Kallam Anji Reddy Molecular Genetics Laboratory
The Kallam Anji Reddy Molecular Genetics Laboratory, established with the generous support of Dr K Anji Reddy of Dr Reddy's Laboratories, Hyderabad, conducts research leading to the understanding of underlying molecular mechanisms in various inherited eye disorders. This laboratory has facilities for advanced research in molecular genetics and molecular biology and is equipped with thermal cyclers, gel documentation units, spectrophotometer, electrophoresis equipment, dHPLC - a Real Time PCR and two automated DNA sequencers.
The primary focus lies in identifying and characterizing the genes involved in ocular disorders, understanding their mutation spectrum, screening SNPs that could be potential risk factors for the disease condition and generating haplotypes to understand the origin, evolution and differentiation of the mutations. Based on this an attempt is made towards establishing a genotype-phenotype correlation that may be useful to monitor prognosis. Identification of gene mutations and variants can further lead to devising molecular diagnostics for rapid screening and early intervention. In addition, functional studies are also being undertaken by cloning and expressing the disease-causing genes, and studying the resultant proteins so as to determine the molecular phenotype based on the function of the proteins and their interactions.
Kallam Anji Reddy Molecular Genetics Laboratory and Champalimaud Translational Centre for Eye Research (C-TRACER)
Genetic evaluation of factor B and complement component C2 in the susceptibility to age related macular degeneration
Investigators: Inderjeet Kaur, Rajeev K Reddy, Saritha Katta, Raja Narayanan, Annie Mathai, Ajit B Majji, Subhabrata Chakrabarti
Support: Department of Science and Technology, India
Age related macular degeneration (AMD) has been implicated to multiple variations in several complement factor genes. Factor B (CFB) and component C2 genes are located in the major histocompatibility complex class III region (6p21) and are found to be expressed in the neural retina, retinal pigment epithelium (RPE) and choroids. Our study results have indicated that SNPs in C2 and CFB gene appear to confer significant protection to AMD in India. Also, we found a potential risk haplotype within an extended region of CFH (without Y402H) with AMD susceptibility in the Indian cohort.
Establishing a “risk assessment chip” for the eye disease age related macular degeneration
Investigators: Subhabrata Chakrabarti, Raja Narayanan, Rajeev K Reddy, Inderjeet Kaur, Paul N Baird,1 Robyn H Gyner1
Support: Indo-Australia Biotechnology Fund, Department of Biotechnology, India
AMD is the most frequent cause of blindness in Australia and has been recognized as an increasingly major cause of blindness in India. AMD is now known to have strong genetic as well as environmental risk factors, the latter including smoking, diet, inflammatory factors and vascular parameters. Discovery of the CFH gene and other susceptibility genes have led to a renewed push to identify those gene variants as well as explore gene-environmental interactions associated with the disease. This project seeks to identify variants through genome-wide association study (GWAS) using high density SNP and copy umber microarray that would accurately identify disease risk across different ethnic groups in Australia and India. The outcomes would help to offer targeted treatment options to the susceptible patients thereby improving their quality of life and reducing the burden of AMD in the wider community.
Genetic and phenotypic comparison of primary congenital glaucoma in India and Brazil
Investigators: Subhabrata Chakrabarti, Anil K Mandal, Ivan M Tavares,2 Jose P C Vasconcellos,3 Monica Mello3
Support: Department of Science and Technology, India (Indo-Brazil collaborative program)
Primary congenital glaucoma (PCG) results in an irreversible blindness in children and is largely attributed to mutations in the CYP1B1 gene. While the estimates of mutation frequencies vary widely across populations, there are subtle commonalities with respect to the prevalent mutation among different populations on a uniform haplotype background as evidenced from the mutation spectrum among PCG patients from Brazil and India. The present study would try to unravel the similarities and dissimilarities in the genetic basis of PCG among the Brazilian and Indian patients and understand the origin and migration of the mutations across these populations.
Central India eye & medical study
Investigators: Subhabrata Chakrabarti, Jonas Jost,4 Vinay Nangia,5 Inderjeet Kaur
Support: University of Heidelberg, Germany
The Central India Eye and Medical Diseases (CIEMS) is a large population study in a rural central Indian region (Nagpur) on 5000 individuals above 40 years of age. This study aims to understand the prevalence of various eye and other systemic diseases in this population. As part of this study, we would characterize the genetic risk factors in this population for the prevalent eye diseases based on whole genome and candidate gene screening, genotype-phenotype correlation and gene-environment interactions.
