Interactions of Flaviviruses with host cellular mechanisms and implications for pathogenesis

Host-pathogen interaction is a series of complex and intertwined cellular and signalling events that determine disease outcome. Understanding these interactions is crucial for identification and development of therapies, vaccines and anti-viral drugs. Our research theme is to understand how Flaviviruses [positive-stranded RNA viruses- Japanese Encephalitis Virus (JEV) and Dengue virus] interact with and modulate cellular pathways to establish infection. Both viruses are spread by infected mosquito bites and pose a significant health burden for India. We aspire to understand the mechanisms leading to disease, identify & validate drug-targets, develop therapeutics and improve vaccine efficacy.

Our focus is the host Membrane trafficking, Autophagy and ER-associated degradation (ERAD) pathway.

Our studies on the membrane trafficking requirements for JEV infection have shown how the virus can exploit alternate endocytic pathways (clathrin independent) depending on the target cell (neuronal vs epithelial). This has enabled us to identify novel drug-targets that are in the process of being validated. Autophagy, a basic cellular housekeeping pathway, is closely linked to virus pathogenesis. Our studies have highlighted the role of this pathway as an anti-viral defence mechanism, and its modulation by oxidative and ER stress. Interestingly, some autophagy proteins play an independent role in virus replication.

Our current research themes are-

• Molecular Regulation of Autophagy & ERAD pathway during virus infection
• Mechanisms of the anti-viral role of autophagy
• Regulation and enhancement of immune response to virus infection by autophagy modulation
• Validation of drug targets against flavivirus infections in vitro and in animal model

• Eira Choudhary, PhD
  SERB-NPDF
  eira.choudhary@rcb.res.in
• Riya Sarkar
  Senior Research Fellow
  riya.sarkar@rcb.res.in
• Surendra Kumar Prajapat
  Senior Research Fellow
  surendra.prajapat@rcb.res.in
• Puja Sharma
  Senior Research Fellow
  puja.sharma@rcb.res.in
• Sakshi Khera
  Junior Research Fellow
  sakshi.khera@rcb.res.in
• Simran Chhabra
  Integrated MSc-PhD student
  simran.chhabra@rcb.res.in
• Laxmi Mishra
  Junior Research Fellow
  laxmi.mishra@rcb.res.in
• Ananya De
  Integrated MSc-PhD student
  ananya.de@rcb.res.in

• SERC Fast Track Fellowship for Young Scientists (DST) 2003-2006
• Innovative Young Biotechnologist Award (DBT) 2007-2010

