Recent Publications

Govindaraj GM, Jain A, Peethambaran G, Bhoyar R, Vellarikkal SK, Ganapati A, Sandhya P, Edavazhippurath A, Dhanasooraj D, Puthenpurayil JM, Chakkiyar K, Mishra A, Batra A, Punnen A, Kumar S, Sivasubbu S, Scaria V
Spectrum of clinical features and genetic variants in mevalonate kinase (MVK) gene of South Indian families suffering from Hyperimmunoglobulin D Syndrome 
PLoS ONE (2020) Accepted

Mhaske A, Dileep KV, Kumar M, Poojary M, Pandhare K, Zhang KYJ, Scaria V, and Binukumar BK (2020) 
ATP7A Clinical Genetics Resource - a comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Computational and Structural Biotechnology Journal. Accepted (2020)

Kumar M, Gaharwar U, Paul S, Poojary M, Pandhare K, Scaria V, Binukumar BK
Scientific Reports (2020) 10, : 9037 

Sharma S, Rophina M, Poojary M and Scaria V
circad: a comprehensive manually curated resource of circular RNA associated with diseases
Database (2020) Accepted [circAD Resource]

Jagtap U, Sivadas A, Basu S, Verma A, Sivasubbu S, Scaria V, Sachidanandan C.
A Temporal Map of Gene Expression Pattern During Zebrafish Liver Regeneration.
Zebrafish. 2020 Feb;17(1):1-10. doi: 10.1089/zeb.2019.1790. Epub 2019 Nov 26.

GUaRDIAN Consortium
Genomics of rare genetic diseases—experiences from India
Human Genomics (2019) Accepted

Biswas A, Raza A, Das S, Kapoor M, Jayarajan R, Verma A, Shamsudheen KV, Murry B, Seth S, Bhargava B, Scaria V, Sivasubbu S, Rao VR.
Loss of function mutation in the P2X7, a ligand-gated ion channel gene associated with hypertrophic cardiomyopathy.
Purinergic Signal. 2019 Jun;15(2):205-210. doi: 10.1007/s11302-019-09660-7. Epub 2019 May 31.

Thottath J, Vellarikkal SK, Jayarajan R, Verma A, Manamel M, Singh A, Rajendran VR, Sivasubbu S and Scaria V
A novel cathepsin D mutation in 2 siblings with late infantile neuronal ceroid lipofuscinosis
Neurol Genet 5:e302 (2019). doi:10.1212/NXG.0000000000000302

Sivadas A, Scaria V
Population-scale genomics—Enabling precision public health
Advances in Genetics (Academic Press) (2019)

Genomics of Hyper IgD Syndrome - Founder variants dominate the disease in India

posted Sep 6, 2020, 11:47 PM by Vinod Scaria   [ updated Sep 6, 2020, 11:51 PM ]

Hyper-IgD syndrome (HIDS, OMIM #260920) is a rare autosomal recessive autoinflammatory disorder caused by pathogenic variants in the mevalonate kinase (MVK) gene. HIDS has an incidence of 1:50,000 to 1:5,000, and is thought to be prevalent mainly in northern Europe. Here, we report a case series of HIDS from India, which includes ten patients from six families who presented with a wide spectrum of clinical features such as recurrent fever, oral ulcers, rash, arthritis, recurrent diarrhea, hepatosplenomegaly, and high immunoglobulin levels. Using whole exome sequencing (WES) and/or Sanger capillary sequencing, we identified five distinct genetic variants in the MVK gene from nine patients belonging to six families. The variants were classified as pathogenic or likely pathogenic as per the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines for annotation of sequence variants. Over 70% of patients in the present study had two recurrent mutations in MVK gene i.e. a nonsynonymous variant p.V377I, popularly known as the ‘Dutch mutation’, along with a splicing variant c.226+2delT in a compound heterozygous form. Identity by descent analysis in two patients with the recurrent variants identified a 6.7 MB long haplotype suggesting a founder effect in the South Indian population. Our analysis suggests that a limited number of variants account for the majority of the patients with HIDS in South India. This has implications in clinical diagnosis, as well as in the development of cost-effective approaches for genetic diagnosis and screening. To our best knowledge, this is the first and most comprehensive case series of clinically and genetically characterized patients with HIDS from India.