Genetic comparison of primary congenital glaucoma in India and Tunisia – Understanding the possible founder effects
Investigators: Subhabrata Chakrabarti, Anil K Mandal, Guemira Fethi,6 E A Mhd Ali,7 Douik Hayet,7 G Abderraouf,8 Harzallah Latifa,8 Bouassida Jihene8
Support: Department of Science and Technology, India (Indo-Tunisia collaborative program)
Primary congenital glaucoma (PCG) attributed to mutations in the CYP1B1 gene affects different populations worldwide. These mutations exhibit a strong geographical clustering based on a uniform haplotype background as evidenced from the mutation spectrum among PCG patients in Morocco, Saudi Arabia and India. So far, there are no reports on the genetics of PCG in Tunisia. The present study would try to unravel the similarities and dissimilarities in the genetic basis of PCG in Tunisian and Indian patients and understand the origin and migration of common mutations across these two populations.
Developing a global blueprint for zero PCG: Understanding the molecular basis of PCG
Investigators: Subhabrata Chakrabarti, Partha P Majumder,1 Luba Kalaydijeva,2 Inderjeet Kaur, Anil K Mandal, K Narayanasamy,3 Jamie Craig,4 Ivailo Tournev,5 Silvia Cherninkova
Support: Indo-Australia Biotechnology Fund, Department of Biotechnology, India
In continuation to the ongoing genetics work in PCG, the present study is based on identifying the n characterized genes in PCG through the model of human evolution. The premise is based on the background of the evolution and migration of gypsies from India. The cohort comprises an isolated population (gypsies) derived from an ancestral population (Indian), which was founded in the recent timescale of evolution, as a result of which it would have undergone a minimum number of genetic recombinations. Gypsy patients exhibit 20% CYP1B1 mutations in PCG, while it is around 40% for Indian patients. The study employs a GWAS in PCG cases and controls in both the cohorts using the 1.8 million SNP Affymetrix array. We plan to derive the regions of shared haplotypes across the genomes and identify the conserved regions between these two groups, which would harbor mutations in gene(s) causing PCG.
Genetics of retinal dystrophies
Investigators: Chitra Kannabiran, Hardeep Singh, Rachna Shukla, Subhadra Jalali, R Narayanan
Support: Champalimaud Foundation, Portugal, Department of Biotechnology, India
Retinal dystrophies are degenerative disorders of the retinal photoreceptors resulting in irreversible blindness. They are caused by single gene defects and are extremely heterogeneous in genetic causation. We are studying the genetics of different types of dystrophies including congenital (LCA) and later-onset forms. Mapping and candidate gene screening have led to identifi cation of novel mutations in genes for autosomal recessive retinal dystrophy in a few families. Screening of candidate genes in Lebers congenital amaurosis (LCA) is being done to determine the major causes of LCA in the Indian population.
Novel causes of congenital hereditary cataract
Investigators: Chitra Kannabiran, Surya Prakash G Ponnam, Ramesh Kekunnaya, Jyoti Matalia, Sushma Tejwani, BSR Murthy.
Support: Council of Scientifi c and Industrial Research, India
Collaborators: Ghanshyam Swarup,6 Linda Musil7
Congenital hereditary cataracts occur in infants and children and are inherited as single gene defects
commonly through autosomal dominant and recessive modes of inheritance. We carried out a genetic screen of several known genes for hereditary cataract in several families with autosomal forms of cataract. Interesting pathogenic mutations were found in gap junction and lens membrane protein genes. These are being studied further using molecular and cell biologic approaches for changes in the properties of the protein to understand the basis for cataract.
Characterization of the SLC4A11 gene responsible for corneal endothelial dystrophy
Investigators: Chitra Kannabiran, Neerja Sharma
Support: Champalimaud Foundation, Portugal
Our previous studies involved mapping and identifi cation of the causative gene for the recessive form of congenital hereditary endothelial dystrophy (CHED), a disease involving corneal opacities in infants and young children. The gene identifi ed by ourselves and others was the sodium bicarbonate transporter-related gene, SLC4A11. We are studying the wild type and mutant proteins (found in CHED patients) encoded by this gene in order to understand its properties and its pathogenic basis usinf suitable experimental systems.
