Name of the PhD Student

Name of the Supervisor

Brief Description of Project

Abarna Sinha

Sharmila Sengupta

Cervical cancer is one of the leading causes of cancer related deaths among Indian women. One of the major risk factors, which accounts for 99.7% cases of the cervical cancer is persistent infection with a sexually transmitted, high risk Human Papilloma Virus (HPV). It has been found that E6 and E7, two oncoproteins encoded by HPV, deregulates p53 and pRb and promotes cervical cancer in the hosts. It is seen that non-coding RNAs (miRNA and lnc-RNAs) play differential roles in the normal cellular physiology and molecular pathogenesis of several diseases, including cancer. My aim is to explore the involvement of miRNAs in HPV16 driven cervical cancers specifically associated with viral oncoprotein E7, the interaction or the crosstalk of lncRNA with cellular miRNAs, under the influence of E7 expression and to investigate how they influence HPV16 related CaCx pathogenesis.

Abhisikta Ghosh

Sharmila Sengupta

Cervical cancer is one of the leading causes of cancer related deaths among Indian women. Persistent infection with oncogenic Human Papillomavirus (HPV) is the major etiology of the disease. Expression of the viral oncoproteins E6 and E7 are critical for malignant transformation of the host cells and is mediated through the interaction with other host encoded molecules. E6 regulates the decay of tumor suppressor p53, while E7 interacts with pRb leading to cellular transformation and neoplastic progression of the cervical epithelial cells. My aim is to identify the intrinsic HPV 16 E7 mediated pathways relevant for cervical cancer pathogenesis, focusing majorly on the immune pathway molecules and correlate such intrinsic host molecular factors with some of the extrinsic phenomena of tumor immune microenvironment in cervical cancer pathogenesis.

Anand Bhushan

Sreedhar Chinnaswamy One of the important events in a pathogen infection is the host-pathogen interaction that is critical to decide its outcome.  In this event there are two major players, host and the pathogen (virus, bacteria, parasite etc.).Host immune system plays a major role for the elimination of the pathogen and pathogen also tries different options to escape from the immune system of the host. In this episode if pathogen succeeds then the host will come down with the disease otherwise the pathogen is likely to be eliminated. I am is interested to learn how genetic variation in the immune response genes particularly those in innate immunity pathways decide on the outcome of an infection at the population level and also to learn the molecular mechanisms leading to these decisions. Currently, I am focusing on host-pathogen interactions in RNA viral diseases and intracellular parasitic diseases.

Ankit Patel

Sandeep Singh

My overall research goal is to contribute to the better understanding of cancer progression and metastasis. Tumor cells have the properties to convert its niche as a supportive environment for cancer progression.  I am interested in exploring how tumor micro-environment supports progression of solid cancers like oral squamous cell carcinoma.

Antara Biswas

Kartiki V Desai

JMJD6 is a putative histone arginine demethylase and lysyl hydroxylase, robustly associated with poor prognosis in breast cancer. It rapidly increases proliferation and motility of breast cancer cells, and our preliminary data suggests it interacts with long non-coding HOX Transcript Antisense RNA (HOTAIR). HOTAIR and its binding partner Enhancer of Zeste Homolog 2 (EZH2) correlate with poor survival in breast cancer patients. We therefore hypothesize that JMJD6, EZH2 and HOTAIR may together as a complex to play important role(s) in modulating gene expression towards enhanced oncogenesis. Exploring these molecular mechanisms forms the basis of my thesis. In the long run, this may steer us towards developing effective drugs against advance breast cancer.

