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.

Anuradha Gautam

Bhaswati Pandit

Tuberculosis (TB) is primarily an infection of the lungs caused by Mycobacterium tuberculosis complex (MTBC). This complex comprises of upto seven Mycobacterium species including but not limited to Mycobacterium tuberculosis (M.tb) and M. bovis. This disease is a major public health burden for the country with India accounting for 27% of the world TB cases. This strain on the health care system is further compounded by the emergence of drug resistance. Multi-drug resistant (MDR)-TB is the resistance against at least two first line drugs: Isoniazid (INH) and Rifampicin (RIF). Resistance to standard antibiotic therapy allows for the drug-resistant M.tb to linger longer in the host and induce immunopathological changes which may differ from those caused by its drug-susceptible counterparts. The common determinants for developing drug resistant TB have been identified to include non-adherence to therapy, inadequate drug regimens, drug metabolism and immunological state of the host. Host genetic factors have been known to modulate drug metabolism genes. This has been exemplified in the studies regarding the NAT2 genotypes which are associated with the rates of acetylation of isoniazid. This clearly indicates at the involvement of host genetic factors in susceptibility to MDR-TB. The primary objective of my research is to explore the host genomics and functional genomics to dissect TB susceptibility and to determine host genetic basis of emergence of drug resistance. In doing so, I am studying the involvement of host genetic variants in susceptibility to drug resistant and drug sensitive TB cases through genome wide genotyping followed by identification of associated variants including variants in drug metabolism genes and validating these via targeted re-sequencing. Simultaneously in the functional genomics aspect, I am looking into the whole transcriptome to identify a gene signature which discriminates drug resistant and drug sensitive TB cases.

Arghya Dey

Analabha Basu

The overarching goal of my research is to study the ancestry of Indian populations, mainly the Ancestral South Indians (ASI) and the admixture of ASI with other populations. The early migration and ancestries of Indian populations are hugely debated and there is a lack of consensus on important issues. I will use advanced statistical methods, simulation studies and genomic data to gain further insight into the peopling of India. I will also look at the ancient gene flow from East and Southeast Asia into South Asia and ideally connect that to the ‘Out-of-Africa’ migration of anatomically modern humans.  I want to create new statistical methods for this purpose, as required, to supplement the existing methodology.

Aritra Gupta   

Kartiki V Desai

JMJD6 has diverse enzymatic activities including histone arginine demethylation, lysyl hydroxylation, and is recently shown to phosphorylate proteins. It’s high expression is robustly associated with poor prognosis in breast cancer. JMJD6 binds RNA but lacks a DNA binding domain. However, by interacting with other transcription factors like BRD4, it was recently shown to regulate the anti-pause release of RNA pol-II on poised sites. To determine its complete function in tumorigenesis, we have haveperformed mass spectrometric analysis of proteins immunoprecipitated using JMJD6 specific antibodies. Many transcription and DNA binding factors were found and one such protein was Y-box interacting protein 1 (Ybox-1), a transcription factor that has both DNA and RNA binding activities.  This protein is also associated with poor prognosis and metastasis in breast cancer. We hypothesize that JMJD6 and Ybox1 may physically interact and influence gene expression to promote breast cancer progression leading to poor patient survival. 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.

Debopriyo Ganguly

Priyadarshi Basu

Nonalcoholic fatty liver disease (NAFLD) is a complex disorder. Both genetic and environmental factors affect disease pathogenesis. NAFLD begins with aberrant accumulation of triglycerides in the liver which is called hepatic steatosis. In some individuals it can lead to inflammatory responses and causes progression to Nonalcoholic steatohepatitis to cirrhosis, and subsequently hepatocellular carcinoma. The pathogenicity of the disease is poorly understood and therapeutic options are very limited. My work emphasizes on understanding the molecular mechanisms and the role of related pathways involved in disease progression from mild to advanced stages and validation of the role of some specific genes associated with NAFLD in the Indian population in in vitro and in vivo models.

Esha Bhattacharjee

Arindam Maitra

Period of gestation being an important determinant of infant’s health, adverse live birth outcomes are major public health concerns of global importance.Complications from preterm birth, which is defined as any live birth before 37 completed weeks of gestation, is the leading cause of mortality of children below 5 years. Interplay between environment and underlying genomics of both the mother and the fetus results in the preterm birth outcome. To combat the global health burden, early detection of the women having higher risk for delivering preterm is highly crucial which will help to provide personalized medical care to them. Since genomic markers have the potential to identify the high-risk women even to prior to pregnancy, so I intend to study the maternal genetic influences on preterm birth.

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.

