Bio

Professional Education


  • Bachelor of Science, Delhi University (2006)
  • Master of Science, Delhi University (2008)
  • Doctor of Philosophy, Homi Bhabha NationalHomi Bhabha National Institute (2015)

Stanford Advisors


Publications

All Publications


  • Distinct genome-wide methylation patterns in sporadic and hereditary nonfunctioning pancreatic neuroendocrine tumors. Cancer Tirosh, A., Mukherjee, S., Lack, J., Gara, S. K., Wang, S., Quezado, M. M., Keutgen, X. M., Wu, X., Cam, M., Kumar, S., Patel, D., Nilubol, N., Tyagi, M. V., Kebebew, E. 2019

    Abstract

    BACKGROUND: Aberrant methylation is a known cause of cancer initiation and/or progression. There are scant data on the genome-wide methylation pattern of nonfunctioning pancreatic neuroendocrine tumors (NFPanNETs) and sporadic and hereditary NFPanNETs.METHODS: Thirty-three tissue samples were analyzed: they included samples from sporadic (n=9), von Hippel-Lindau (VHL)-related (n=10), and multiple endocrine neoplasia type 1 (MEN1)-related NFPanNETs (n=10) as well as normal islet cells (n=4) for comparison. Genome-wide CpG methylation profiling was performed with the Infinium MethylationEPIC BeadChip assay and was analyzed with R-based tools.RESULTS: In unsupervised hierarchical clustering, sporadic and MEN1-related NFPanNETs clustered together, and the VHL group was in a separate cluster. MEN1-related NFPanNETs had a higher rate of hypermethylated CpG sites in comparison with sporadic and VHL-related tumor groups. Differentially methylated region analysis confirmed the higher rate of hypermethylation in MEN1-related tumors. Moreover, in an integrated analysis of gene expression data for the same tumor samples, downregulated gene expression was found in most genes that were hypermethylated. In a CpG island methylator phenotype analysis, 3 genes were identified and confirmed to have downregulated gene expression: secreted frizzle-related protein 5 (SFRP5) in sporadic NFPanNETs and cell division cycle-associated 7-like (CDCA7L) and RNA binding motif 47 (RBM47) in MEN1-related NFPanNETs.CONCLUSIONS: MEN1 NFPanNETs have a higher rate of geno me-wide hypermethylation than other NFPanNET subtypes. The similarity between the pathways enriched in a methylation analysis of known genes involved in NFPanNET tumorigenesis suggests a key role for aberrant methylation in the pathogenesis of NFPanNETs.

    View details for PubMedID 30620390

  • Genomic characterization and dynamic methylation of promoter facilitates transcriptional regulation of H2A variants, H2A.1 and H2A.2 in various pathophysiological states of hepatocyte INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY Tyagi, M., Reddy, D., Gupta, S. 2017; 85: 15-24

    Abstract

    Differential expression of homomorphous variants of H2A family of histone H2A.1 and H2A.2 have been associated with hepatocellular carcinoma and maintenance of undifferentiated state of hepatocyte. However, not much is known about the transcriptional regulation of these H2A variants. The current study revealed the presence of 43bp 5'-regulatory region upstream of translation start site and a 26bp 3' stem loop conserved region for both the H2A.1 and H2A.2 variants. However, alignment of both H2A.1 and H2A.2 5'-untranslated region (UTR) sequences revealed no significant degree of homology between them despite the coding exon being very similar amongst the variants. Further, transient transfection coupled with dual luciferase assay of cloned 5' upstream sequences of H2A.1 and H2A.2 of length 1.2 (-1056 to +144) and 1.379kb (-1160 to +219) from experimentally identified 5'UTR in rat liver cell line (CL38) confirmed their promoter activity. Moreover, in silico analysis revealed a presence of multiple CpG sites interspersed in the cloned promoter of H2A.1 and a CpG island near TSS for H2A.2, suggesting that histone variants transcription might be regulated epigenetically. Indeed, treatment with DNMT and HDAC inhibitors increased the expression of H2A.2 with no significant change in H2A.1 levels. Further, methyl DNA immunoprecipitation coupled with quantitative analysis of DNA methylation using real-time PCR revealed hypo-methylation and hyper-methylation of H2A.1 and H2A.2 respectively in embryonic and HCC compared to control adult liver tissue. Collectively, the data suggests that differential DNA methylation on histone promoters is a dynamic player regulating their expression status in different pathophysiological stages of liver.

