- Department of Health Sciences, College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - B K Thelma
- Department of Genetics, University of Delhi, New Delhi, India
| | - Urmila M Thatte
- Department of Clinical Pharmacology, King Edward Memorial Hospital and Seth Gordhandas Sunderdas Medical College, Mumbai, Maharashtra, India
| | - Nilima A Kshirsagar
- Department of Clinical Pharmacology, ESI PGIMSR MGM Hospital, Mumbai, Maharashtra, India
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Senapati S, Sood A, Midha V, Sood N, Sharma S, Kumar L, Thelma BK. Shared and unique common genetic determinants between pediatric and adult celiac disease. BMC Med Genomics 2016; 9:44. [PMID: 27449795 PMCID: PMC4957920 DOI: 10.1186/s12920-016-0211-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 06/09/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Based on age of presentation, celiac disease (CD) is categorised as pediatric CD and adult CD. It however remains unclear if these are genetically and/or phenotypically distinct disorders or just different spectrum of the same disease. We therefore explored the common genetic components underlying pediatric and adult CD in a well characterized north Indian cohort. METHODS A retrospective analysis of children (n = 531) and adult (n = 871) patients with CD between January 2001 and December 2010 was done. The database included basic demographic characteristics, clinical presentations, associated diseases and complications, if any. The genotype dataset was acquired for children (n = 217) and adult CD patients (n = 340) and controls (n = 736) using Immunochip. Association analysis was performed using logistic regression model to identify susceptibility genetic variants. RESULTS The predominant form of CD was classical CD in both pediatric and adult CD groups. There was remarkable similarity between pediatric and adult CD except for quantitative differences between the two groups such as female preponderance, non-classical presentation, co-occurrence of other autoimmune diseases being more common amongst adult CD. Notably, same HLA-DQ2 and -DQ8 haplotypes were established as the major risk factors in both types of CD. In addition, a few suggestively associated (p < 5 × 10(-4)) non-HLA markers were identified of which only ANK3 (rs4948256-A; rs10994257-T) was found to be shared and explain risk for ~45 % of CD patients with HLA allele. DISCUSSION Overall phenotypic similarity between pediatric and adult CD groups can be explained by contribution of same HLA risk alleles. Different non-HLA genes/loci with minor risk seem to play crucial role in disease onset and extra intestinal manifestation of CD. None of the non-HLA risk variants reached genome-wide significance, however most of them were shown to have functional implication to disease pathogenesis. Functional relevance of our findings needs to be investigated to address clinical heterogeneity of CD. CONCLUSIONS This present study is the first comparative study based on common genetic markers to suggest that CD in pediatric age group and in adults are the spectrum of the same disease with novel and shared genetic risk determinants. Follow-up fine mapping studies with larger study cohorts are warranted for further genetic investigation.
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Affiliation(s)
- Sabyasachi Senapati
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
- Present Address: Centre for Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Neena Sood
- Department of Pathology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Suresh Sharma
- Department of Nursing, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Lalit Kumar
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India.
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Sudhaman S, Muthane UB, Behari M, Govindappa ST, Juyal RC, Thelma BK. Evidence of mutations inRIC3acetylcholine receptor chaperone as a novel cause of autosomal-dominant Parkinson's disease with non-motor phenotypes. J Med Genet 2016; 53:559-66. [DOI: 10.1136/jmedgenet-2015-103616] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/10/2016] [Indexed: 12/18/2022]
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Taur SR, Kulkarni NB, Gandhe PP, Thelma BK, Ravat SH, Gogtay NJ, Thatte UM. Association of polymorphisms of CYP2C9, CYP2C19, and ABCB1, and activity of P-glycoprotein with response to anti-epileptic drugs. J Postgrad Med 2016; 60:265-9. [PMID: 25121365 DOI: 10.4103/0022-3859.138739] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Epilepsy, the most common neurological disorder, has treatment failure rate of 20 to 25%. Inter-individual variability in drug response can be attributed to genetic polymorphism in genes encoding different drug metabolizing enzymes, drug transporters (P-gp), and enzymes involved in sodium channel biosynthesis. The present study attempted to evaluate association of polymorphisms of CYP2C9, CYP2C19, and ABCB1, and P-gp activity with treatment response in patients with epilepsy. MATERIALS AND METHODS Patients with epilepsy on phenytoin and/or phenobarbital and/or carbamazepine were categorized into responders and non-responders as per the International League Against Epilepsy. Plasma drug concentration was estimated by high-performance liquid chromatography. P-gp activity was measured by flow cytometry using rhodamine efflux. The polymerase chain reaction (PCR-RFLP) was used to study polymorphisms of ABCB1 (C3435T), CYP2C9 (416 C > T, and 1061 A > T), and CYP2C19 (681 G > A and 636 G > A). RESULTS Of total 117 patients enrolled in this study, genotype data was available for 115 patients. P-gp activity was higher in non-responders (n = 68) compared to responders (n = 47) (P<0.001). No association of 416 C > T and 1061 A > T in CYP2C9 or 681 G > A and 636 G > A in CYP2C19 was observed with response phenotype in genotypic analysis. Significant genotypic (odds ratio, OR = 4.5; 95% CI, 1.04 to 20.99) and allelic association (OR = 1.73; 95% CI, 1.02 to 2.95) was observed with ABCB1 C3435T and response phenotype. CONCLUSIONS The response to antiepileptics seems to be modulated by C3435T in ABCB1 or P-gp activity. At present, role of other genetic factors in treatment responsiveness in epilepsy appears limited, warranting analysis in a larger cohort.