Moumita Mukherjee

Srikanta Goswami

Pancreatic cancer is the seventh leading cause of cancer-related deaths worldwide with a lowest 5-year survival rate (<5%) and poor diagnosis among other cancers. This intractable malignancy is often caused by some genetic alterations and also by pancreatic damage due to recurrent bouts of inflammation of chronic pancreatitis. In recent years, several regulatory functions of long non-coding RNAs (lncRNAs) have come to picture which were initially considered to be junk elements of the genome with no function. Role of lncRNAs in various types of cancer has been gradually revealed and in the case of pancreatic cancer also, intricate role of lncRNAs have been uncovered with implications in cell cycle, apoptosis, autophagy, epithelial-mesenchymal transition (EMT), metastasis and immune responses. But still there are several important lncRNAs which have significantly altered expression in pancreatic cancer and their functions are yet to unfold. Aim of my research project is to functionally characterize few such lncRNAs in pancreatic carcinogenesis and also to find out if they have any role in progression of pancreatitis to pancreatic cancer.

Mousumi Sarkar

Souvik Mukherjee

Pregnancy is a complex physiological process associated with successive changes in the uterine environment that facilitates childbirth. The period of gestation varies from 37-42 weeks in Term Birth and <37 weeks in Preterm Birth (PTB).  Globally, PTB is one of the leading cause of child mortality and morbidity. Many preterm survivors face a lifetime of disability, including respiratory, learning, visual disability and the number of premature babies is increasing exponentially with time. Identification of the complex aetiologies behind premature delivery is a big challenge worldwide. The vagina plays an important role in childbirth and is also home to a population of facultative and obligate anaerobic microorganisms that maintains the hygiene and pH of the vaginal milieu. This polymicrobial community is difficult to characterise through conventional microbiological culture based methods and are collectively termed as the Vaginal Microbiome. Recently, the role of oral as well as placental microbiome in preterm birth has also gained much interest. I am interested to investigate the change in composition and diversity of the Maternal Microbiome associated with Preterm birth in India. A multi-omics approach will be undertaken to dissect the host-microbiome interactions between host factors and differentially enriched microbial gene families as well as functional pathways that ultimately lead to Preterm Birth.

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.

 

Samadrita Ojha

Bhaswati Pandit

Tuberculosis is a potentially serious infectious disease and still a major health problem worldwide.  Pathogenesis of this disease is driven by a complex interaction between the host immune system and immune escaping strategies of the pathogen. Cytokines and chemokines produced by host immune cells play vital role in elimination of infection.  Bio fluid level of one such chemokine, CXCL10, is found to be elevated in active TB patients. The effect of elevated CXCL10 on immune cells is not well studied. My aim of research is to explore the role of CXCL10 in alteration of downstream signaling pathways involved in host defense mechanism in context of TB using high throughput genomic tools. I am also interested to understand the influence of the chemokine in the immunological processes with advent of M.tb infection. These approaches will help us in better understanding of potential regulatory role of CXCL10 for tuberculosis disease progression.

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

Congenital muscular dystrophies (CMD) and congenital myopathies (CM) are a group of rare genetically and clinically heterogeneous degenerative primary muscle disorders with onset at birth or during infancy. Due to vast heterogeneity, clinical examination and protein-based analyses often fail to identify the genetic causes of these diseases making it challenging for the clinician to make an accurate diagnosis.  My research therefore focuses on investigating the genomic signatures causal to CMD and CM in Indian patients. I analyse whole exome sequence data using variant calling and stringent variant filtration process to identify pathogenic mutations and achieve a genetic diagnosis.
I'm also interested in functionally characterizing the candidate variants in an in vivo zebrafish model and do a mechanistic evaluation in primary muscle cells using the efficient CRISPR-Cas genome editing tools.

Shouvik Chakravarty

Nidhan K Biswas

Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) is a form of Head and Neck Squamous cell carcinoma (HNSCC).             Recent epidemiological studies reported – (i) India has one-third of all oral cancer cases in the world and (ii) oral cancer accounts for 30% of all cancers reported from India. Oral cancer is the topmost cancer among males in India and linked to tobacco chewing and smoking habits. Few driver genes were recently identified for late-stage OSCC-GB from genome-scale studies. Identification of early stage OSCC-GB biomarkers is of extreme importance, because it might potentially lead to precise understanding of the molecular mechanisms of tumor initiation, as well as the factors whose alteration might lead to progression of tumor. My research objective is to leverage state-of-the-art genomic technologies for understanding the profile of the genomic drivers of early stage OSCC-GB tumors. Deeper understanding of the molecular underpinnings of the alterations of these drivers will provide improved diagnosis, more precise risk prediction as well as better response to therapy.

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.