1. KB, Kalia M (2022). Human Guanylate-binding Protein 1 positively regulates Japanese encephalitis virus replication in an interferon gamma primed environment. Front Cell Infect Microbiol 2022 May 19;12:832057. doi: 10.3389/fcimb.2022.832057. eCollection
2. Agarwal A, Alam MF, Basu B, Pattanayak S, Asthana S, Syed GH, Kalia M, Vrati S (2022). Japanese Encephalitis Virus NS4A protein interacts woth PTEN-Induced Kinase 1 (PINK1) and promotes mitophagy in infected cells. Microbiology Spectrum. 2022 May 23:e0083022. doi: 10.1128/spectrum.00830-22.
3. KB, Aggarwal S, Yadav AK, Vrati S, Kalia M (2022). Studying Autophagy using a TMT-based quantitative proteomics approach. Methods Mol Biol. 2022;2445:183-203. doi: 10.1007/978-1-0716-2071-7_12.
4. Sharma KB, Chhabra S, Aggarwal S, Tripathi A, Banerjee A, Yadav AK, Vrati S, Kalia M (2021). Proteomic landscape of Japanese encephalitis virus-infected fibroblasts. J Gen Virol. 2021 Sep;102(9). Doi:10.1099/jgv.0.001657
5. Nath P, Chauhan NR, Jena KK, Datey A, Kumar ND, Mehto S, De S, Nayak TK, Priyadarsini S, Rout K, Bal R, Murmu KC, Kalia M, Patnaik S, Prasad P, Reggiori F, Chattopadhyay S, Chauhan S. Inhibition of IRGM establishes a robust antiviral immune state to restrict pathogenic viruses (2021). EMBO Rep. 2021 Nov 4;22(11): e52948. doi: 10.15252/embr.202152948. Epub 2021 Sep 1.
6. Vedagiri D, Gupta D, Mishra A, Krishna G, Bhaskar M, Sah V, Basu A, Nayak D, Kalia M, Valiya Veettil M, Harshan KH. (2021) Retinoic Acid-Inducible Gene I-Like Receptors Activate Snail To Limit RNA Viral Infections. J Virol. 2021 Oct 13;95(21): e0121621.doi: 10.1128/JVI.01216-21. Epub 2021 Aug 11.
7. Sharma KB, Vrati S, Kalia M (2021) Pathobiology of Japanese encephalitis virus infection. Mol Aspects Med. 2021 Oct;81:100994. doi: 10.1016/j.mam.2021.100994. Epub 2021 Jul 15.
8. Shailendra Chauhan, Deepak Kumar Rathore, Shilpa Sachan, Sebastien Lacroix-Desmazes, Nimesh Gupta, Amit Awasthi, Sudhanshu Vrati and Manjula Kalia (2021) “Japanese Encephalitis Virus Infected Human Monocyte-Derived Dendritic Cells Activate a Transcriptional Network Leading to an Antiviral Inflammatory Response” Frontiers in Immunology 12: 638694.doi: 10.3389/fimmu.2021.638694
9. Sapna Sherawat, Renu Khasa, Arundhati Deb, Surendra Kumar Prajapat, Suvadip Mallick, Anirban Basu, Milan Surjit, Manjula Kalia, Sudhanshu Vrati (2021) “Valosin-containing protein/p97 plays critical roles in the Japanese encephalitis virus life cycle” Journal of Virology 2021 Mar 17: JVI.02336-20. doi: 10.1128/JVI.02336-20.
10. Klionsky DJ et al., (2021) “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) Autophagy 2021 Jan;17(1):1-382. doi: 10.1080/15548627.2020.1797280. Epub 2021 Feb 8.
11. Riya Sarker, Kiran Bala Sharma, Anita Kumari, Shailendra Asthana, Manjula Kalia (2020) “Japanese encephalitis virus capsid protein interacts with non-lipidated MAP1LC3 on replication membranes and lipid droplets” Journal of General Virology. 2021 Jan;102(1). doi: 10.1099/jgv.0.001508. Epub 2020 Oct 23.
12. Renu Khasa, Puja Sharma, Anuradha Vaidya, Sudhanshu Vrati, Manjula Kalia (2020) “Proteins involved in actin filament organization are key host factors for Japanese encephalitis virus life-cycle in human neuronal cells” Microbial Pathogenesis 2020 Dec;149:104565. doi: 10.1016/j.micpath.2020.104565. Epub 2020 Oct 12.
13. Garima Sharma, Shweta Dang, Aruna K, Manjula Kalia, Reema Gabrani (2020) “Synergistic antibacterial and anti-biofilm activity of nisin like bacteriocin with curcumin and cinnamaldehyde against ESBL and MBL producing clinical strains” Biofouling. 2020 Jul; 36 (6): 710-724. doi: 10.1080/08927014.2020.1804553. Epub 2020 Aug 9.