    View details for DOI 10.1016/j.biocel.2017.01.019

    View details for Web of Science ID 000399630500003

    View details for PubMedID 28163185

  • Trichostatin A decreases the levels of MeCP2 expression and phosphorylation and increases its chromatin binding affinity. Epigenetics Good, K. V., Martínez de Paz, A., Tyagi, M., Cheema, M. S., Thambirajah, A. A., Gretzinger, T. L., Stefanelli, G., Chow, R. L., Krupke, O., Hendzel, M., Missiaen, K., Underhill, A., Landsberger, N., Ausió, J. 2017; 12 (11): 934–44

    Abstract

    MeCP2 binds to methylated DNA in a chromatin context and has an important role in cancer and brain development and function. Histone deacetylase (HDAC) inhibitors are currently being used to palliate many cancer and neurological disorders. Yet, the molecular mechanisms involved are not well known for the most part and, in particular, the relationship between histone acetylation and MeCP2 is not well understood. In this paper, we study the effect of the HDAC inhibitor trichostatin A (TSA) on MeCP2, a protein whose dysregulation plays an important role in these diseases. We find that treatment of cells with TSA decreases the phosphorylation state of this protein and appears to result in a higher MeCP2 chromatin binding affinity. Yet, the binding dynamics with which the protein binds to DNA appear not to be significantly affected despite the chromatin reorganization resulting from the high levels of acetylation. HDAC inhibition also results in an overall decrease in MeCP2 levels of different cell lines. Moreover, we show that miR132 increases upon TSA treatment, and is one of the players involved in the observed downregulation of MeCP2.

    View details for DOI 10.1080/15592294.2017.1380760

    View details for PubMedID 29099289

    View details for PubMedCentralID PMC5788420

  • Y-labelled microspheres for therapy of hepatocellular carcinoma. Indian journal of medical research Subramanian, S., Pandey, U., Chaudhari, P., Tyagi, M., Gupta, S., Singh, G., Dash, A., Samuel, G., Venkatesh, M. 2016; 143: S74-S81

    Abstract

    Yttrium-90 ( 90 Y)-based radioembolization has been employed to treat hepatocellular carcinoma (HCC) as commercial radioactive glass and polymeric resin microspheres. However, in India and other Asian countries, these preparations must be imported and are expensive, validating the need for development of indigenous alternatives. This work was aimed to develop an economically and logistically favourable indigenous alternative to imported radioembolizing agents for HCC therapy.The preparation of 90 Y-labelled Biorex 70 microspheres was optimized and in vitro stability was assessed. Hepatic tumour model was generated in Sprague-Dawley rats by orthotopic implantation of N1S1 rat HCC cell line. In vivo localization and retention of the 90 Y-labelled Biorex 70 microspheres was assessed for seven days, and impact on N1S1 tumour growth was studied by histological examination and biochemical assays.Under optimal conditions, >95% 90 Y-labelling yield of Biorex70 resin microspheres was obtained, and these showed excellent in vitro stability of labelling (>95%) at seven days. In animal studies, 90 Y-labelled Biorex 70 microspheres were retained (87.72±1.56% retained in liver at 7 days). Rats administered with 90 Y-labelled Biorex 70 microspheres exhibited lower tumour to liver weight ratio, reduced serum alpha-foetoprotein level and greater damage to tumour tissue as compared to controls.90 Y-labelled Biorex 70 microspheres showed stable retention in the liver and therapeutic effect on tumour tissue, indicating the potential for further study towards clinical use.

    View details for DOI 10.4103/0971-5916.191786

    View details for PubMedID 27748281

    View details for PubMedCentralID PMC5080932

  • Chromatin remodelers: We are the drivers!! NUCLEUS Tyagi, M., Imam, N., Verma, K., Patel, A. K. 2016; 7 (4): 388-404

    Abstract

    Chromatin is a highly dynamic structure that imparts structural organization to the genome and regulates the gene expression underneath. The decade long research in deciphering the significance of epigenetics in maintaining cellular integrity has embarked the focus on chromatin remodeling enzymes. These drivers have been categorized as readers, writers and erasers with each having significance of their own. Largely, on the basis of structure, ATP dependent chromatin remodelers have been grouped into 4 families; SWI/SNF, ISWI, IN080 and CHD. It is still unclear to what degree these enzymes are swayed by local DNA sequences when shifting a nucleosome to different positions. The ability of regulating active and repressive transcriptional state via open and close chromatin architecture has been well studied however, the significance of chromatin remodelers in regulating transcription at each step i.e. initiation, elongation and termination require further attention. The authors have highlighted the significance and role of different chromatin remodelers in transcription, DNA repair and histone variant deposition.

    View details for DOI 10.1080/19491034.2016.1211217

    View details for Web of Science ID 000384442800008

    View details for PubMedID 27429206

    View details for PubMedCentralID PMC5039004

  • Techniques to access histone modifications and variants in cancer. Methods in molecular biology (Clifton, N.J.) Tyagi, M., Khan, S. A., Bhattacharya, S., Reddy, D., Sharma, A. K., Khade, B., Gupta, S. 2015; 1238: 251-272

    Abstract

    Recent years have witnessed an explosion of epigenetic research on the role of histone variants and modifications in cancer. To understand the global dynamics of chromatin structure and function, analysis of histone variants incorporated into the nucleosome and their covalent modifications, is required. The nucleosome is the fundamental structural unit of chromatin, contains an octamer of core histones H3, H4, H2A, and H2B. The differential alterations in diverse histone variants and their accompanying modifications patterns will provide a deeper insight into their biological role in structural and functional properties of chromatin. Here we provide a step-by-step protocol to investigate these aspects, the histone modifications and variants, their localization and dynamics within specific regions of chromatin under distinct condition and the recruitment/retention of epigenetic regulators at their target sites in chromatin to influence cell growth and differentiation.

