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

Rescue of neural crest derived phenotypes in a zebrafish CHARGE model by sox10 downregulation

posted Jul 21, 2016, 4:44 AM by Vinod Scaria   [ updated Jul 21, 2016, 4:47 AM ]

CHD7 mutations are implicated in a majority of cases of the congenital disorder, CHARGE syndrome. CHARGE, an autosomal dominant syndrome, is known to affect multiple tissues including eye, heart, ear, craniofacial nerves and skeleton and genital organs. Using a morpholino-antisense-oligonucleotide-based zebrafish model for CHARGE syndrome, we uncover a complex spectrum of abnormalities in the neural crest and the crest-derived cell types. We report for the first time, defects in myelinating Schwann cells, enteric neurons and pigment cells in a CHARGE model. We also observe defects in specification of peripheral neurons and craniofacial skeleton as previously reported. Chd7 morphants have impaired migration of neural crest cells and deregulation of sox10 expression from the early stages. Knocking down sox10 in the zebrafish CHARGE model rescued the defects in Schwann cells and craniofacial cartilage. Our zebrafish CHARGE model thus reveals important regulatory roles for Chd7 at multiple points of neural crest development viz., migration, fate choice and differentiation and we suggest that sox10 deregulation is an important driver of the neural crest-derived aspects of chd7 dependent CHARGE syndrome.

Asad Z, Pandey A, Babu A, Sun Y, Shevade K, Kapoor S, Ullah I, Ranjan S, Scaria V, Bajpai R, Sachidanandan C.
Hum Mol Genet. 2016 Jul 13. pii: ddw198. [Epub ahead of print]

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Case Report: Whole exome sequencing reveals a novel frameshift deletion mutation p.G2254fs in COL7A1 associated with autosomal recessive dystrophic epidermolysis bullosa

posted Jun 19, 2016, 5:36 AM by Vinod Scaria   [ updated Jun 27, 2016, 2:32 AM ]

Dystrophic epidermolysis bullosa simplex (DEB) is a phenotypically diverse inherited skin fragility disorder. It is majorly manifested by appearance of epidermal bullae upon friction caused either by physical or environmental trauma. The phenotypic manifestations also include appearance of milia, scarring all over the body and nail dystrophy. DEB can be inherited in a recessive or dominant form and the recessive form of DEB (RDEB) is more severe. In the present study, we identify a novel p.G2254fs mutation in COL7A1 gene causing a sporadic case of RDEB by whole exome sequencing (WES). Apart from adding a novel frameshift Collagen VII mutation to the repertoire of known mutations reported in the disease, to the best of our knowledge, this is the first report of a genetically characterized case of DEB from India.

F1000Research 2016, 5:900 (doi: 10.12688/f1000research.8380.1)

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mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets

posted Jan 24, 2016, 4:19 AM by Vinod Scaria   [ updated Jun 19, 2016, 5:32 AM ]

The human mitochondrial genome has been reported to have a very high mutation rate as compared with the nuclear genome. A large number of mitochondrial mutations show significant phenotypic association and are involved in a broad spectrum of diseases. In recent years, there has been a remarkable progress in the understanding of mitochondrial genetics. The availability of next-generation sequencing (NGS) technologies have not only reduced sequencing cost by orders of magnitude but has also provided us good quality mitochondrial genome sequences with high coverage, thereby enabling decoding of a number of human mitochondrial diseases. In this study, we report a computational and experimental pipeline to decipher the human mitochondrial DNA variations and examine them for their clinical correlation. As a proof of principle, we also present a clinical study of a patient with Leigh disease and confirmed maternal inheritance of the causative allele. The pipeline is made available as a user-friendly online tool to annotate variants and find haplogroup, disease association, and heteroplasmic sites. The "mit-o-matic" computational pipeline represents a comprehensive cloud-based tool for clinical evaluation of mitochondrial genomic variations from NGS datasets. The tool is freely available at 

Human Mutation. 2015 Apr;36(4):419-24.

Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis

posted Aug 25, 2015, 12:32 AM by Vinod Scaria   [ updated Jun 19, 2016, 5:37 AM ]

Lamellar ichthyosis (LI), considered an autosomal recessive monogenic genodermatosis, has an incidence of approximately 1 in 250,000. Usually associated with mutations in the transglutaminase gene (TGM1), mutations in six other genes have, less frequently, been shown to be causative. Two siblings, born in a collodion membrane, presented with fish like scales all over the body. Karyotyping revealed duplication of the chromosome arm on 22q12+ in the father and two siblings. Whole exome sequencing revealed a homozygous p.Gly218Ser variation in TGM1; a variation reported earlier in an isolated Finnish population in association with autosomal recessive non-syndromic ichthyosis. This concurrence of a potentially benign 22q12+ duplication and LI, both rare individually, is reported here likely for the first time.

Gupta A, Sharma Y, Deo K et al. 
Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis. 
F1000Research 2015, 4:446 (doi:10.12688/f1000research.6779.1)

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