NIBMG

Shouvik PaulSupervisor: SOUVIK MUKHERJEE

Brief Description of Project

Diabetes affects almost 537 million people worldwide and 71 million people in India. Diabetic Foot Ulcers (DFUs) are a dreaded complication of Diabetes and 15-25% of diabetic patients run the risk of developing DFU in their lifetime. DFU infections are polymicrobial and bacterial biofilm formation in chronic wounds leads to persistent antibiotic resistance often resulting in limb amputation and de
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ath. Conventional culture-based methods cannot detect the viable but non-culturable (VBNCs) microbes. Massively parallel sequencing can identify both culturable and non-culturable microbes collectively termed as the microbiome. My research interest is to characterize (a) longitudinal shift in the composition and diversity of DFU microbiome both pre and post antibiotic treatment, (b) biofilm formation by confocal microscopy and (c) antibiotic resistance profiling of clinical isolates. Besides these, I will also identify host gene expression patterns in different cell types in chronic non-healing DFUs and integrate it with metagenomic as well as clinical factors to understand their contribution in impairment of wound healing. Read less
Shrayashi BiswasSupervisor: SAMSIDDHI BHATTACHARJEE

Brief Description of Project

Genome wide association studies (GWAS) are used to discover association of genetic variants with various complex diseases and traits. However, testing markers across the genome in an unbiased manner leads to loss of power for such studies. My research project deals with increasing the power of such genome wide studies by incorporating information from other sources. Knowledge from pathways,
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gene expression/eQTL studies and transcriptional regulation can be integrated with the information from GWAS to help in identifying variants that could be otherwise missed in an unbiased genome-wise search. My work emphasizes on building a pipeline for integrative statistical analysis of such multi-omics data. The pipeline will enable investigators to discover novel genetic variants and understand their mode of action, thus helping to elucidate the underlying genetic makeup of complex diseases.
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Subhashis GhoshSupervisor: SANDEEP SINGH

Brief Description of Project

Human oral squamous cell carcinoma (OSCC) is the eighth most common cancer worldwide; and, the most prevalent cancer among men and fourth most common among women in India. Owing to the highly heterogeneous nature of oral carcinoma at both cellular and molecular levels, it is important to investigate the functions of altered pathways with respect to distinct cancer cell-types present wit
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hin the tumor as well as in its microenvironment. In the context of cell-cell interactions, NOTCH related signaling is intriguing because of its juxtacrine mode of action. Therefore, I am interested in studying the functional consequences of altered NOTCH related genes and its regulation within oral tumors. My focus is to examine the mechanisms of reciprocal interactions between diverse cell-types and its significance in oral cancer initiation and progression.
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Sukanya MitraSupervisor: Moulinath Acharya

Brief Description of Project

Congenital muscular dystrophy and myopathy belong to a group of rare neuromuscular disorders. A common subtype of these heterogeneous disorders caused by mutations in nuclear proteins is Emery-Dreifuss muscular dystrophy (EDMD). Mutation in emerin (EMD) causes X-linked EDMD and autosomal dominant EDMD is caused due to mutations in muscle specific nuclear envelop transmemebrane proteins - lamin A (
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LMNA), nesprin1, nesprin2, SUN1 and FHL1. Using whole exome sequencing in Indian patients, a number of mutations in EMD and LMNA were reported from our lab. My research is focused on functional characterization of these mutants in vivo in both human skeletal muscle cells and in zebrafish which would provide a better insight of heterogeneity in EDMD pathogenesis. Further, by understanding the process of myogenesis in human skeletal muscle myoblasts, I would like to investigate the interplay among various molecular players in background of EMD and LMNA mutants towards progression of EDMD pathogenesis. Read less
Sumitava RoySupervisor: ARINDAM MAITRA

Brief Description of Project

Intratumor heterogeneity is among the greatest challenges in treatment of cancer. In spite of disruptive advances in sequencing technologies achieved over the last decade, high resolution comprehension of such heterogeneity has been beyond our reach until recently. Developments in high-throughput Single Cell RNA-Seq (SC-RNASEQ) may now enable us to dissect the diverse cellular populations of
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tumors. In the future these technologies might inform the selection of targeted combination therapies and enrollment criteria for clinical trials. I am working on single cell RNA-Seq approaches to investigate the role of intratumour heterogeneity in tumour recurrence in Oral squamous cell carcinoma gingivo-buccal (OSCC-GB). My objective is to excavate the landscape of intratumor heterogeneity at single cell resolution and identify important clues on how cell type diversity relates to cancer recurrence.
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Supratim GhoshSupervisor: ARINDAM MAITRA

Brief Description of Project

Understanding the genomics of health and wellbeing is essential for unravelling of genomic underpinnings of diseases. Expression quantitative trait loci (eQTLs) are known to play an important role in the various biological processes which determine health. However, analysis of eQTLs in gene expression data from bulk tissues is challenging due to the use of average gene expression across multiple c
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ell types as input for eQTL mapping. In recent years, single-cell RNA sequencing has led to the understanding that each cell type has unique gene expression signatures and cell state. Elucidation of the role of eQTLs in defining the healthy state can be achieved by using single-cell-based studies of the immune cells. My interest is to investigate the role of genomic variations in regulating cell-type-specific gene expression in peripheral blood immune cells which may provide important insights into blood immunity and thereby our health and wellbeing. Read less
Tahseen AhmedSupervisor: Moulinath Acharya

Brief Description of Project

Developmental glaucoma spectrum disorders include conditions such as aniridia, Axenfeld-Rieger syndrome, Peter's anomaly and primary congenital glaucoma that severely affect the eye anterior segment along with the retina and optic nerve. Ten genes were found mutated in a cohort of patients having this disease spectrum. Bioinformatic analyses indicated possible interactions between two mutated gene
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s; WT1 and MMP9 and further in silico investigation suggested presence of putative WT1 binding site on MMP9 promoter. WT1, being a transcription factor is known for its promiscuity, acting as both activator and repressor of transcription in various tissue types. Interestingly, WT1 is also in close genomic proximity with another transcription factor, PAX6, which is reportedly a master regulator of eye anterior segment development. We are currently doing reverse genetics in zebrafish along with other molecular biology techniques to elucidate any underlying interactions and possible role of these transcription factors in developmental glaucoma spectrum disorders. Read less
Vijay Laxmi RoySupervisor: PARTHA PRATIM MAJUMDER

Brief Description of Project

An individual is provided medication, whether vaccine or drug, without taking into account the genomic background of the individual; i.e., a one-size-fits-all approach is used. However, it is known that genetic differences strongly account for inter-individual variability in treatment response, leading to huge wastage of funds and resources. This economic burden can be drastically minimize
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d by genomic technologies. Very little is known in India about drug-response in relation to the genomic background of medication-recipient. The investigation of genetic backgrounds of recipients of medication can unfold key mechanisms associated with medication efficacy, which could be harnessed to design better medications for overcoming failure and poor response of current therapies.

Aim of the current study is to identify the genomic correlates of medication response to design a well represented panel of pharmacogenetic markers which will enable screening of individuals. These will help clinicians in selection of appropriate drug and genotype-specific dose. With plummeting cost of DNA sequencing technologies, genetic testing using such a panel will augment clinical decision making to meet personalized needs of each patient providing quality health care, while preventing adverse events and improve many lives.
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