14. Kiran Bala Sharma, Manish Sharma, Suruchi Aggarwal, Amit Kumar Yadav, Shinjini Bhatnagar, Sudhanshu Vrati, Manjula Kalia (2019) “Quantitative Proteome Analysis of Atg5- Deficient Mouse Embryonic Fibroblasts Reveals the Range of the Autophagy-Modulated Basal Cellular Proteome” mSystems. Nov 5;4(6). pii: e00481-19. doi: 10.1128/mSystems.00481-19.
15. Renu Khasa, Anuradha Vaidya, Sudhanshu Vrati, Manjula Kalia (2018) “Membrane trafficking RNA interference screen identifies a crucial role of the clathrinendocytic pathway and ARP2/3 complex for Japanese encephalitis virus infection in HeLa cells” Journal of General Virology. 2018 Nov 29. doi: 10.1099/jgv.0.001182. [Epub ahead of print] PMID: 30489239.
16. Manish Sharma, Kiran Bala Sharma, Shailendra Chauhan, Sankar Bhattacharyya, Sudhanshu Vrati, Manjula Kalia (2018) “Diphenyleneiodonium enhances oxidative stress and inhibits Japanese encephalitis virus induced autophagy and ER stress pathways” Biochem Biophys Res Commun. 2018 May 22. pii: S0006-291X(18)31218-X. doi: 10.1016/j.bbrc.2018.05.149. [Epub ahead of print] PMID:29792860
17. Vikas Sood, Kiran Bala Sharma, Vishal Gupta, D Saha, P Dhapola, Manish Sharma, Utsav Sen, S. Kitajima, S Chowdhury, Manjula Kalia, Sudhanshu Varti (2017) “ATF3 negatively regulates cellular antiviral signaling and autophagy in the absence of type I interferons” Scientific Reports 2017 Aug 18;7(1):8789. Doi:10.1038/s41598-017-08584-9. PMID: 28821775
18. A Madhvi, S Hingane, R Srivastav, N Joshi, C Subramani, R Muthumohan, R Khasa, S Varshney, Manjula Kalia, Sudhanshu Vrati, Milan Surjit, Ranjith-Kumar CT (2017) “A screen for novel hepatitis C virus RdRp inhibitor identifies a broad-spectrum antiviral compound” Scientific Reports 2017 Jul 10;7(1): 5816. Doi: 10.1038/s41598-017-04449-3. PMID: 28725041
19. Manish Sharma, Sankar Bhattacharyya, Kiran Bala Sharma, Shailendra Chauhan, Suramya Asthana, Mailk Zainul Abdin, Sudhanshu Vrati and Manjula Kalia (2017) “Japanese encephalitis virus activates autophagy through XBP1 and ATF6 ER stress sensors in neuronal cells” Journal of General Virology 2017 May;98(5):1027-1039. doi: 10.1099/jgv.0.000792. Epub 2017 May 23. PMID: 28535855
20. Minu Nain, Sriparna Mukherjee, Sonali Porey Karmakar, Adrienne W. Paton, James C. Paton, M.Z. Abdin, Anirban Basu, Manjula Kalia*, Sudhanshu Vrati* (2017) “GRP78 is an Important Host Factor for Japanese Encephalitis Virus Entry and Replication in Mammalian Cells” Journal of Virology 2017 Feb 28;91(6). pii: e02274-16. doi: 10.1128/JVI.02274-16. Print 2017 Mar 15. PMID: 28053106
21. Daniel J. Klinosky et al., Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) Autophagy 2016 Jan 2:12(1): 1-222
22. Minu Nain, M.Z.Abdin, Manjula Kalia* and Sudhanshu Vrati* (2015) “Japanese encephalitis virus invasion of cell: allies and alleys” Reviews in Medical Virology 2015 Dec23:doi:10.1002/rmv.1868 [Epub ahead of print] [*Co-corresponding Author]
23. Nimesh Gupta, Melissanne de Wispelaere, Maxime Lecerf, Manjula Kalia, Tobias Scheel, Sudhanshu Vrati, Claudia Berek, Srinivas V. Kaveri, Philippe Despres, Sebastien Lacroix-Desmazes, Jordan D. Dimitrov (2015) “Neutralization of Japanese Encephalitis Virus by heme-induced broadly reactive human monoclonal antibody” Scientific Reports. 2015 Nov6:5:16248. Doi: 10.1038/srep16248
24. Deepika Bhullar, Richa Jalodia, Manjula Kalia, Sudhanshu Vrati (2014) “Cytoplasmic Translocation of Polypyrimidine Tract-Binding Protein and Its Binding to Viral RNA during Japanese Encephalitis Virus Infection Inhibits Virus Replication” PLoS ONE 9(12):e114931. doi:10.1371/journal.pone.0114831