Arindam Palodhi

Arindam Maitra

Head and neck cancer, especially oral and oropharyngeal cancer, is one of the major threats to public health. Investigations of genomic, epigenomic and transcriptomic alterations that are associated with initiation and progress of tumerigenesis might lead to the complete understanding of the underlying molecular processes and result in improved prediction of risk and response to therapy. My goal is to harness the cutting edge genomic technologies to identify the major genomic alterations in head and neck cancer and use such information for development of biomarkers for improved diagnosis and patient care. Specifically, I am working on identification of the genomic drivers of Warburg Effect in gingivobuccal oral cancer by performing comprehensive analysis of exome and mitochondrial DNA mutations as well as alterations in mitochondrial biogenesis.

Barsha Saha

Srikanta Goswami

Chronic pancreatitis (CP) is an irreversible disease characterized by progressive inflammation, fibrosis of pancreas, and loss of pancreatic functions. Epidemiological studies have identified CP to be a major risk factor for pancreatic ductal adenocarcinoma (PDAC). PDAC is one of the most lethal diseases with an incidence rate almost equal to the rate of mortality. Elucidation of the molecular mechanism driving the development of the diseases will not only help us understanding the disease biology but also help us identifying key molecules which could be used as potential biomarkers for early detection of the malignant disease. Regulation of gene expression by epigenetic mechanisms has gained much importance due to their important role in disease pathophysiology and my work revolves around delineating the role of key epigenetic factors in the development of chronic pancreatitis and pancreatic ductal adenocarcinoma.

Bishnupriya Chhatriya

Srikanta Goswami

Chronic pancreatitis (CP) is a condition characterized by progressive and irreversible damage to both exocrine and endocrine components of the pancreas, eventually resulting in significant exocrine insufficiency and diabetes. In the recent years, several genetic risk factors for chronic pancreatitis have been identified in genes like PRSS1, PRSS2, SPINK1, CFTR, CTRC etc. In view of these findings, my proposed work aim to find out the prevalence of these common genetic changes causative to CP in the population of North-Eastern Region (NER) of India where CP and CP related death are of high incidence. Such population specific variations have significant contribution towards the formulation of diagnostic and therapeutic strategies specific for those individuals. The outcome of the study is also believed to add substantial information to the existing knowledge of the molecular mechanism of the development of CP. Furthermore, chronic pancreatitis (CP) is a progressive benign fibro-inflammatory disease of the pancreas and is one of the risk factors of pancreatic cancer. The development of pancreatic cancer in CP is a classic example of chronic inflammation progressing to cancer that is also found in other organs of the body. Pancreatic Cancer (CAPan) is one of the most aggressive forms of cancers, with only 4-5% 5-year survival. Not much is known about the molecular changes that lead to the development of CAPan in CP patients. Therefore, another important aspect of my research objective is to delineate that process and to find out whether these changes can be used for development of biomarkers for early detection of pancreatic cancer in CP patients, as well.

Debashree Tagore

Analabha Basu

Modern human originated in Africa nearly 150K YBP (Years Before Present) from where they spread to different parts of the world. This “out-of-Africa” migration took place nearly 60-75K YBP. The migrating population carried with them the genetic variants inherited from their parents but simultaneously, with the passage of time, accumulated mutations which gave rise to new variants. This migrating population entered into India through different corridors and created a rich pool of variants. My research objective is to study these variants to unravel finer intricacies of population migration in the Indian sub-continent. The Indian population harbors common and unique variations which have serious implications on human health and diseases. I, therefore, intend to study the genomic variations in detail and use this knowledge in deciphering association of genomic variants with diseases.

Jagyashila Das

Arindam Maitra

Birth outcome is an important determinant of an infant’s survival and health even during adulthood. Identifying the complex physiological and molecular pathways involved in modulation of pregnancy outcomes is thus of paramount importance for understanding and developing strategies to reduce adverse birth outcomes like preterm birth (PTB). Genetic markers alone may not provide sufficient insights into these processes. Epidemiologic observations, mostly from neonatal genomes, suggest probable role of epigenetic disruptions in enhancement of risk of PTB. However, very limited information is available on the role of maternal epigenome in PTB till date. My goal is to study the temporal variations in maternal DNA methylation landscape that occur during pregnancy and identify those that are associated with adverse outcomes.