Govindaraj GM, Jain A, Peethambaran G, Bhoyar R, Vellarikkal SK, Ganapati A, Sandhya P, Edavazhippurath A, Dhanasooraj D, Puthenpurayil JM, Chakkiyar K, Mishra A, Batra A, Punnen A, Kumar S, Sivasubbu S, Scaria V
PLoS ONE (2020) 

Chemical screens in a zebrafish model of CHARGE syndrome identifies small molecules that ameliorates disease like phenotypes in embryo

posted May 2, 2019, 3:03 AM by Vinod Scaria   [ updated May 2, 2019, 3:04 AM ]

CHARGE syndrome is an autosomal dominant congenital disorder caused primarily by mutations in the CHD7 gene. Using a small molecule screen in a zebrafish model of CHARGE syndrome, we identified 4 compounds that rescue embryos from disease-like phenotypes. Our screen yielded DAPT, a Notch signaling inhibitor that could ameliorate the craniofacial, cranial neuronal and myelination defects in chd7 morphant zebrafish embryos. We discovered that Procainamide, an inhibitor of DNA methyltransferase 1, was able to recover the pattern of expression of isl2a, a cranial neuronal marker while also reducing the effect on craniofacial cartilage and myelination. M344, an inhibitor of Histone deacetylases had a strong recovery effect on craniofacial cartilage defects and could also modestly revert the myelination defects in zebrafish embryos. CHIC-35, a SIRT1 inhibitor partially restored the expression of isl2a in cranial neurons while causing a partial reversion of myelination and craniofacial cartilage defects. Our results suggest that a modular approach to phenotypic rescue in multi-organ syndromes might be a more successful approach to treat these disorders. Our findings also open up the possibility of using these compounds for other disorders with shared phenotypes.

Cite this Resource:

Zainab Asad and Chetana SachidanandanEuropean Journal of Medical Genetics (2019) In Press.

From Chetana Sachidanandan Lab at CSIR-Institute of Genomics and Integrative Biology

Related Links

Small Molecule Inhibitors of NFkB Reverse Iron Overload and Hepcidin Deregulation in a Zebrafish Model for Hereditary Hemochromatosis Type 3

posted Jul 18, 2018, 11:50 PM by Vinod Scaria   [ updated Feb 1, 2019, 9:05 PM ]

Hereditary hemochromatosis (HH) is one of the most common genetic disorders in Caucasian populations, with no viable therapeutic options except phlebotomy. We describe a zebrafish model of human HH (HH) created by targeted mutagenesis of the gene encoding transferrin receptor 2 (tfr2). TFR2 mutations in humans lead to HH Type 3, a rare but severe form of the disease. The tfr2 mutant model in zebrafish recapitulates the defining features of HH3: iron overload and suppression of hepcidin, the iron regulatory hormone. Using in vivo chemical screens in zebrafish embryos, we identify a new small molecule inducer of hepcidin: SC-514, a specific chemical inhibitor of NFkB signaling. Using independent small molecule inhibitors of the NFkB pathway, we demonstrate that inhibition of NFkB signaling causes induction of hepcidin transcription and reduction of iron overload in the HH3 model. This first successful chemical intervention for hereditary hemochromatosis may also have relevance in treatment of other very prevalent iron regulatory iron overload disorders such as thalassemia.

Cite this Resource:
Basu S, Jalodia K, Ranjan S, Yeh JJ, Peterson RT, Sachidanandan C
Small Molecule Inhibitors of NFkB Reverse Iron Overload and Hepcidin Deregulation in a Zebrafish Model for Hereditary Hemochromatosis Type 3
ACS Chem. Biol.,(2018) DOI: 10.1021/acschembio.8b00317

From Chetana Sachidanandan Lab at CSIR-Institute of Genomics and Integrative Biology

Related Links

Whole exome sequencing in a multi-generation family from India reveals a genetic variation c.10C>T (p.Gln4Ter) in keratin 5 gene associated with Dowling–Degos disease

posted Apr 13, 2018, 10:32 PM by Vinod Scaria   [ updated Apr 13, 2018, 10:33 PM ]

Dowling–Degos disease (OMIM: 179850) is a rare genodermatosis characterized by reticulate pigmentation of the flexures. This disease is inherited in an autosomal dominant pattern, with onset typically in early adulthood. The clinical presentation is with development of hyperpigmented, reticular macules on the face, trunk, axillae and groin. The mutations causing the disease are usually found in the keratin 5 (KRT5) gene and rarely in the protein O-fucosyl transferase 1 (POFUT1) and protein O-glucosyltransferase 1 (POGLUT1) genes. POGLUT1 and POFUT1 are components of the Notch signaling pathway, involved in the differentiation and migration of cells. Mutations in these genes affect the skin more than the hair. Only a few cases suffering from this disease have been described previously from India, as it is a rare disorder with an unknown population frequency. In the current report, we emphasize the utility of whole exome sequencing in the molecular characterization of the genetic defect, in a rare familial case of a reticular pigmentation disorder.