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Affiliation(s)
| | | | | | | | | | - N J Gogtay
- Department of Clinical Pharmacology, Seth GS Medical College and KEM Hospital, Mumbai, India
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Sudhaman S, Prasad K, Behari M, Muthane UB, Juyal RC, Thelma BK. Discovery of a frameshift mutation in podocalyxin-like (PODXL) gene, coding for a neural adhesion molecule, as causal for autosomal-recessive juvenile Parkinsonism. J Med Genet 2016; 53:450-6. [DOI: 10.1136/jmedgenet-2015-103459] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 01/18/2016] [Indexed: 12/30/2022]
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Gupta A, Thelma BK. Identification of critical variants within SLC44A4, an ulcerative colitis susceptibility gene identified in a GWAS in north Indians. Genes Immun 2016; 17:105-9. [PMID: 26741288 DOI: 10.1038/gene.2015.53] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Abstract
SLC44A4 is one of the seven novel susceptibility genes that were discovered in the first ever genome-wide association study (GWAS) on ulcerative colitis (UC) in the genetically distinct north Indians. This gene seems to be functionally relevant to disease biology as it may contribute to the associated phenotype of Vitamin B1 deficiency among UC patients, hence playing a role in disease pathogenesis. A large number of single-nucleotide polymorphisms (SNPs) are known to be distributed throughout this gene, but the functional status of most are not known. Thus, an extensive investigation of structural and regulatory variants within this gene was undertaken in this study to identify the critical variants amongst them using a combination of fine mapping, in silico and in vitro approaches. A few intronic SNPs were predicted to have regulatory roles on the basis of in silico analysis, suggesting that they may be the critical variants within SLC44A4. This highlights the importance of this gene in UC biology, thus confirming the finding of the GWAS and also warranting additional studies.
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Affiliation(s)
- A Gupta
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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Dey SK, Joseph T, Kumar S, Kamaladevi A, Sarkar N, Thelma BK, Sarkar S, Balamurugan K, Kundu S. Abstract P067: Novel Antagonists of Dopamine-β-hydroxylase Identified and Validated Through Structure Based Approach to Combat Hypertension. Hypertension 2015. [DOI: 10.1161/hyp.66.suppl_1.p067] [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
Human dopamine β-hydroxylase (hDBH), expressed in noradrenergic nerve terminals of nervous system and in chromaffin cells of adrenal medulla, is a key constituent of catecholamine biosynthetic pathway. DBH inhibition has been shown to help the treatment of hypertension, cardiac hypertrophy and cardiac heart failure, which are major causes of mortality and morbidity worldwide. Existing hDBH inhibitors are too few, often result in side effects and are frequently non-responsive to specific population. Since no three-dimensional structure existed for full-length hDBH, structure based rational drug design was elusive till date, an issue to which we provided solution lately by building an experimentally validated in silico model for hDBH. The model was used in Autodock, Glide SP and XP software for structure based virtual screening against small molecule databases from NCI, USA. The docked structures were scored using Autodock, X-Score and Prime MMGBSA. Thus, 69 compounds were identified as prospective inhibitors of DBH, which were then tested in vitro against human serum DBH and its nearly identical homologue, bovine DBH (586 of 617 amino acids homologous), with known inhibitors nepicastat and disulfiram as positive controls. Three lead molecules UDSC171, UDSC180 and UDSC142 were discovered in the process as potent inhibitors of DBH with IC50s of 1μM, 5.5μM and 18μM, respectively. The binding of the inhibitors to the enzyme were validated using fluorescence and CD spectroscopy as well as ITC, revealing KD values in the range of 100nm to 1μM. In silico pharmacokinetic analysis indicated the molecules to be latest generation of DBH inhibitors having very high cell permeability and inability to cross the blood brain barrier. High doses (up to 50μM) of the lead compounds showed acceptable cellular tolerance against HEK 293 cell line and insignificant hemo-toxicities against human RBCs. Hence, in vivo evaluation of the lead molecules were done in small model systems like C. elegans and D. melanogaster reconfirming their nontoxic properties up to 15μM doses. These three leads are now being tested in cardiac hypertrophy and hypertension rat models with exciting preliminary results.