Kavya Vipparthi

Sandeep Singh My research goal is to explore the role of tumor initiating or cancer stem cells in oral squamous cell carcinoma, one of the most aggressive cancers in Indians with high rates of metastasis. According to Cancer Stem Cell theory, targeting stem-like cells would be more helpful rather than the whole tumor because only these cells would have the potential to self-renew and maintain tumor growth and spreading while other cells do not. I am interested in learning the molecular mechanisms underlying the self- renewal and differentiation of stem-like cancer cells in oral cancer and how they contribute in tumor spread and metastasis. I am developing methods to identify and isolate these cells from oral-tumor tissue for its genomic and functional characterization. 

Krittika Bhattacharyya

Samsiddhi Bhattacharjee

Identification of causal variants together with the potential mechanism contributing to differential disease risk among individuals can offer most critical insights into the proper understanding of complex diseases. So far, Genome-Wide Association Studies have been remarkably successful in identifying genetic variants associated with various complex diseases. However, the interpretation of GWAS variants in terms of causality and the perception regarding the role played by these variants in the etiology of complex diseases have remained significantly ambiguous. Hence, we require robust statistical methods to efficiently integrate epigenomic and transcriptomic signatures and the intricate network of gene-regulation in relevant tissues along with functional annotations, pathways, and other evidence from publicly available databases. My primary interest lies in developing statistical methods for integrative analysis of multi-omics data to systematically identify causal variants within an associated region and to elucidate the causal mechanism through which they act. Methods developed will facilitate interpretation of complex disease associated loci not only to infer genetic causality through the epigenomic, transcriptomic and functional landscape in relevant tissues but also to highlight the upstream genes, pathways directly modulated by these genetic variants and consequent downstream changes.

Paromita Mitra

Sandeep Singh

Oral cancer is the most common cancer among Indian men. In spite of many therapeutic advancements, there has been no significant improvement in the survival outcome of head and neck squamous cell carcinoma. Five year survival rate in advanced stage  carcinoma is only 27% & it has high chance of relapse. Recently it is known that tumor microenvironment and stromal components (e.g- fibroblasts, immune cells, endothelial cells), are as important as genetic mutations and play critical role in cancer development. Tumor contains different subpopulations in terms of mutations and make tumor heterogeneous. These subpopulations may differ in genetic, epigenetic level resulting in variation of the gene expression and protein function. However the reciprocal interaction between cancer cell and stromal component have not been studied in oral cancer. Therefore  I am interested in finding the interaction between heterogeneous tumor and its microenvironment. By understanding the cross-talk and reciprocal interaction between tumor cells and stromal components, we can predict novel target against tumor-stromal interaction.

Partha Das

Kartiki V Desai

Breast cancer is one of the most common cancers and the second most leading of cancer death in women. Breast cancer is hormone dependent tumor and estrogen is known to play a major role in the initiation and progression of this cancer. Endocrine therapy is the best therapy for breast cancer. But resistance to endocrine therapy is common. Previous studies account for only 40% of such mechanisms. The aim of my research is to discover newer mechanism using genomics and epigenomics tools to identify novel candidates to combat endocrine resistance.

