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«Aravind Medical Research Foundation is recognized as Scientific and Industrial Research Organization (SIRO) by the Department of Scientific and ...»

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Aravind Medical Research Foundation is recognized as

Scientific and Industrial Research Organization (SIRO) by the

Department of Scientific and Industrial Research (DSIR)

MISSIOn

To eliminate needless blindness by providing

evidence through research and evolving methods

to translate existing evidence and knowledge

into effective action.

bASIC RESEARCH IN

oPHTHALMIC SCIENCES

Annual Report 2011 - 2012

Much has been done, but much remains to be done… we look to the future with renewed strength to continue the mission of providing quality eye care and hope that some of what we have learned will be useful to other eye care workers around the world.

ARAvInD MeDIcAl ReSeARch FOunDAtIOn BOARD OF MAnAgeMent mr. r.D. thulasiraj, Dr. P. NamPerumalsamy, Dr. G. Natchiar, ms, Do er. G. sriNivasaN, be, ms mba ms, fams Dr. r. Kim, Do., DNb Dr. s.r. KrishNaDas, Dr.N.veNKatesh PrajNa Dr. s. araviND, ms, mba Do., DNb., frcophth Do., DNb ReSeARch ADvISORy cOMMIttee InStItutIOnAl RevIew BOARD (IRB) MeMBeRS Chairman Chairman Dr. P. NamPerumalsamy ms. shobhaNa ramaChaNDhraN Chairman - Emeritus Managing Director Aravind Eye Care System TVS Sri Chakra Ltd.

1, Anna Nagar, Madurai – 625 020 Madurai Member-Secretary Member-Secretary Dr.Vr. muthukkaruPPaN Dr. lalitha PrajNa Director - Research Chief Microbiolgist Aravind Medical Research Foundation Aravind Eye Hospital 1, Anna Nagar, Madurai – 625 020 1, Anna Nagar, Madurai - 625 020 MeMberS Members Prof. C. sriNiVasaN Dr. C. mohaN rao UGC Emeritus Professor Director School of Chemistry, Madurai Kamaraj University Centre for Cellular & Molecular Biology 7th Street, Kalvi Nagar, Uppal Road, Hyderabad – 500 007 Nagamalai, Madurai Dr. kumaraVel somasuNDaram Dr. l. thayumaNaVaN Associate professor Sr. Consultant, Gastroenterologist Microbiology and Cell Biology Indian Institute of Science

–  –  –

Research Scholars at AMRF 46 IntRODuctIOn Fundamental research is essential for the design of optimal treatment options in ophthalmic diseases in addition to the understanding of the disease process. Genetic architecture, metabolic status, predisposition to diseases as well as cultural habits play a direct role in disease onset, progression, severity and response to treatment. Next generation sequencing is now creating a wealth of data, which will go a long way in the understanding of human genome in general. Recent introduction of Smart-seq methodologies allows the transcriptome analysis of a single human cell, which carries just ten picograms of RNA. High throughput analysis brings genetics to general medical practice at an affordable cost. These and other related developments in technologies have to be in place to understand ophthalmic diseases. Aravind Medical Research Foundation is harnessing many of these modern techniques towards the analysis of ophthalmic diseases. Another area of research is retinoblastoma, a pediatric cancer. Genetic and functional organization of selected genes will be examined in this important disease.

Molecular Ophthalmic Genetics group is focusing on the genetics of various inherited eye diseases in Indian population. The ongoing research programmes include primary open angle glaucoma, albinism, diabetic retinopathy, keratoconus, globe anomalies, leber hereditary optic neuropathy, leber congential amaurosis and retinoblastoma. Various genetic changes involved directly or indirectly in the pathogenesis of these disorders were identified using direct sequencing method. Recently next generation sequencing and microarray based chip analysis were also used. In addition, expression, function and structure of selected proteins are also being studied with the help of bioinformatics tools. In a new dimension of genetics, studies correlating mitochondrial dysfunction with some of the age related ocular disorders and tumor initiation and progression have been initiated. The involvement of some ambiguous genetic changes like synonymous variations and copy number alteration in the pathogenesis of these ocular disorders are also examined. These studies will help to understand molecular mechanism and find new candidate genes/biomarkers involved in the pathogenesis of eye diseases.