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Affiliation(s)
- Sanjay K Dey
- Dept of Biochemistry, Univ of Delhi South Campus, New Delhi, India
| | - Toyanji Joseph
- Dept of Genetics, Univ of Delhi South Campus, New Delhi, India
| | - Santosh Kumar
- Institute of Genomics and Integrative Biology, New Delhi, India
| | - A Kamaladevi
- Dept of Biotechnology, Alagappa Univ, Karaikudi, India
| | - Nabanita Sarkar
- Dept of Genetics, Univ of Delhi South Campus, New Delhi, India
| | - B K Thelma
- Dept of Genetics, Univ of Delhi South Campus, New Delhi, India
| | - Surajit Sarkar
- Dept of Genetics, Univ of Delhi South Campus, New Delhi, India
| | - K Balamurugan
- Dept of Biotechnology, Alagappa Univ, Karaikudi, India
| | - Suman Kundu
- Dept of Biochemistry, Univ of Delhi South Campus, New Delhi, India
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Juyal G, Negi S, Sood A, Gupta A, Prasad P, Senapati S, Zaneveld J, Singh S, Midha V, van Sommeren S, Weersma RK, Ott J, Jain S, Juyal RC, Thelma BK. Genome-wide association scan in north Indians reveals three novel HLA-independent risk loci for ulcerative colitis. Gut 2015; 64:571-9. [PMID: 24837172 DOI: 10.1136/gutjnl-2013-306625] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [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] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Over 100 ulcerative colitis (UC) loci have been identified by genome-wide association studies (GWASs) primarily in Caucasians (CEUs). Many of them have weak effects on disease susceptibility, and the bulk of the heritability cannot be ascribed to these loci. Very little is known about the genetic background of UC in non-CEU groups. Here we report the first GWAS on UC in a genetically distinct north Indian (NI) population. DESIGN A genome-wide scan was performed on 700 cases and 761 controls. 18 single-nucleotide polymorphisms (SNPs) (p<5×10(-5)) were genotyped in an independent cohort of 733 cases and 1148 controls. A linear mixed model was used for case-control association tests. RESULTS Seven novel human leucocyte antigen (HLA)-independent SNPs from chromosome 6, located in 3.8-1, BAT2, MSH5, HSPA1L, SLC44A4, CFB and NOTCH4, exceeded p<5×10(-8) in the combined analysis. To assess the independent biological contribution of such genes from the extended HLA region, we determined the percentage alternative pathway activity of complement factor B (CFB), the top novel hit. The activity was significantly different (p=0.01) between the different genotypes at rs12614 in UC cases. Transethnic comparisons revealed a shared contribution of a fraction of UC risk genes between NI and CEU populations, in addition to genetic heterogeneity. CONCLUSIONS This study shows varying contribution of the HLA region to UC in different populations. Different environmental exposures and the characteristic genetic structure of the HLA locus across ethnic groups collectively make it amenable to the discovery of causative alleles by transethnic resequencing. This may lead to an improved understanding of the molecular mechanisms underlying UC.
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Affiliation(s)
- Garima Juyal
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sapna Negi
- National Institute of Immunology, New Delhi, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Aditi Gupta
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Pushplata Prasad
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | | | - Jacques Zaneveld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shalini Singh
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Vandana Midha
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Suzanne van Sommeren
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Jurg Ott
- Key Laboratory of Mental Health Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Sanjay Jain
- Departments of Physics and Astrophysics, University of Delhi, Delhi, India
| | | | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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Senapati S, Gutierrez-Achury J, Sood A, Midha V, Szperl A, Romanos J, Zhernakova A, Franke L, Alonso S, Thelma BK, Wijmenga C, Trynka G. Evaluation of European coeliac disease risk variants in a north Indian population. Eur J Hum Genet 2014; 23:530-5. [PMID: 25052311 PMCID: PMC4666579 DOI: 10.1038/ejhg.2014.137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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] [Received: 10/14/2013] [Revised: 06/10/2014] [Accepted: 06/18/2014] [Indexed: 01/06/2023] Open
Abstract
Studies in European populations have contributed to a better understanding of the genetics of complex diseases, for example, in coeliac disease (CeD), studies of over 23 000 European samples have reported association to the HLA locus and another 39 loci. However, these associations have not been evaluated in detail in other ethnicities. We sought to better understand how disease-associated loci that have been mapped in Europeans translate to a disease risk for a population with a different ethnic background. We therefore performed a validation of European risk loci for CeD in 497 cases and 736 controls of north Indian origin. Using a dense-genotyping platform (Immunochip), we confirmed the strong association to the HLA region (rs2854275, P=8.2 × 10−49). Three loci showed suggestive association (rs4948256, P=9.3 × 10−7, rs4758538, P=8.6 × 10−5 and rs17080877, P=2.7 × 10−5). We directly replicated five previously reported European variants (P<0.05; mapping to loci harbouring FASLG/TNFSF18, SCHIP1/IL12A, PFKFB3/PRKCQ, ZMIZ1 and ICOSLG). Using a transferability test, we further confirmed association at PFKFB3/PRKCQ (rs2387397, P=2.8 × 10−4) and PTPRK/THEMIS (rs55743914, P=3.4 × 10−4). The north Indian population has a higher degree of consanguinity than Europeans and we therefore explored the role of recessively acting variants, which replicated the HLA locus (rs9271850, P=3.7 × 10−23) and suggested a role of additional four loci. To our knowledge, this is the first replication study of CeD variants in a non-European population.
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Affiliation(s)
| | - Javier Gutierrez-Achury
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, India
| | - Agata Szperl
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Jihane Romanos
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Gosia Trynka
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
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