    View details for DOI 10.1007/978-1-4939-1804-1_13

    View details for PubMedID 25421664

  • Expression of histone variant, H2A.1 is associated with the undifferentiated state of hepatocyte EXPERIMENTAL BIOLOGY AND MEDICINE Tyagi, M., Khade, B., Khan, S. A., Ingle, A., Gupta, S. 2014; 239 (10): 1335-1339

    Abstract

    Recent studies suggest the incorporation of histone variants into the chromatin regulate cellular proliferation, differentiation, and de-differentiation. We have earlier reported the increase of H2A.1 variant during sequential de-differentiation of hepatocyte to hepato-cellular carcinoma. Here, we decipher the alterations in expression of H2A.1 and H2A.2 variants during rat liver embryogenesis and regeneration. The expression of H2A.1 and H2A.2, at protein and mRNA level, does not alter in normal cellular proliferation associated with regeneration of liver post PH. In contrast, gradual decrease of H2A.1 with increase of H2A.2 is observed during differentiation of embryonic to adult liver. Furthermore, the accumulation of H2A.1 is higher in embryonic stem cells compared to normal adult liver. Collectively, these data support a strong correlation of H2A.1 expression with undifferentiated cells and overall epigenetic reprogramming in dedifferentiation and maturation of undifferentiated cells, rather than with normal cellular proliferation.

    View details for DOI 10.1177/1535370214531869

    View details for Web of Science ID 000343003300007

    View details for PubMedID 24764240

  • Cell-type specificity of beta-actin expression and its clinicopathological correlation in gastric adenocarcinoma WORLD JOURNAL OF GASTROENTEROLOGY Khan, S. A., Tyagi, M., Sharma, A. K., Barreto, S. G., Sirohi, B., Ramadwar, M., Shrikhande, S. V., Gupta, S. 2014; 20 (34): 12202-12211

    Abstract

    To investigate cell type specific distribution of β-actin expression in gastric adenocarcinoma and its correlation with clinicopathological parameters.β-actin is a housekeeping gene, frequently used as loading control, but, differentially expresses in cancer. In gastric cancer, an overall increased expression of β-actin has been reported using tissue disruptive techniques. At present, no histological data is available to indicate its cell type-specific expression and distribution pattern. In the present study, we analyzed β-actin expression and distribution in paired normal and tumor tissue samples of gastric adenocarcinoma patients using immunohistochemistry (IHC), a tissue non-disruptive technique as well as tissue disruptive techniques like reverse transcriptase-polymerase chain reaction (RT-PCR) and western blotting. Correlation of β-actin level with clinicopathological parameters was done using univariate analysis.The results of this study showed significant overexpression, at both mRNA and protein level in tumor tissues as confirmed by RT-PCR (1.47 ± 0.13 vs 2.36 ± 0.16; P < 0.001) and western blotting (1.92 ± 0.26 vs 2.88 ± 0.32; P < 0.01). IHC revealed that β-actin expression is majorly distributed between epithelial and inflammatory cells of the tissues. Inflammatory cells showed a significantly higher expression compared to epithelial cells in normal (2.46 ± 0.13 vs 5.92 ± 0.23, P < 0.001), as well as, in tumor tissues (2.79 ± 0.24 vs 6.71 ± 0.14, P < 0.001). Further, comparison of immunostaining between normal and tumor tissues revealed that both epithelial and inflammatory cells overexpress β-actin in tumor tissues, however, significant difference was observed only in inflammatory cells (5.92 ± 0.23 vs 6.71 ± 0.14, P < 0.01). Moreover, combined expression in epithelial and inflammatory cells also showed significant increase (4.19 ± 0.15 vs 4.75 ± 0.14, P < 0.05) in tumor tissues. In addition, univariate analysis showed a positive correlation of β-actin level of inflammatory cells with tumor grade (P < 0.05) while epithelial cells exhibited negative correlation (P > 0.05).In gastric cancer, β-actin showed an overall higher expression predominantly contributed by inflammatory or tumor infiltrating immune cells of the tissue microenvironment and correlates with tumor grade.

    View details for DOI 10.3748/wjg.v20.i34.12202

    View details for Web of Science ID 000341719100027

    View details for PubMedID 25232253

    View details for PubMedCentralID PMC4161804