How to cite this article:
Virmani N, Vellarikkal SK, Verma A, Jayarajan R, Sakhiya J, Desai C, Sivasubbu S, Scaria V. Whole exome sequencing in a multi-generation family from India reveals a genetic variation c.10C>T (p.Gln4Ter) in keratin 5 gene associated with Dowling–Degos disease. Indian J Dermatol Venereol Leprol 2018;84:344-6

Chemical and genetic rescue of an ep300 knockdown model for Rubinstein Taybi syndrome in zebrafish

posted Feb 7, 2018, 8:11 PM by Vinod Scaria   [ updated Feb 7, 2018, 8:11 PM ]

EP300 is a member of the EP300/CBP family of lysine acetyltransferases (KATs) with multiple roles in development and physiology. Loss of EP300/CBP activity in humans causes a very rare congenital disorder called Rubinstein Taybi Syndrome (RSTS). The zebrafish genome has two co-orthologs of lysine acetyltransferase EP300 (KAT3B) in zebrafish viz. ep300a and ep300b. Chemical inhibition of Ep300 with C646, a competitive inhibitor and morpholino-based genetic knockdown of ep300a and ep300b cause defects in embryonic development reminiscent of the human RSTS syndrome. Remarkably, overexpression of Ep300a KAT domain results in near complete rescue of the jaw development defects, a characteristic feature of RSTS in human suggesting the dispensability of the protein-interaction and DNA-binding domains for at least some developmental roles of Ep300. We also perform a chemical screen and identify two inhibitors of deacetylases, CHIC35 and HDACi III, that can partially rescue the RSTS-like phenotypes. Thus, modeling rare human genetic disorders in zebrafish allows for functional understanding of the genes involved and can also yield small molecule candidates towards therapeutic goals.

Babu A; Kamaraj M; Basu M; Mukherjee D; Kapoor S; Ranjan S; Swamy MM; Kaypee S; Scaria V; Kundu TK; Sachidanandan C.
Chemical and genetic rescue of an ep300 knockdown model for Rubinstein Taybi Syndrome in zebrafishBBA - Molecular Basis of Disease (2018) 

Genetic epidemiology of Familial Mediterranean Fever through integrative analysis of whole genome and exome sequences from Middle East and North Africa

posted Jun 10, 2017, 6:00 AM by Vinod Scaria

Familial Mediterranean fever (FMF), an autosomal recessive and rare autoinflammatory disease is caused by genetic mutations in the MEFV gene and is highly prevalent in the Mediterranean basin. Though the carrier frequency of specific disease variants in the MEFV gene has been reported from isolated studies, a comprehensive view of variants in the Mediterranean region has not been possible due to paucity of data. The recent availability of whole-genome and whole-exome datasets prompted us to study the genetic epidemiology of MEFV variants in the region. We assembled data from five datasets encompassing whole-genome and whole-exome datasets for 2115 individuals from multiple subpopulations in the region and also created a compendium for MEFV genetic variants, which were further systematically annotated as per the ACMG guidelines. Our analysis points to significant differences in allele frequencies in the subpopulations, and the carrier frequency for MEFV genetic variants in the population to be about 8%. The MEFV gene appears to be under natural selection from our analysis. To the best of our knowledge, this is the most comprehensive study and analysis of population epidemiology of MEFV gene variants in the Middle East and North African populations.

Clinical Genetics (2017) DOI: 10.1111/cge.13070

Development of a Clinical Diagnostic Matrix for characterising Inherited Epidermolysis Bullosa.

posted May 1, 2017, 12:35 AM by Vinod Scaria   [ updated May 1, 2017, 12:35 AM ]

Accurately diagnosing the subtype of Epidermolysis Bullosa (EB) is critical for management and genetic counseling. Modern laboratory techniques are largely inaccessible in developing countries, where the diagnosis remains clinical and often inaccurate. We developed a matrix indicating presence or absence of a set of distinctive clinical features (rows) for the 9 more prevalent EB subtypes (columns). To test an individual patient, the presence or absence of these features was compared to the findings expected in each of the 9 subtypes to see which corresponded the best. If two or more diagnoses scored equally, that with more specific features was selected. The matrix was tested using findings from 74 genetically characterized patients with EB aged >6 months by an investigator blinded to molecular diagnosis. Matrix diagnoses were compared with molecular diagnoses for concordance.Overall, the concordance between the matrix and molecular diagnosis for the 4 major types of EB was 91.9% (kappa co-efficient: 0.88±0.07; p<0.001). The matrix achieved a 75.7% agreement (kappa co-efficient: 0.73±0.04; p<0.001) in classifying EB into its 9 sub-types. The matrix appears to be simple, valid and useful in predicting the type and subtype of EB. An electronic version will facilitate further testing.

