Translational Health

MEDICAL BIOTECHNOLOGY / Recombinant Diagnostics and Vaccines

Research Interests

Tuberculosis, Proteomics, Metabolomics, volatile organic compounds (VOCs), eNOSE.

Description of Research

Tuberculosis perturbs miRNAome, proteome and metabolome of human body fluids
Global profiling of genes, proteins and metabolites using complementary OMICS platforms portrays the footprint and signatures of normal physiology as well as perturbed states of an organism. By this approach an atlas of pattern recognition representing specific and nonspecific condition of different variability can be established at population level. Combined effort of molecular details at separate hierarchical levels could help to put the pieces of puzzle together to elucidate their role to explain variability at population levels to explain the bigger picture in relation to normal and diseased conditions. These complementary techniques can be employed to discover bio-signature for various purposes like disease diagnosis and monitoring therapeutic outcomes as well as to gain understanding host pathogen relationship in tuberculosis (TB) patients.

Expression, regulation and dynamics of biofluid miRNAome, proteome and metabolome are influenced by cell processes and perturbed by external factors like infection in a steady state. Therepetuic interventions also affect fluid state of biofluid molecular constituents inside the body to sum the effect on different cell and tissue types. With the advancement of quantitative proteomics, metabolomics tools like mass spectrometry and microarray techniques it is possible to compare multiple study groups representing different stages of disease progression or treatment response to discover stage specific bio-signature. Our focus is to identify panels of marker molecules from different biological fluids like saliva, serum and urine of active TB patients recruited from our collaborative clinical sites. Molecules showing significant up or down regulations in TB patients will be identified as putative marker molecules and their specificity to TB will be established using other similar respiratory disease states (e.g. pneumonia, lung cancer). In addition we are also attempting to elucidate the role of identified altered marker molecules from different bio-fluids in host pathogen interactions using a systems biology approach.

eNOSE for early Tuberculosis diagnosis
A non-invasive method of TB diagnosis using either urine and/or breath volatile organic compounds (VOCs) biomarkers is a major focus. Our earlier findings showed that a molecular signature of six VOCs identified from urine head space could diagnose TB with high sensitivity using gas chromatography and mass spectroscopy. Similarly a signature of seven molecules was identified from the breath of TB patients with high discriminatory power. We have also observed alterations in abundance of these VOCs during anti-TB therapeutic interventions. Preliminary results on breath VOCs showed drug resistance in pulmonary TB patients, active drug curable TB patients, lung cancer and COPD patients cluster separately.
With support from Bill and Melinda Gates Foundation and Grand Challenges Canada our present focus is to validate those signatures and to identify novel marker molecules in a longitudinal study including diverse study populations. Presently we are collaborating with six clinical sites representing diverse locations in India. After careful validation of the marker molecules, partnering with Next Dimensional Technologies, USA we are exploring the possibility of developing an easy to use eNOSE as a point of care TB diagnosis method by developing sensor arrays and integrating them with decision making algorithm.

Recent Publications

Meitei, H.N., Pandey, A., Faruquee, HMd., Thokchom, M., Athokpam, S., Guha, H., Das, R., Saha, S., Kupa, R., Kapfo, W., Keppen, J., Mohapatara, A.K., Priyadarsini, H., Koijam, A.S., Dasgupta, A., Goswami, B., Thong, A., Meru, K., Konyak, W., Gupta, D., Das, A., Khamo, V., Huidrom, L.S., Haobam ,S., Nanda, R.K., Haobamm R. 2021. Polymorphism of NAT2, PXR, ABCB1, and GSTT1 genes among tuberculosis patients of North Eastern States of India. medRxiv 2021.06.09.21258600; doi: https://doi.org/10.1101/2021.06.09.21258600

Faruquee, HMd,, Meitei, H.N., Pandey, A., Pahwa, F., Thokchom,  M., Sonia, A., Chaudhary, S., Gupta, D., Singh, H.L., Haobam, S., Haobam, R., Nanda, R.K. 2021.  Urine metabolome of tuberculosis patients receiving intensive phase of treatment show diurnal variations. medRxiv, doi: https://doi.org/10.1101/2021.03.30.21254606

Mohapatra, P., Shriwas, O., Mohanty, S., Kaushik, S.R., Arya, R., Rath, R., Majumdar, S.K.D., Muduly, D.K., Nanda, R.K., Dash, R. 2021. CMTM6 drives cisplatin resistance in OSCC by regulating AKT mediated Wnt signaling. bioRxiv  2020.03.18.993774;  doi: https://doi.org/10.1101/2020.03.18.993774. JCI Insight 6(4):e143643 PubMed link

Shriwas, O., Arya, R., Mohanty, S., Kumar, S., Rath, R., Kaushik, S.R., Thakur, M.C., Pahwa, F., Majumdar, S.K.D., Muduly, D.K., Nanda, R.K., Dash, R. 2021. RRBP1 rewires cisplatin resistance in Oral Squamous Cell Carcinoma by regulating YAP-1. bioRxiv 2020.03.18.998070;  Br J Cancer 124(12):2004-2016. https://doi.org/10.1038/s41416-021-01336-7

Arya, R., Dabral, D., Faruquee, H.M., Mazumdar, H., Patgiri, S.J., Deka, T., Basumatary, R., Kupa, R., Semy, C., Kapfo, W., Liegise, K., Kaur, I., Choedon, T., Kumar, P., Behera, R.K., Deori, P., Nath, R., Khalo, K.P., Saikia, L., Khamo, V., Nanda, R.K. 2020. Serum Small Extracellular Vesicles Proteome of Tuberculosis Patients Demonstrated Deregulated Immune Response. Proteomics Clin Appl 14,1,1900062 PubMed link

Meher, A., Guha, H., Pemmadi, R.V., Akram, S., Faruquee, H.M., Arya, R., Ghosh, H., Nikam, C., Saha, S., Das, R., Dasgupta, A., Goswami, B., Gupta, D., Das, A., Nanda, R.K. 2020. Whole-Genome sequence of drug-resistant Mycobacterium tuberculosis strain S7, isolated from a patient with pulmonary tuberculosis. Microbiol Resour Announce 9,17,e01567-19 PubMed link