MAJOR AREAS OF RESEARCH:
- Profiling of DNA methylation in human cancers prevalent in North-eastern states of India with the intension of identifying new “biomarkers”.
- Study of Metallotheinein genes as biomarkers for heavy metal pollution in Chironomous and fish in water bodies of Meghalaya.
- Profiling DNA methylation in skin cancer using mouse model
- Discovery of DNA methylation biomarkers in human cervical cancer
- Analyses of pathways controlling neurodegeneration of polyglutamine diseases using Drosophila model
- Generation of Drosophila model of Amyotrophic lateral sclerosis (ALS) also called motor neuron disease
- Study of chromatin compaction in Drosophila polytene chromosomes
SUMMARY OF RESEARCH EXPERIENCE:
2009-present: Dept. of Zoology, North Eastern Hill University, Meghalaya, India
- We have been profiling oral cancer with special reference to the ethnic population of Meghalaya, North East India. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome. Our study identified 27,205 CpG sites and 3,811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes, some of which are tumor suppressor genes, were found to be similar to that of the TCGA-HNSCC study. However, a number of “novel genes” were also identified which may serve as candidate methylation “biomarkers” for OSCC in this poorly characterized ethnic group. Currently studies are ongoing to characterize these candidate novel genes as suitable “biomarkers” of oral cancer.
- Similar methylation based whole genome profiling is also being done for stomach cancer and oropharyngeal cancers that are prevalent in the NE states of India. Many novel genes have been identified for these two types of cancers. Currently further characterization of these genes are being carried out for identifying them as “biomarkers” of the relevant cancers.
- Metallothioneins(MTs) are cysteine-rich, non-enzymatic proteins in the animal kingdom, that can bind various heavy metals, including mercury, silver, copper, cadmium, lead, zinc, and cobalt, with varying affinities. MTs are widely expressed in organisms and are responsible for essential metal metabolism and heavy metal detoxification. We are presently studying the expression of these MTs in Chironomous and common carp from various water bodies of Meghalaya, India with the intension of using them as indicators of heavy metal toxicity in these animals.
2004-2009: Roswell Park Cancer Institute, Buffalo, NY, USA
Labs of Dr. Hiroki Nagase and Dr. William Held (Oct 2005-2009):
There is considerable evidence, which show that the susceptibility to cancer development in humans involves the same processes as those seen in mouse. Besides genetic variations, epigenetic modifications, most importantly DNA methylation, plays a role in human cancer development and risk. We wanted to probe this event by using the two-stage mouse skin carcinogenesis model. Using the technique of Restriction Landmark Genomic Scanning (RLGS) with the enzyme combination of NotI-EcoRV-HinfIto globally scan the genome for methylation events associated with skin cancer in mouse, we have compiled a list of genes that are methylated and call them skin tumor-specific differences in methylation (ST-DMRs). We have confirmed some of this methylation data by methylation specific MassArray technique (MALDI-TOF MS system from Sequenom). We also performed whole genome expression analyses using Agilent arrays to identify the correlation between expression and DNA methylation at some ST-DMR. We also used CGH BAC array analyses of these cancer samples and found a correlation between BAC loss and DNA methylation at the same locus for a candidate gene. We are presently analyzing the functional role of candidate genes, which are located near the ST-DMRs, using skin cancer cell lines. Since most of the ST-DMRs are conserved between mouse and humans, we are choosing some orthologous regions of these ST-DMRs and elucidating their methylation status in some human cancers (melanoma, colon and lung cancer). This work furthers our understanding of how DNA methylation status impacts on each step of tumor development. It could also identify potentially new pathways of tumorigenesis. In the future, the novel targets identified may have broad applications in defining patient populations that are more susceptible to poor prognostic cancer and possibly monitoring methylation changes with age or during administration of drugs for treatment or early diagnosis and prevention.
We have performed methylated DNA immunoprecipitation (MeDIP) assay of multipotent mammalian cells using CpG island and promoter arrays in order to find novel genes that are methylated during differentiation. Also our results on tissue specific methylation during mouse development indicate that some genomic regions with tissue-specific methylation and expression are conserved between mouse and human and suggest that DNA methylation may have an important role in regulating differentiation and tissue-/cell-specific gene expression of some genes.
Lab of Dr. Dominic Smiraglia (Jan 2004-Sept 2005):
- Methylation of CpG islands within promoter regions of genes has been associated with gene silencing, suggesting loss of tumor suppressor function and tumorigenesis. Promoter hypermethylation is a frequent, non-random event in cancers of most organs including the cervix, breast, prostate etc. Hypermethylation may occur in cancer precursors and that the number of methylation events increases with progression, paralleling the accumulation of genetic changes. Using RLGS, we focused on genome wide scanning for frequently methylated genes, including genes not previously implicated in carcinogenesis that may be used to develop promising panels of biomarkers for cancer screening and other applications. We compiled an extensive list of possible methylation targets in cervical neoplasia, breast cancer and prostate cancer using RLGS. From our panel of most frequently methylated genes in cervical cancer that we identified by RLGS, we developed quantitative Methylation Specific PCR (MethLight) assays for two novel DNA methylation biomarkers that are specific for cervical cancer and have validated the results. We have identified a list of novel genes that are epigenetically altered in human breast and prostate cancers. Work is in progress to validate these results in larger sample sets. Our RLGS studies have also identified a few novel genes that are methylated in tissue specific as well as germ layer specific manner in normal human adults. We have confirmed these results by Methylation specific massArray.
