Profile

Dr. Santosh Chauhan- Significant achievements

Please visit http://autophagylab.com for more details.

1. Elected Fellow of National Academy of Sciences (NASI)-2020
2. S Ramachandran-National Bioscience Award for Career Development- DBT-2019
3. EMBO Global Investigator Fellowship-EMBO- 2019-2023
4. Runner up- Merck young Scientist Award-2019
5. Selected for Wellcome-DBT intermediate fellowship-2015
6. Selected for Ramanujan Fellowship-2015
7. Selected for Ramalingaswami Fellowship-2015
8. Associate Faculty Member for F1000Prime, 2014-present
9. Associate of Indian Academy of Sciences, 2009-2013.
10. Research Associateship CSIR, New Delhi. India, 2009.
11. Junior and Senior Research Fellowship, CSIR, India 2004-2009.
12. Qualified Graduate Aptitude Test in Engineering-2003, India.
13. Qualified national level combined biotechnology test, 2001 for M.Sc (Biotechnology).
14. Topper in M.Sc (Biotechnology), GNDU, Amritsar.

Lab awards and achievements

1. Parej Nath– Sunpharma Science Scholar Award-2020
2. Kautilya Kumar Jena– NASI-Young Scientist Platinium Jubilee Award-2020
3. Kautilya Kumar Jena– INSA Young Scientist Medal-2020
4. Dr. Subhash Mehto– Inspire Faculty Fellowship-2020
5. Dr. Subhash Mehto– Merit certificate “NPDF online poster competition” organized by DST-SERB and ACS publication-2020
6. Dr. Subhash Mehto – DST-DFG Young Scientist Award for attending Lindau Nobel Laureate Meeting-2020/21
7. Kautilya Kumar Jena – DST-DFG Young Scientist Award for attending Lindau Nobel Laureate Meeting-2020/21
8. Dr. Subhash Mehto– TNQ-Cell Press Inspiring Science Award Winner-2020
9. Dr. Subhash Mehto– NASI-Young Scientist Platinum Jubilee Award-2019
10. Kautilya Kumar Jena– TNQ-Inspiring Science Award Runner up-2019
11. AWSAR DST Award in pdf category- Dr. Nuzhat Ahsan
12. Paper selected for a short talk in Keystone conference on innate immunity, Taipei, Taiwan, 2019- Dr. Subhash Mehto 
13. Travel award from DST and Immunology Foundation to attend the conference- Dr. Subhash Mehto (Postdoctoral Fellow)

Please visit http://autophagylab.com for more details.

Major Interests of the Lab:

1. Mechanistic understanding of the role of autophagy and inflammation in diseases.

2. Understanding the host response to viruses.

3.  Understanding the mechanisms of cancer development.

   Please visit http://autophagylab.com for more details.

Summary of Selected Publications:

1. Santosh Chauhan*, Suresh Kumar *, Ashish Jain*, Marisa Ponpuak*, Michal H. Mudd, Tomonori Kimura, Seong Won Choi, Ryan Peters, Michael Mandell, Terje Johansen, and Vojo Deretic. TRIMs and Galectins globally cooperate and TRIM16 and Galectin-3 codirect autophagy in endomembrane damage homeostasis. * Equal authorships. Developmental Cell. DOI: http://dx.doi.org/10.1016/j.devcel.2016.08.003
2. Selective autophagy performs an array of tasks to maintain intracellular homeostasis, sterility, and organellar and cellular functionality. The fidelity of these processes depends on precise target recognition and limited activation of the autophagy apparatus in a localized fashion. Here we describe cooperation in such processes between the TRIM family and Galectin family of proteins. TRIMs, which are E3 ubiquitin ligases, displayed propensity to associate with Galectins. One specific TRIM, TRIM16, interacted with Galectin-3 in a ULK1-dependent manner. TRIM16, through integration of Galectin- and ubiquitin-based processes, coordinated recognition of membrane damage with mobilization of the core autophagy regulators ATG16L1, ULK1, and Beclin 1 in response to damaged endomembranes. TRIM16 affected mTOR, interacted with TFEB, and influenced TFEB’s nuclear translocation. The cooperation between TRIM16 and Galectin-3 in targeting and activation of selective autophagy protects cells from lysosomal damage and Mycobacterium tuberculosis invasion.