Yenamandra, V.K., Moss, C., Sreenivas, V., Khan, M., Sivasubbu, S., Sharma, V.K. and Sethuraman, G.
Development of a Clinical Diagnostic Matrix for characterising Inherited Epidermolysis Bullosa. 
Br J Dermatol. (2016) Accepted Author Manuscript. doi:10.1111/bjd.15221

Unilateral monomorphic hypopigmented macules: A variant of Darier disease

posted Apr 29, 2017, 4:31 AM by Vinod Scaria   [ updated Apr 29, 2017, 4:32 AM ]

Darier disease, also known as keratosis follicularis, is an autosomal dominant genodermatosis that occurs as a result of mutation in the ATP2A2 gene, located on chromosome 12q23-24.1. It encodes the sarcoplasmic/endoplasmic reticulum Ca 2+-ATP isoform 2 protein, which is a calcium pump that transports calcium ions from the cytosol into the sarcoplasmic/endoplasmic reticulum, catalyzing the hydrolysis of adenosine triphosphate. It is classically characterized by follicular and nonfollicular skin colored to reddish brown hyperkeratotic papules, primarily on the seborrheic areas, along with a cobblestone appearance of the buccal mucosa and white/red longitudinal bands on the nail plates that frequently end in V-shaped notching. Zosteriform or linear, cornifying, vesiculobullous, isolated acral hemorrhagic, acrokeratosis verruciformis of Hopf, comedonal and hypopigmented/leukodermic macules are its rare morphological variants.

Sakhiya J, Virmani NC, Sharma YK, Khopkar U, Vellarikkal SK. 
Unilateral monomorphic hypopigmented macules: A variant of Darier disease. 
Indian J Dermatol Venereol Leprol (2017) Apr 29;83:369-71. 

Elucidating the Phenotype and Genotype Spectrum of Junctional Epidermolysis Bullosa in India

posted Feb 21, 2017, 7:52 AM by Vinod Scaria

  • Junctional epidermolysis bullosa (JEB) is a clinically and genetically heterogenous group of genetic skin disorders.•
  • We show the utility of WES in understanding the phenotype and genotype spectrum in four Indian JEB families.•
  • Computational modeling studies have been used to understand the probable molecular consequence of a missense mutation on the structure-function relationship of lamininβ3 protein.•
  • This is the first report documenting the phenotype-genotype correlations of JEB patients from India.
Yenamandra VK, Vellarikkal SK, Kumar M, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Ray SB, Dinda AK, Kabra M, Kaur P, Sharma VK, Sethuraman G
Application of Whole Exome Sequencing in Elucidating the Phenotype and Genotype Spectrum of Junctional Epidermolysis Bullosa: A Preliminary Experience of a Tertiary Care Centre in India
J Dermatol Sci (2017) in press.

Egyptian tale from India: application of whole-exome sequencing in diagnosis of atypical familial Mediterranean fever

posted Feb 21, 2017, 7:48 AM by Vinod Scaria

Autoinflammatory diseases encompass a spectrum of diseases characterized by dysfunction of the innate immune system. Until recently, these diseases were largely classified and diagnosed by the clinical presentation. The recent years have seen the delineation of the molecular mechanisms and specific molecular markers for diagnosing these illnesses.A number of autoinflammatory diseases have well established genetic basis and associated variations as described in literature. Several such diseases also have strong geographical preponderance. Diagnosis of these conditions, therefore, requires an intense clinical suspicion and sound molecular evidence, especially in regions where the prevalence is low. In this manuscript, we report a case of atypical familial Mediterranean fever (FMF) in an Asian Indian patient whose ancestry could be traced to Egypt.

Sandhya P, Vellarikkal SK, Nair A, Ravi R, Mathew J, Jayarajan R, Kumar A, Verma A, Sivadas A, Danda D, Sivasubbu S*, Scaria V*
Egyptian tale from India - application of whole-exome sequencing in diagnosis of atypical Familial Mediterranean Fever
Int J Rheum Dis (2017) DOI: 10.1111/1756-185X.13042

1-10 of 18