2003-2004: State University of New York at Buffalo, Buffalo, NY, USA
- Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder caused by expansion of polyglutamine [Poly (Q)] repeats beyond the threshold value of 38, in the amino terminal portion of a predominately cytosolic protein, huntingtin (htt). This results in the appearance of intranuclear inclusions in affected neurons and cytosolic aggregates in the neuronal processes (neuropil) of HD patient brains. Our laboratory identified the protein product Drosophila myeloid leukemia factor (dMLF) because of its similarity to human protein MLF and also an orthlog of a brain enriched chaperone, the human MRJ (mammalian relative of DnaJ), both of which colocalize with the aggregates and suppresses Poly (Q) toxicity in a Drosophila model of Poly (Q) diseases. My work was to identify the domains of dMLF required for suppression of Poly (Q) toxicity and also to identify the roles played by modifiers of dMLF on its suppressing effect of polyglutamine toxicity and colocalization with the aggregates.We also showed that in the photoreceptors, expression of another suppressor with a J domain, dHDJ1, but not dMRJ, prior to expression of expanded Poly (Q)s dramatically promoted cytoplasmic aggregation. Biochemical analyses of both proteins showed increased level of detergent-soluble, monomeric Poly (Q)-expanded proteins. These findings exemplified the functional similarities and differences between J domain proteins in suppressing Poly (Q) toxicity.
2000- 2003: Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Most human neurodegenerative diseases have a number of features in common including adult onset, progressive degeneration of selected neuronal populations, and the formation of abnormal protein aggregates. Although these shared characteristics raise the possibility of conserved pathogenic mechanisms, the diverse clinical and pathologic features of each disorder indicate significant differences as well. By directly comparing modifiers isolated in Drosophila models of polyglutamine diseases and from a Drosophila model of tauopathy we find a final common pathway of cell death involving apoptosis. Among the polyglutamine diseases, protein folding and histone acetylation are key common mediators. In addition, two novel modifiers suggest shared pathways of toxicity among all the disorders. Since cell type specificity is a highly salient feature of all neurodegenerative diseases, but most work to date in Drosophila models has been performed in the retina, we determined if similar pathways of toxicity operate in neurons of the Drosophila brain. Many, but not all, retinal modifiers also modify toxicity in postmitotic neurons in the brain. Analysis of polyglutamine toxicity in the adult brain facilitated identification of nicotinamide (Vitamin B3), a vitamin with histone deacetylase inhibiting activity, as a potent suppressor of polyglutamine toxicity. These findings outline common pathways of neurotoxicity, demonstrate of disease- and cell-type specific pathways, and identify a common vitamin as a potential therapy in polyglutamine disorders.
- Amyotrophic lateral sclerosis (ALS) is one of the most common adult onset neurodegenerative diseases and is characterized by selective loss of motor neurons, ultimately leading to progressive atrophy of skeletal muscles. The discovery of missense mutations in genes coding for Cu/Zn superoxide dismutase 1 (SOD1) in familial cases has led to the development of mouse models that portray the motor neuron degeneration syndrome of the human disease. We have generated several transgenic flies using different Cu/Zn hSOD1 mutations. Work is in progress to establish them as a faithful model of the toxic human disease and effectively use them for genetic dissection of the fundamental pathogenetic mechanisms underlying the disease.
- 1992: Junior Research Fellowship: Graduate Aptitude Test in Engineering (GATE) Basic Sciences and Engineering, India
- 1993-1996: Junior Research Fellowship: Position effect variegation (PEV) as a system to expose genomic domains that are involved in the control of PEV, homeotic pathway, developmental regulations and retrotransposons insertional mutations in D. melanogaster (funded by Dept. of Atomic Energy, Govt. of India awarded to Principal Investigator
- 1997-1998: Research Fellowship: Polymorphism at the level of DNA and protein as genetic marker in response to heavy metal stress, insecticides, detergents and crude oil surfactants (funded by Dept. of Science and Technology, West Bengal, India awarded to Principal Investigator)
- 2000-2003:Postdoctoral Fellowship: Drosophila models of human neurodegenerative diseases (funded by National Institute of Health, USA awarded to Principal Investigator)
- 2003-2004: Postdoctoral Fellowship: Characterization of modifiers of Polyglutamine diseases in Drosophila models (funded by National Institute of Health, USA awarded to Principal Investigator)
- 2004-2005: Postdoctoral Fellowship: Methylation profiling in cervical and breast cancers (funded by Dept. of Defense, USA awarded to Principal Investigator)
- 2005-2009: Postdoctoral Fellowship: Genomic sites of developmental and tissue specific DNA methylation (funded by National Institute of Health, USA awarded to Principal Investigator)
NUMBER OF PH. D. STUDENTS SUBMITTED / WORKING FOR THE DEGREE:
||Title of Thesis
|Mr. Shngainlang Khongsti
||Whole genome DNA methylation profiling of oral cancer patients from Meghalaya (awarded)
|Mr. Frederick A. Lamare
||Assessment of DNA methylation biomarkers for stomach cancer in patients from Mizoram
|Mr. Diwakar Kshetriya
||Expression of metallothionein and heat shock protein genes in Chironomus sp. of Meghalaya as a potential biomarker for environmental toxicity
|Mr. Calvin D. Warjri
||Studies on effects of heavy metals on metallothionein gene expression in common carp, Cyprinus carpio Linnaeus, 1758
|Mr. Lastborn Marthong
|| Yet to be registered
- Serving as Warden of Umiam Hostel for PG Girls (hostel No. 5) since October 2009 till date.