Faculty Members

Research

Sepsis is a lethal disorder in all age groups including the newborn, and accounts for one-fifth of all deaths globally. One approach to reduce mortality is by rapid detection of the virulent pathogens (especially of the ESKAPE group) causing neonatal sepsis in India. Virulent phenotype is coded by certain genes in the bacteria. In our first attempt, we have developed a molecular diagnostic assay based on multiplex PCR for rapid detection of ESKAPE pathogens in clinical isolates. We plan to go deeper with genomic characterization of hyper-virulent bacteria causing sepsis.

What is the consequence of infection by a virulent pathogen? The host response to a serious bacterial pathogen, such as Klebsiella, is complex and dynamic. A series of molecular and cellular events shape the clinical trajectory of sepsis. In sepsis patients, some patterns emerge from analysis of blood transcriptomic datasets of the patients, such as up-regulation of pro-inflammatory cytokines and down-regulation of adaptive immunity. The current motivation is to dissect the clinically meaningful patterns and to discover the biological processes underlying non-survival from sepsis [PMID:28199355] and related disorders like COVID-19 (DOI: 10.1101/2020.10.13.20211425).

In addition to pathogen virulence and host immune-inflammatory responses, failure of antimicrobial treatment is an important cause of mortality due to sepsis. Antimicrobial

resistance, like virulence, is also encoded by genes in the bacteria, and are targeted for rapid detection.

Modern biological investigations are premised on generation of genome-scale data and sophisticated computational algorithms. For example, pathway-centric analysis of transcriptome data conducted at our laboratory revealed insights into sepsis [PMID:28199355] and sepsis-like cancers [PMID: 32293345] that were not possible with gene-level analysis alone. Ultimately, we are grounded on the notion that computational analysis must be driven by the quest for biological insights and societal impact.

Current Project

A diagnostic panel for rapid detection of early onset sepsis in high-risk neonates (DBT and ICMR)

CV

Education

Professional Appointments

Assistant Professor, National Institute of Biomedical Genomics, Kalyani, West Bengal, India (2010 - present)

Research Associate, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA (2005 - 2009)

Research Associate, Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA (2003 - 2005)

SRA, Scientists' Pool Scheme, CSIR, India (2000 - 2002)

Assistant Professor, Department of Biochemistry, BP Koirala Institute of Health Sciences, Dharan Nepal (1997 - 1999)

Senior Resident, Department of Biochemistry, Maulana Azad Medical College, New Delhi, India (1994 - 1997)

Professional Memberships

Member, Society of Biological Chemists (India)

Member, Indian Society of Human Genetics

Awards/Honors

Invited/Special lectures

• Year     Institute/meeting, Title of the talk
• 2018 Asean Institute of Public Health (Bhubaneswar). “Genomics of sepsis”.
• 2014 Lecture Series on Recent Advances in Mathematical and Computational Biology (Tezpur University). “Analysis of the dynamic transcriptomic changes in critical illness”.
• 2013 Asean Institute of Public Health (Bhubaneswar). “Genomics in medical research”.
• 2012    Annual Conference of Indian Society of Human Genetics (BHU, Varanasi). “Host transcriptional response to bacterial infection”.
• 2012 Cancer Informatics Workshop and Mini-symposium (NCCS, Pune). “Differential Expression Case Study”.
• 2012 National Workshop on Statistical Computing in Life Sciences (Pondicherry University). “Transcriptome Analysis with Bioconductor”.
• 2012 Workshop on Bioinformatics (ISI, Kolkata). “Bioinformatic analyses of protein microarrays”.
• 2012 Bioinformatics Workshop 2012 on High-throughput Data Analysis using R Packages (ICGEB, Delhi). “Transcriptome analysis with Bioconductor”.
• 2011 Discussion Meeting on Computational Biology in India – Status and Prospects (Coorg, Karnataka). “Global gene expression profiling using DNA microarrays”.

Past major projects

Leukocyte transcriptome signature of outcome of severe sepsis/septic shock (DBT)

A unified web-portal for analysis, integration and visualization of multiomics data (DBT)

