Research

Understanding lung Cancer Susceptibility, Prognosis and Metastasis

Lung cancer is found to be the most prevalent malignancy with the highest mortality rates worldwide and is the fourth most prevalent malignancy ranked at the third position in causing cancer-related mortalities in India. The conventional methods of treatment for lung cancer have not been entirely successful in increasing the survival of the patients. Therefore, more precise and targeted approaches such as chemoprevention and precision genomics are necessary for effective treatment of the patients to ensure better survival. The identification of molecular targets for early detection, treatment, and management of lung cancer is essential in this regard. I am working in a two-pronged approach to understand the molecular genetic basis of lung cancer susceptibility, progression and pathogenesis: 

(a) Understanding the inherited susceptibility among cigarette smokers

It has been reported that about 15-20% of tobacco smokers develop lung cancer while the rest somehow evade the disease, which indicates an operant genetic predisposition to lung cancer. Lung carcinogenesis involves aberrant expression of xenobiotic metabolism and DNA repair genes as critical modulators of differential susceptibility among individuals. Such differential expression of genes could be attributed to variants in the cis-regulatory regions regulating the transcription of the respective genes. My team in the Department of Genetics, University of Calcutta has been engaged in identification, prioritisation and validation of variants as cis-regulatory markers regulating the differential expression of the candidate xenobiotic metabolism and DNA repair genes conferring risk to lung cancer in smokers. To-date, we have been able to identify 2984 variants within 531 gene-expression correlated DNaseI hyper sensitive sites (DHS) associated with 23 DNA repair and 25 xenobiotic metabolizing genes that have the potential of acting as cis-regulatory markers for lung cancer. The 2984 variants were prioritized further based ontheir transcription factor binding site altering potential, and being in cis-eQTL in lung tissue.The exercise identified 22 regulatory SNVs (rSNVs) for 7 xenobiotic metabolismand 7 DNA repair genes through a pipeline developed in our laboratory. Case-control analysis in lung cancer smokers and non lung cancer smokers has revealed the identified variants of of ALDH3B1 and of RAD52 to be strongly associated associated with cigarette smoke induced lung cancer in the Indian population, as also with lung cancer modified by pack-years of smoking, tobacco and betel quid chewing. Interestingly, the rSNVs were also found to be associated with different histological subtypes and TNM stages that provide an insight into personalised therapy with the application of precision medicine in a population-specific manner.

(b) Identifying the molecular basis of long non-coding RNA-mediated regulation of ROS metabolism, cytoprotection and induction of stemness in lung cancer

It has been well-established that the progression of lung cancer depends on the balance of ROS generation and adequate clearance of ROS by phase I and phase II detoxification pathway. When produced in excess amount, ROS results in damage to DNA triggering lung carcinogenesis. It has been suggested that lung cancer cells hijack the ROS metabolism pathway, which clears out intracellular ROS effectively and enhances the survival of the lung tumour cells. A lncRNA, SCAL1 was found to play a critical role inNRF2/KEAP1-mediated detoxification and ROS clearance conferring cytoprotection to the lung cancer cells. SCAL1 has also been found to induce cell proliferation by epigenetic silencing of p21 and p57 in NSCLC cells. Therefore, it is evident that the lncRNA SCAL1 plays a critical regulatory role in tumour cell cytoprotection and growth in lung cancer pathogenesis. Cytoprotection and tumour growth is the principal characteristic of the small population of cancer stem cells in the tumour bulk. Thus, we are trying to elucidate of the role of SCAL1 in the induction and maintenance of cancer stem cells leading to tumorigenic transformation in normal human bronchial epithelial (BEAS-2B) cells under cigarette smoke exposure as an aqueous extract. Real-time quantitative PCR analysis revealed the lncRNA to be significantly overexpressed in BEAS-2B cells under the exposure to 20% cigarette smoke extract (CSE). CSE exposure was also found to induce the upregulation of cancer stem cell markers of lung cancer, such as CD44 and CD133. Further, our experiments revealed SCAL1 to play a role in P53/TCTP-mediated tumorigenic transformation of non-tumorigenic BEAS-2B cells, by upregulating TCTP and downregulating P53 expression. siRNA-mediated silencing of SCAL1 resulted in the significant downregulation of cancer stem cell markers, accumulation of intracellular ROS even at higher incubation time, decrease in cell survival even at higher incubation time, upregulation of P53 and low expression of TCTP. The findings are suggestive of SCAL1 to be a prognostic biomarker and a critical pharmacologic target for effective treatment and management of lung cancer. Presently, we are trying to target-inhibit SCAL1 with different dietary plant-based products that could act as a potential therapy to prevent de-differentiation of lung cancer cells.