25. Manish Sharma, Sankar Bhattacharyya, Minu Nain, Manpreet Kaur, Vikas Sood, Vishal Gupta, Renu Khasa, Malik Abdin, Sudhanshu Vrati* and Manjula Kalia* (2014) “Japanese Encephalitis Virus Replication is Negatively Regulated by Autophagy and Occurs on LC3-I- and EDEM1-containing Membranes. Autophagy. 2014 Sep; 10(9): 1637-51. Doi: 10.4161/auto.29455. Epub 2014 July16
26. Nimesh Gupta, Pushpa Hegde, Maxime Lecerf, Minu Nain, Manpreet Kaur, Manjula Kalia, Sudhanshu Vrati, Jagadeesh Bayry, Sebastien Lacroix-Desmazes and Srini V. Kaveri (2014) “Japanese encephalitis virus expands regulatory T cells by increasing the expression of PD-L1 on dendritic cells” Eur.J.Immunol. 2014 May;44(5):1363-74. [Epub 2014 Mar24]
27. Manjula Kalia*, Renu Khasa, Manish Sharma, Minu Nain and Sudhanshu Vrati (2013) “Japanese Encephalitis Virus Infects Neuronal Cells through a Clathrin Independent Endocytic Mechanism” J Virology. 2013 Jan; 87(1):148-162. [Epub 2012 Oct 10]. [*Corresponding Author]
28. Vivek Chandra, Manjula Kalia, Krishan Hajela and Shahid Jameel (2010) “The ORF3 protein of hepatitis E virus delays degradation of activated growth factor receptors by interacting with CIN85 and blocking formation of the Cbl-CIN85 complex” J Virology. 2010 Apr; 84(8):3857-67. [Epub 2010 Feb 3].
29. Manjula Kalia and Shahid Jameel (2011) Virus entry paradigms. Amino Acids Nov; 41(5):1147-57. [Epub 2009 Oct 15]. Review
30. Manjula Kalia*, Vivek Chandra, Sheikh Abdul Rahman, Deepak Sehgal and Shahid Jameel (2009) “Heparan Sulfate Proteoglycans are Required for Cellular Binding of the Hepatitis E Virus ORF2 Capsid Protein and for Viral Infection” J. Virology Vol 83, No24:12714-24 [Epub 2009 Oct7]. [*Corresponding Author]
31. Vivek Chandra, Shikha Taneja, Manjula Kalia and Shahid Jameel (2008) “Molecular Biology and Pathogenesis of Hepatitis E Virus” J.Biosciences 33:451-64
32. Manjula Kalia, Sudha Kumari, Rahul Chadda, Michelle M. Hill, Robert G. Parton, and Satyajit Mayor (2006) “Arf6-independent GEECs fuse with sorting endosomes via a Rab5/PI-3’ kinase dependent machinery” Mol Biol Cell 17: 3689-3704
33. M. Awasthi-Kalia, K.V. Bhat and R.K. Anand. (2002) “Genetic characterization of Mus musculus and related forms from India”. Experimental Animals 51: No 1. 103-107
34. M. Mishra, N. Dubey, S.M. Totey, K.V. Bhat, S. Babu, M. Awasthi-Kalia and R.K. Anand. (2002) “Phylogenetic relationships and genetic polymorphisms in wild Indian mice”. Biomolecular Engineeering 18: No 6. 281-288
35. M. Awasthi-Kalia, P.P.M. Schnetkamp and J.P. Deans. (2001). “Differential effects of Filipin and Methyl--cyclodextrin on B Cell Receptor Signaling”. Biochemical and Biophysical Research Communications 287: 77-82
36. R.J. Petrie, P.P.M. Schnetkamp, K.D. Patel, M. Awasthi-Kalia and J.P. Deans. (2000) "Transient Translocation of the B Cell Receptor and Src Homology 2 Domain- Containing Inositol Phosphatase to Lipid Rafts: Evidence Toward a Role in Calcium Regulation". Journal of Immunology. 165: 1220-1227
37. M. Awasthi, K.V. Bhat and R.K. Anand. (1999) "Allozyme variation in four Indian species of genus Mus: A comparative analysis ". Journal of Genetics. 78: No 2. 73-80
38. M. Awasthi, S. Rath, P.A. Cazenave and R.K. Anand. (1999) "TCR V 17 gene polymorphism in the Indian Mus musculus". Journal of Biosciences. 24: 163-169
39. M. Awasthi, K.V. Bhat and R.K. Anand. (1998) "Genetic heterogeneity in the Indian Mus musculus". Biochemical Genetics. 36: Nos. 7/8 245-258.