Publications

• Chhatriya B, Mukherjee M, Ray S, Saha B, Lahiri S, Halder S, Ghosh I, Khamrui S, Das K, Bhattacharjee S, Mohapatra SK, Goswami S. Transcriptome analysis identifies putative multi-gene signature distinguishing benign and malignant pancreatic head mass. J Transl Med. 2020 Nov 7;18(1):420. doi: 10.1186/s12967-020-02597-1. PMID: 33160365; PMCID: PMC7648960.
• Tripathi H, Mukhopadhyay S, Mohapatra SK. Sepsis-associated pathways segregate cancer groups. BMC Cancer. 2020 Apr 15;20(1):309. doi: 10.1186/s12885-020-06774-9. PMID: 32293345; PMCID: PMC7160985.
• Mukhopadhyay S, Thatoi PK, Pandey AD, Das BK, Ravindran B, Bhattacharjee S, Mohapatra SK. Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock. PLoS One. 2017 Feb 15;12(2):e0171689. doi: 10.1371/journal.pone.0171689. PMID: 28199355; PMCID: PMC5310888.
• Ghosh A, Ghosh A, Datta S, Dasgupta D, Das S, Ray S, Gupta S, Datta S, Chowdhury A, Chatterjee R, Mohapatra SK*, Banerjee S. Hepatic miR-126 is a potential plasma biomarker for detection of hepatitis B virus infected hepatocellular carcinoma. Int J Cancer. 2016 Jun 1;138(11):2732-44. doi: 10.1002/ijc.29999. Epub 2016 Feb 8. PMID: 26756996. (* Joint corresponding author)
• Irshad K, Mohapatra SK, Srivastava C, Garg H, Mishra S, Dikshit B, Sarkar C, Gupta D, Chandra PS, Chattopadhyay P, Sinha S, Chosdol K. A combined gene signature of hypoxia and notch pathway in human glioblastoma and its prognostic relevance. PLoS One. 2015 Mar
• 10(3):e0118201. doi: 10.1371/journal.pone.0118201. PMID: 25734817; PMCID: PMC4348203.
• Bassaganya-Riera J, Dominguez-Bello MG, Kronsteiner B, Carbo A, Lu P, Viladomiu M, Pedragosa M, Zhang X, Sobral BW, Mane SP, Mohapatra SK, Horne WT, Guri AJ, Groeschl M, Lopez-Velasco G, Hontecillas R. Helicobacter pylori colonization ameliorates glucose homeostasis in mice through a PPAR γ-dependent mechanism. PLoS One. 2012;7(11):e50069. doi: 10.1371/journal.pone.0050069. Epub 2012 Nov 15. PMID: 23166823; PMCID: PMC3499487.
• Mohapatra SK, Krishnan A. Microarray data analysis. Methods Mol Biol. 2011;678:27-43. doi: 10.1007/978-1-60761-682-5_3. PMID: 20931370.
• Guri AJ, Mohapatra SK, Horne WT 2nd, Hontecillas R, Bassaganya-Riera J. The role of T cell PPAR gamma in mice with experimental inflammatory bowel disease. BMC Gastroenterol. 2010 Jun 10;10:60. doi: 10.1186/1471-230X-10-60. PMID: 20537136; PMCID: PMC2891618.
• Mohapatra SK, Guri AJ, Climent M, Vives C, Carbo A, Horne WT, Hontecillas R, Bassaganya-Riera J. Immunoregulatory actions of epithelial cell PPAR gamma at the colonic mucosa of mice with experimental inflammatory bowel disease. PLoS One. 2010 Apr 20;5(4):e10215. doi: 10.1371/journal.pone.0010215. PMID: 20422041; PMCID: PMC2857885.
• Mohapatra SK, Cole LE, Evans C, Sobral BW, Bassaganya-Riera J, Hontecillas R, Vogel SN, Crasta OR. Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection. BMC Infect Dis. 2010 Jan 18;10:10. doi: 10.1186/1471-2334-10-10. PMID: 20082697; PMCID: PMC2826305.
• Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Mégraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J. Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses. J Bacteriol. 2010 Jun;192(12):3078-92. doi: 10.1128/JB.00063-10. Epub 2010 Apr 16. PMID: 20400544; PMCID: PMC2901691.
• Li XL, Ezelle HJ, Kang TJ, Zhang L, Shirey KA, Harro J, Hasday JD, Mohapatra SK, Crasta OR, Vogel SN, Cross AS, Hassel BA. An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20816-21. doi: 10.1073/pnas.0807265105. Epub 2008 Dec 15. PMID: 19075243; PMCID: PMC2634919.x
• Lin HS, Talwar HS, Tarca AL, Ionan A, Chatterjee M, Ye B, Wojciechowski J, Mohapatra SK, Basson MD, Yoo GH, Peshek B, Lonardo F, Pan CJ, Folbe AJ, Draghici S, Abrams J, Tainsky MA. Autoantibody approach for serum-based detection of head and neck cancer. Cancer Epidemiol Biomarkers Prev. 2007 Nov;16(11):2396-405. doi: 10.1158/1055-9965.EPI-07-0318. PMID: 18006929; PMCID: PMC2575765.
• Nowak JE, Chatterjee M, Mohapatra SK, Dryden SC, Tainsky MA. Direct production and purification of T7 phage display cloned proteins selected and analyzed on microarrays. Biotechniques. 2006 Feb;40(2):220-7. doi: 10.2144/000112099. PMID: 16526412.
• Chatterjee M, Mohapatra SK, Ionan A, Bawa G, Ali-Fehmi R, Wang X, Nowak J, Ye B, Nahhas FA, Lu K, Witkin SS, Fishman D, Munkarah A, Morris R, Levin NK, Shirley NN, Tromp G, Abrams J, Draghici S, Tainsky MA. Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays. Cancer Res. 2006 Jan 15;66(2):1181-90. doi: 10.1158/0008-5472.CAN-04-2962. PMID: 16424057; PMCID: PMC2546578.
• Khan ZH, Mohapatra SK, Khodiar PK, Ragu Kumar SN. Artificial neural network and medicine. Indian J Physiol Pharmacol. 1998 Jul;42(3):321-42. PMID: 9741647

Lab members

Ph.D. students:

Samanwoy Mukhopadhyay (recently submitted thesis)
Manisha Rout

Saroj Kant Mohapatra