Understanding human pigmentation and related disorders

Skin pigmentation in human is one of the most complex quantitative traits ever studied. Epidemiological studies had shown that skin pigmentation is a polygenic trait with high heritability. The key molecule driving variations in pigmentation is melanin and its different forms and the rate limiting enzyme to melanin biosynthesis is Tyrosinase enzyme. Apart from Tyrosinase different other proteins working as channel proteins or differentiation factors, regulate numerous avenues of melanin biosynthesis and its distribution. In our laboratory, we are trying to identify the genetic bases of the pigmentary disorder oculocutaneous albinism (OCA) in Indian population by screening the 8 candidate genes followed by functional validation. Interestingly, in spite of rigorous screening by targeted sequencing method, ~40% of all the alleles screened remain uncharacterized for OCA, worldwide. These uncharacterised mutations (UCMs) have been hypothesised to be located in the regulatory regions of the candidate gene(s), which are not screened in most of the studies, or these may be indicative of new locus/loci precipitating the disease. Thus, we are also trying to identify the missing heritability in OCA cases with missing heritability through Exome analysis. 

My team also explores the public domain datasets and bioinformatically assess relevant functional and statistical association data to fish out hitherto unexplored genes and polymorphisms that might have an implication in human pigmentation and the related disorder vitiligo, a very common acquired depigmentation problem characterized by white patches due to the loss of the melanocytes distributed over the skin.

Lastly, in collaboration with Dept. of Anthropolgy, University of Calcutta, we aim to assess to assess the human skin pigmentation variation quantitatively with regard to latitude and altitude and solar flux, in some of the particularly vulnerable tribal populations of eastern India and correlate the same with the genetic polymorphisms. This woud help us assess fixation index as measure of population differentiation due to genetic structure with skin colour as biomarker.

Deciphering the neurogenetic link between well-being and sleep

Over the past decade, there has been a tremendous rise in research concerning sleep science; involving aspects like sleep latency, number of arousals from sleep, sleep depth, restfulness, and sensations upon awakening and their association with psychiatric behaviors. It is well-perveived that having a more positive outlook towards life is inherrently associated with improved sleep quality and vice versa; however, there has been a lack of comprehensive research on sleep parameters and their probable role in modulating both positive and negative aspects of well-being. In our laboratory, we are studying the neurogenetic interplay between sleep quality and well-being considering i) all the possible parameters involved in maintaining sleep quality, and ii) its impact on modulating the overall well-being of an individuals from West Bengal.  We are assessing the sleep and well-being parameters through established questionnaires and on the basis of Receiver Operating Characteristic curves, segregating the recuited individuals into positive sleep quality-higher subjective happiness-lower depressive scores and negative sleep quality-lower subjective happiness-higher depressive scores. Through whole exome sequencing of individuals, we are trying to identify discrete genetic signature patterns in the two grpups. We plan to do EEG fluctuation mapping in the individuals with highest deviation from the mean scores for each scale and check for their genetic patterns.

This study thus aims to identify novel genetic components which are involved in sleep regulated well-being. The outcome of the study may develop a simple screening protocol for the individuals susceptible to negative aspects of well-being customized for study population.