Developing a global blueprint for zero PCG: Understanding the molecular basis of PCG
Investigators:Subhabrata Chakrabarti, Partha P Majumder,1 Luba Kalaydijeva,2 Inderjeet Kaur, Anil K Mandal, K Narayanasamy,3 Jamie Craig,4 Ivailo Tournev,5 Silvia Cherninkova5
Support: Indo-Australia Biotechnology Fund, Department of Biotechnology, India
In continuation to the ongoing genetics work in PCG, the present study is based on identifying the n characterized genes in PCG through the model of human evolution. The premise is based on the background of the evolution and migration of gypsies from India. The cohort comprises an isolated population (gypsies) derived from an ancestral population (Indian), which was founded in the recent timescale of evolution, as a result of which it would have undergone a minimum number of genetic recombinations. Gypsy patients exhibit 20% CYP1B1 mutations in PCG, while it is around 40% for Indian patients. The study employs a GWAS in PCG cases and controls in both the cohorts using the 1.8 million SNP Affymetrix array. We plan to derive the regions of shared haplotypes across the genomes and identify the conserved regions between these two groups, which would harbor mutations in gene(s) causing PCG.
Novel causes of congenital hereditary cataract
Investigators: Chitra Kannabiran, Surya Prakash G Ponnam, Ramesh Kekunnaya, Jyoti Matalia, Sushma Tejwani, BSR Murthy.
Support: Council of Scientifi c and Industrial Research, India
Collaborators: Ghanshyam Swarup,6 Linda Musil7
Congenital hereditary cataracts occur in infants and children and are inherited as single gene defects commonly through autosomal dominant and recessive modes of inheritance. We carried out a genetic screen of several known genes for hereditary cataract in several families with autosomal forms of cataract. Interesting pathogenic mutations were found in gap junction and lens membrane protein genes. These are being studied further using molecular and cell biologic approaches for changes in the properties of the protein to understand the basis for cataract.
Characterization of the SLC4A11 gene responsible for corneal endothelial dystrophy
Investigators:Chitra Kannabiran, Neerja Sharma
Support: Champalimaud Foundation, Portugal
Our previous studies involved mapping and identifi cation of the causative gene for the recessive form of congenital hereditary endothelial dystrophy (CHED), a disease involving corneal opacities in infants and young children. The gene identifi ed by ourselves and others was the sodium bicarbonate transporter-related gene, SLC4A11. We are studying the wild type and mutant proteins (found in CHED patients) encoded by this gene in order to understand its properties and its pathogenic basis usinf suitable experimental systems.
Genetics of Retinoblastoma
Investigators: Chitra Kannabiran, Vidya Parsam, Md Javed Ali, Santosh Honavar, Geeta Vemuganti
Support: Champalimaud Foundation, Portugal
Retinoblastoma is an intraocular malignancy involving the retinal precursor cells and affects children below the age of 5 yrs. It is caused by mutations in the RB1 gene. We developed an effective screening protocol for retinoblastoma using patients' genomic DNA, that can potentially identify the oncogenic mutation in >80% of patients. We have also performed analysis of the RB1 mRNA in patients to further detect changes that were not detectable in DNA analysis.
Ocular Microbiology Service, LVPEI, Bhubaneswar
Ocular infections caused by Staphylococcus species: Study of clinico-microbiologic features, virulence markers and genome profile
Investigators: Savitri Sharma, DV Singh1
Support: Department of Science and Technology, India
Staphylococci are normal flora in the conjunctiva and at the same cause a variety of eye infections. This project aims to determine the clinical profile of various ocular infections caused by different species of Staphylococcus, identify Staphylococcus species causing ocular infections by phenotypic methods, determine antibiotic susceptibility of the clinical isolates of staphylococci from ocular infections and normal eyes, determine virulence factors of the clinical isolates of staphylococci from ocular infections and from normal eyes, perform genetic profiling of methicillin sensitive and resistant Staphylococcus species and compare clinical, phenotypic and genotypic features of methicillin sensitive and resistant Staphylococcus species. Sixty staphylococcal isolates from clinical samples and 35 isolates from normal individuals have been characterized phenotypically using ATB system and their antibiotic susceptibility has been tested by minimum inhibitory concentration of number of antibiotics. Currently, the isolates are being tested for the presence of mecA gene that determines methicillin resistance.
1Centre for Eye Research Australia (CERA), University of Melbourne, Australia
2Vision Institute, Federal University of Sao Paolo, Brazil
3Campinas State University, Sao Paolo, Brazil
4Department of Ophthalmology, University of Heidelberg, Manheim, Germany
5Suraj Eye Institute, Nagpur, India
6Institut Salah Azaiz, Tunis, Tunisia
7Service d’Ophthalmologie, Habib Thameur Hospital, Tunis, Tunisia
8Service de Biologie Clinique, Institut Salah Azaiz, Tunis, Tunisia