Main focus of the research of Ocular Microbiology group is on understanding the immune response in fungal and bacterial corneal ulcers with the aim of identifying potential targets that can be used in treatment. The pathogenesis and virulence mechanisms of other common ocular conditions caused by mycobacterial, leptospiral and trematode infections are also being studied. The thrust areas of research also include detection and discovery of novel pathogens causing various eye infections using both conventional and newer molecular technologies. These studies will help ophthalmologists and vision scientists working with infectious eye diseases to devise newer strategies to combat and prevent blindness due to infections.

The study of proteomics is important because proteins are responsible for both the structure and functions of the living organisms. The levels of proteins and interactions at the cellular level help in understanding the disease progression better. The function and localization of proteins are important assessors for the proper functioning of the cells. The Proteomics Group at Aravind Medical Research Foundation is engaged in using this leading technology to understand ocular diseases such as fungal keratitis, diabetic retinopathy and glaucoma, which are widely prevalent in Indian population. Understanding of the disease and progression at the protein level will help us to assess the host response to pathogen as well. Such gained knowledge will ultimately personalize the treatment strategies for individual patients. The diagnosis of potential biomarkers may help to understand the population at risk, so that effective and early treatment strategies can be planned in a cost effective manner. Fungal keratitis is a disease, most common in developing countries such as India, Bangladesh, Nepal and China; hence knowledge gained will immensely benefit people from the lower socio economic group. The sheer importance of diabetic retinopathy and the lack of effective screening mechanisms for primary open angle glaucoma have prompted this group to concentrate on these two common eye diseases also. The aim of the research carried out is to apply a variety of proteomic tools to understand the host pathogen interactions and to identify new diagnostic, prognostic and therapeutic biomarkers for these clinical conditions.





The main focus of research of the Immunology group is to understand the pathogenic mechanism associated with development of infectious uveitis. Extensive studies on leptospiral uveitis, which occurs weeks to months after systemic infection, are being carried out. The current thrust of research is to understand (i) the host immune response to leptospiral infection at cellular level in the eye of patients with leptospiral uveitis and (ii) the role of autoimmune mechanisms in the development of cataract, in leptospiral uveitis patients.

The concept of stem cells in regenerative medicine is gaining prominence in recent times. The Stem Cell Group has developed a simpler method for the identification and quantification of human corneal epithelial stem cells using fluorescence microscopy. Current focus of this group is (i) understanding the human limbal stem cell biology with reference to characterization of limbal niche factors that are responsible for their maintenance and expansion and (ii) identification of their molecular signature using an enriched stem cell population.

Ocular Pharmacology group has been interested in understanding the pathogenic mechanism of diabetic retinopathy and age-related macular degeneration and in developing methods to identify glaucoma in donor eyes in addition to ocular pharmacokinetics.

MOleculAR genetIcS Molecular ophthalmic genetics laboratory at Aravind medical research foundation is focusing on the genetics of various inherited eye diseases in Indian population. The ongoing research programme involves primary open glaucoma, albinism, diabetic retinopathy, keratoconus, globe anomalies, leber hereditary optic neuropathy, leber congenital amaurosis and retinoblastoma. Various genetic changes involved directly or indirectly in the pathogenesis of these disorders have been identified by the institute with the aid of gold standard direct sequencing method. Recently, the institute has moved forward in advanced sequencing technologies like next generation sequencing and microarray based chip analysis. In addition, gene coded protein expression, function and structures are also being studied with the help of bioinformatic tools. In a new dimension of genetics, studies correlating mitochondrial dysfunction with some of the age related ocular disorders and tumor initiation and progression have been initiated. The involvement of some ambiguous genetic changes like synonymous variations and copy number alteration in the pathogenesis of these ocular disorders are also being analysed. These studies will help understand the molecular mechanism and find new candidate genes/biomarkers involved in the pathogenesis of disease.

Molecular genetics of Leber Congenital Amaurosis in South Indian population Investigators : P. Sundaresan, Aravind Medical Research Foundation, Madurai P. Vijayalakshmi, Aravind Eye Hospital, Madurai Research scholar : Anshuman Verma Funding agency : Indian Council of Medical Research (ICMR), University Grant Commission (UGC) Fellowship background and aim Leber Congenital Amaurosis (LCA) is the most severe form of visual impairment found in children. At present, 16 genes have been reported for LCA and among them, RPE65 is a suitable candidate for gene therapy. The aim of this study is to identify mutations in RPE65 and a comprehensive mutational screening of all other LCA genes.

