eSupervisor Detail

About me

Innovative molecular biologist with fundamental understanding in statistics, human genetics, epigenetics & R programming, proven by good publication record. Problem solver with organizational and multitasking abilities. Total 16 years of research journey (in Cancer Biology field) with experience in multidisciplinary collaborative research and project management. Experience in designing experiments, collecting, compiling, & analyzing data, also having excellent presentation & communication skill.

Interests: My specific interest is in Genomics and Epigenomics of Cancer. My long-term research interests lie in characterizing genomic and epigenetic alterations in tumors, especially translational aspect. I am keen to investigate developing biomarkers, target prediction, subtype classification of cancer, understanding drug resistance and selection of therapeutic strategies for cancers. Research Contributions: Research Project Assistant for a Research Project (1 year 10 months) Human Genetics Unit, Indian Statistical Institute, Kolkata, India Title of the Project: “Elucidation of functional significance of potentially susceptible genetic variants of host and virus (HPV) in epithelial cancers (cervical and oral)” Advisor: Prof Sharmila Sengupta Experience: During this period, I have collected both cervical scrapes as well as tissues from a large number of patients along with their demographic and clinical data. I have isolated DNA and RNAs from those, checked their ODs and quality as well. I have screened all of them for HPVs, mostly for 16 and 18. I have checked intactness of a viral gene like E2 by PCR, as well as TaqMan based method (Das et al., 2010). Ph.D. Thesis Work National Institute of Biomedical Genomics, Kalyani, West Bengal, India and Human Genetics Unit, Indian Statistical Institute, Kolkata, India Thesis Project: AN INVESTIGATION ON THE ROLE OF VIRAL AND HOST GENOME METHYLATIONS IN HPV RELATED CERVICAL CANCER PATHOGENESIS Advisor: Prof Sharmila Sengupta, Ex-Director, National Institute of Biomedical Genomics Most significant contribution: My Ph.D. topic was HPV mediated Cervical Cancer Pathogenesis. During my Ph.D. tenure, I have investigated both the genomic and epigenomic factors associated with HPV mediated Cervical Cancer Pathogenesis, including both Host and Viral perspectives. During this period, I continued work done in the period of Project Assistant. I have screened all of the collected samples for HPVs, mostly for 16 and 18, but for few, depending on study need I screened them for other types of HPVs like 31, 52 etc and contributed to various kinds of analysis with demographic and clinical data (Bhattacharya et al., 2018). In my thesis, I have included only HPV 16(+) samples. I have measured viral load for many case samples. I have chosen a sample set based on E2 status. I have studied methylation status of a particular region of early promoter region of HPV 16 by RFLP first, then confirmed it by Bisulphite sequencing. I tried to correlate this methylation status with intactness of E2 gene. I contributed equally as first author to the main publication arising from this work (Das Ghosh, Bhattacharjee, Sen and Premi et al., 2012). I analyzed methylation status of few CpGs in late promoter region of HPV 16 and tried to correlate this methylation status with intactness of E2 gene. I tried to correlate the expression of host innate immunity gene like TLR9 with methylation status of late promoter of HPV16, as it comprises of two immunostimulatory motifs. I have studied expression status of genes by SYBR Green method using Real Time PCR. I have also studied host methylation globally by TaqMan based method using Real Time PCR and tried to correlate this methylation status with disease as well as intactness of E2 gene in case sample (Sen et al., 2017). I have studied the association of SNPs (studied using RFLP) in MTHFR/MS gene (gene involved in folate metabolic pathway) with disease. I also have done immunohistochemistry for lots of virus infected as well as control samples and observed expression of both viral as well as host proteins. Finally, I have studied whole methylome of host using Illumina Infinium 450k bead chip and tried to see what the different sets of genes and pathways are responsible for different kinds of cervical samples and validated few results (Sen et al., manuscript ready for submission). I have used SPSS and R for different kinds of analysis. I have used different web-based primer designing tools, databases like NCBI, UCSC, I have used BLAST. I have used IPA for pathway analysis. Research Contribution other than PhD thesis work: I did PCR for haplotype determination of virus and participated in Viral load and copy no determination and viral E7 mRNA expression analysis (Mandal et al., 2022). I contributed to library preparation for next generation sequencing of different haplotypes using Ion torrent platform as well as data analysis using IGV (Mandal et al., 2016). I contributed to Whole Transcriptome study using Illumina Human HT v.4 bead array-based platform, both in library preparation as well as in data analysis using packages like Limma in “R”. I also contributed to isolation of RNA and then prepared c-DNA for a few miRNAs (Mandal et al., 2019). Postdoctoral Research Work (2 years 3 months) Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India. Advisor: Prof. Tapas K. Kundu Main Research Project for Post-Doctoral Work: "Understanding the Epigenetic Regulation towards Breast Cancer via Autophagy". I demonstrated the status of Autophagy and histone acetylation in context of Triple Negative Breast Cancer. (Corresponding author of a review from this work is under process) Contribution other than the main project: During my postdoctoral training position, I was involved in several ongoing projects in the laboratory. In a mutational screening for p53 gene in oral cancer patient samples, we have identified, a proline to leucine mutation (CCG to CTG) at 152nd position (P152L) in p53 gene of an Indian oral cancer patient sample. We have established P152L p53 as a newly identified gain-of-function mutant thereby rendering the cells with increased oncogenic potential (Singh and Kumar and Kumar et al., 2019). In another project, I have checked expression of mRNA and miRNA in few cancers’ patient samples (Sikder et al., 2019). Postdoctoral Research Work: (3 years 10 months) Under MITACS Elevate Post-Doctoral Program, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada and Research and Development Department, STEMCELL Technologies Canada Inc, Vancouver, BC, Canada. Advisor: Dr Martin Hirst Terry Fox Laboratory, BC Cancer Research, 675 West 10th Avenue, Vancouver, BC, Canada Department of Medical Genetics, 4500 Oak Street-C201, University of British Columbia, Vancouver, BC, Canada Advisor: Dr Connie Eaves Title of the main ongoing project: Comprehensive Molecular Analysis of Pre- and Postmenopausal Human Mammary Cells to Enable Their Optimized Growth as Organoids Ex Vivo I was involved in various ongoing projects. Consented mammary reduction mammoplasty tissue samples of various age group females were collected and viable LPs, BCs, LCs (various cell population of mammary system) were isolated by fluorescent-activated cell sorting (FACS). Whole genome bisulphite sequencing, RNA sequencing and ChIP sequencing (for some selected histone marks) were done on those. My goal was to have an epigenetic map of aging effect in these different cell populations. Right now, I was heavily involved in RNA sequencing, Whole Genome Bisulphite Sequencing (WGBS) and ChIP-sequencing data analysis. Our long-term plan was to translate this dry lab finding to a product. I was working with a big biotech company of Canada, called STEMCELL Technologies as a MITACS-Elevate Fellow for that, trying to make lineage specific organoids from tissue sample of different age group. I successfully developed organoids from different mammary cell populations. Project Scientist I (6 months) Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India Experience: I was getting firsthand exposure in NGS library preparation for various kinds of sequencing platforms, as I was working as a part of service provider group called National Genomics Core (NGC). I was also involved in other projects related to rare genetic disorder, mutation screening in patient samples.