Qazi Faizul Hasan

Souvik Mukherjee

Chronic diseases are determined by the interplay of genetic and environmental factors.  Although genome-wide studies have identified genetic polymorphisms associated with several important chronic diseases, however, studies focusing on gene-environment interactions on majority of these diseases are still lacking. Humans are now considered as a conglomerate of both human and microbial cells – collectively termed as the “human microbiome” – residing in and on various parts of the human body. The human microbiome is composed of trillions of microbial cells that encodes a “second genome” which is much larger than the human genome.  The microbiome is highly variable across individuals and likely contributes to gene-environment interaction. Diabetes is a common chronic metabolic disease globally affecting the humankind. One of the dreaded complications of Diabetes is the chronic non-healing diabetic foot ulcer (DFU) wound, affecting 15-20% of diabetic patients worldwide. The DFU wounds do not follow the precisely orchestrated course of events observed in normal wound healing. Currently, I am focussing on harnessing the modern genomic methodologies to understand the host-microbiome interactions in the development and progression of non-healing diabetic foot ulcers in humans. Besides the host genomics and metagenomics study, our research work also includes both in vitro and ex vivo assays to detect the presence of polymicrobial biofilms and the growing antibiotic resistance in the wound microenvironment in humans. In future, mechanistic studies may be planned to understand the effect of modulating host-microbiome interactions in DFU wound healing in both in vitro and in vivo models.

Samanwoy Mukhopadhyay

Saroj K Mohapatra

Sepsis is one of the leading causes of morbidity and mortality in all age groups, despite improved care in the recent years. In the pediatric group, sepsis accounts for a large fraction of mortality under 5 years of age, and is one of the leading causes of death in neonates. There is no specific drug for treatment, owing to incomplete understanding of the biology of this disease. I believe that genomics of sepsis is an exciting area of research. For example, recent findings hint at reprogramming of the leukocyte transcriptome in the patients; and this change is coordinated, reproducible and linked to the progression of the disease. I am performing whole-genome gene expression profiling in patients of sepsis to detect strong and reliable signature of outcome (e.g., survival versus death). Additionally, I am interested in discovering the genetic and epigenetic underpinnings of the transcriptional signatures.

Seema Bharatiya

Sreedhar Chinnaswamy

Among the recently discovered Type–III interferon family, IFN-λ4 (IFNL4) is thenewest member. I am interested in characterizing the naturally occurring variants of IFNL4 gene for their effect on IFN-λ4’s function and their significance in different human diseases. IFNL4 gene transcription is known to generate several different splice variants. I am also interested to understand if any of the genetic variants within the body of IFNL4 are important in generation of these splice variants.

Shamita Sanga

Moulinath Acharya

There are more than seventy million patients in India, affected by rare diseases, many of which are related to vision. Rare eye diseases (REDs) are often congenital and more than 80% have a genetic basis. These diseases are associated with many genetic and allelic heterogeneity that lead to variable clinical phenotypes in patients.  Mutations in these genes, causal to REDs may cause alteration in regulatory pathways pertinent to eye development, there by leading to various disease conditions including developmental malformations. Mutations in the same genes lead to diverse clinical phenotypes, thereby making it difficult for genetic counsellors and clinicians to counsel the patients accurately. To delineate that,  I hypothesize that  the altered regulation of certain biochemical pathways is responsible for the pathogenesis of REDs and their varied clinical manifestations. Towards that goal, my aim rests on complete identification of the genomic risk factors and their underlying functions in the pathogenesis of REDs.

Shrayashi Biswas

Samsiddhi Bhattacharjee

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, 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.

Subhajit Roy

Sreedhar Chinnaswamy

Viral diseases are outcomes of complex interactions between virus induced pathogenesis and host immune responses. Host immune responses are major contributors to pathogenesis in both viral diseases and inflammatory disorders. IFNλ-4 is comparatively a newer member of type III interferon family whose expression is genetically contolled. Its role in infectious and other inflammatory diseases is yet to be deciphered properly. My research focuses on understanding diseases in light of host IFNλ response, exploring genetic determinants of host and/or virus that are involved in manifestation of disease severity. I am also involved in defining new roles for IFNλ-4 at the genomic scale besides an interest to decipher its subcellular activity and its involvement in different cellular pathways; these approaches will provide complementary insights that will help a better understanding of the functioning of IFNλ-4 in human health and disease.

Subhashis Ghosh

Sandeep Singh

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 within 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.

Sumitava Roy

 

Arindam Maitra

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 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.

Vijay Laxmi Roy

Partha Pratim Majumder

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 minimized 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.