In this study, the three sequencing technologies adopted were: (a) Gold standard direct sequencing to screen RPE65 mutations in 30 LCA probands; (b) Microarray based comprehensive detection for all known LCA pathogenic variations in 25 individual LCA patients without RPE65 mutation; (c) Next generation sequencing (NGS) based targeted exome enrichment in 25 LCA pooled DNA samples to screen coding regions of 56 genes, which includes 15 known and 41 predicted LCA genes.

In five LCA patients, direct sequencing analysis of RPE65 identified four different pathogenic mutations which include two novel - c.361insT, c.939T A and two known c.394GA, c.361delA mutations. In the microarray based chip analysis, 9 of 25 LCA patients revealed twelve known pathogenic mutations in 5 LCA genes – GUCY2D, RPGRIP1, AIPL1, CRX and IQCB1. The targeted resequencing of 56 genes in a separate set of 25 LCA samples uncovered total 97 variations, mostly in known LCA genes and a few predicted genes. However, most of the variations were in flanking intronic regions and found to be as polymorphism.

Implication of the project This is the first study in South Indian LCA cohort, which applies advanced available techniques for a comprehensive mutational analysis of LCA genes. Based on direct sequencing results, RPE65 mutations account for 16% of LCA cases. The chip analysis was instrumental to identify known pathogenic mutations in 38% of the patients with the major involvement of GUCY2D (14%) followed by RPGRIP1 (12%), AIPL1 (4%), CRX (4%) and IQCB1 (4%). The NGS based targeted exome resequencing can be productive for the comprehensive screening of a large number of genes but are unfavourably influenced by various sequencing steps in pooled samples, which results in its limitation to identify rare pathogenic variations and therefore, only common variations could be achieved.

Presentations

• Anshuman Verma, Sundaresan Periasamy, Vijayalakshmi Perumalsamy. A Novel Insertional RPE65 Mutation in Southern Indian Cohort of Leber Congenital Amaurosis (LCA) at ARVO’s 2011 Annual Meeting, Visionary Genomics, in Fort Lauderdale, Florida, USA.

• Anshuman Verma, Sundaresan Periasamy, Vijayalakshmi Perumalsamy. Screening of RPE65 gene in Southern Indian cohort of LCA patients at IERG 19th annual meeting, LVPEI, Hyderabad, July 30 31st, 2011.

evaluation of SNPs on chromosome 2p with Primary Open Angle Glaucoma in the South Indian Cohort Investigators : P. Sundaresan, Aravind Medical Research Foundation, Madurai S.R. Krishnadas, Aravind Eye Hospital, Madurai Collaborator : J. Fielding Hejtmancik, National Eye Institute, NIH, MD, USA Work done by : B. Suganthalakshmi Funded by : Alcon, Aravind Medical Research Foundation background and aim Glaucoma comprises a heterogeneous group of optic neuropathies with a complex genetic basis. It is the second leading cause of irreversible blindness in the world. Primary Open Angle Glaucoma (POAG) is the most common form of glaucoma. Research breakthroughs have shown that many genes have a key role in the pathogenesis of POAG. The prevalence of mutations in the known candidate genes (MYOC, OPTN, WDR36) associated with the disease pathogenesis is only 4-5%. In the earlier studies conducted at the institute, the frequency of MYOC mutations was identified to be about 2% in South Indian POAG population.

Researchers continue to identify the genetic loci that appear to be major risk factors for POAG. In the study from an Afro-Caribbean population in Barbados, a strong association was demonstrated between POAG and a closely spaced group of markers including rs1533428, rs12994401, rs10202118, rs11125375, and rs11889995. In order to investigate the genetic basis of POAG, a possible association of these markers in Indian POAG patients was tested.

A case-control study was performed using unrelated 220 POAG cases and 220 age matched healthy controls recruited through the Aravind Eye Hospital in Madurai. A set of five SNPs (rs1533428, rs12994401, rs10202118, rs11125375 and rs11889995) on chromosome 2p was evaluated in these two groups and genotyped using Taq Man SNP genotyping assay. Statistical analysis was performed using the SVS program package by Golden Helix to identify the distributions of allele, genotype frequencies, fisher exact test p-values, odds ratios and Hardy Weinberg equilibrium. Linkage disequilibrium (LD), haplotype blocks, tagging SNPs, and HWE were examined using Haploview v3.32, and association was calculated using the SVS implementation. The p values 0.05 after correction for multiple testing using a Bonferroni correction were considered to be statistically significant.



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