1. Chauhan, S.*, Mandell, M. and Deretic, V.*. IRGM governs the core autophagy machinery to conduct antimicrobial defense. Volume 58, Issue 3, p507–521, 7 May, 2015 Molecular Cell. * Corresponding author.
2. coupling it to conventional innate immunity receptors. Exposure to microbial products or bacterial invasion increases IRGM expression, which leads to stabilization of AMPK. Specific protein-protein interactions and post-translational modifications such as ubiquitination of IRGM, lead to a co-assembly with IRGM of the key autophagy regulators ULK1 and BECN1 in their activated forms. IRGM physically interacts with two other CD risk factors, ATG16L1 and NOD2, placing these three principal players in CD within the same molecular complex. This explains how polymorphisms altering expression or function of any of the three factors individually can affect the same process – autophagy. Furthermore, IRGM’s interaction with NOD2, and additional pattern recognition receptors such as NOD1, RIG-I and select TLRs, transduces microbial signals to the core autophagy apparatus. This work solves the long-standing enigma of how IRGM controls autophagy.
3. A punctum to this paper is published in Autophagy Journal.
4. DOI: 10.1080/15548627.2015.1084457

1. Chauhan, S., Goodwin, J.G., Chauhan, S., Manyam, G., Wang, J., Kamat, A.M., and Boyd, D.D. (2013). ZKSCAN3 Is a Master Transcriptional Repressor of Autophagy. Molecular Cell. Apr 11, 2013 ;50(1):16-28.
2. Autophagy constitutes a major cell-protective mechanism that eliminates damaged components and maintains energy homeostasis via recycling nutrients under normal/stressed conditions. Although the core components of autophagy have been well studied, regulation of autophagy at the transcriptional level is poorly understood. In this paper, we establish ZKSCAN3, a zinc finger family DNA-binding protein, as a transcriptional repressor of autophagy. Silencing of ZKSCAN3 induced autophagy and increased lysosome biogenesis. Importantly, we show that ZKSCAN3 represses transcription of a large gene set (>60) integral to, or regulatory for, autophagy and lysosome biogenesis/function and that a subset of these genes, including Map1lC3b and Wipi2, represent direct targets. Interestingly, ZKSCAN3 and TFEB are oppositely regulated by starvation and in turn oppositely regulate lysosomal biogenesis and autophagy, suggesting that they act in conjunction. Altogether, our study uncovers an autophagy master switch regulating the expression of a transcriptional network of genes integral to autophagy and lysosome biogenesis/function.
3. This paper was Highlighted in Cancer Discovery (AACR) journal, February 28, 
   2013; doi:10.1158/2159-8290.CD-RW2013-046. In this highlight the ZKSCAN3 is described as switch, controlling the autophagy and lysosome biogenesis.
5. This paper was also Recommended by Faculty of 1000 (http://f1000.com/prime/717980675)

1. Santosh Chauhan*, Zahra Ahmed*, Steven B. Bradfute,….Vincent Piguet, and Vojo Deretic. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential. * Equal authorships. (Nat Commun. 2015 Oct 27;6:8620. doi: 10.1038/ncomms9620.)
2. Autophagy is a conserved homeostatic process active in all human cells and affecting a spectrum of diseases. In this study, we use a pharmaceutical screen (>3000 FDA approved drugs) to discover new mechanisms for activation of autophagy. We identify a subset of pharmaceuticals inducing autophagic flux with effects in diverse cellular systems modelling specific stages of several human diseases such as HIV transmission and hyperphosphorylated tau accumulation in Alzheimer’s disease. One drug, flubendazole, is a potent inducer of autophagy initiation and flux by affecting acetylated and dynamic microtubules in a reciprocal way. Disruption of dynamic microtubules by flubendazole results in mTOR deactivation and  dissociation  from  lysosomes  leading  to  Transcription  Factor  EB nuclear translocation and activation of autophagy. By inducing microtubule acetylation, flubendazole  activates  JNK1  leading  to  Bcl-2  phosphorylation,  causing  release  of Beclin-1 from Bcl-2-Beclin-1 complexes for autophagy induction, thus uncovering a new approach to inducing autophagic flux that may be applicable in disease treatment.
3. Please visit http://autophagylab.weebly.com for more details.

2020

1. Kolapalli SP, Sahu R, Chauhan NR, Jena KK, Mehto S, Das SK, Jain A, Rout M, Dash R, Swain RK, Lee DY, Rusten TE, Chauhan S*, Chauhan S*. RNA binding RING E3-ligase DZIP3/hRUL138 is a novel driver of cell cycle and cancer progression by employing a unique mechanism to stabilize Cyclin D1. Cancer Research, 2020. PMID: 33067265. * Corresponding author
2. Jena KK, Mehto S, Nath P, Chauhan NR, Sahu R, Dhar K, Das SK, Kolapalli SP, Murmu KC, Jain A, Krishna S, Sahoo BS, Chattopadhyay S, Rusten TE, Prasad P, Chauhan S, Chauhan S*. Autoimmunity gene IRGM suppresses cGAS-STING and RIG-I-MAVS signaling to control interferon response. EMBO Rep. 2020 Jul 27:e50051. doi: 10.15252/embr.202050051.* Corresponding author
3. Nath P, Jena KK, Mehto S, Chauhan NR, Sahu R, Dhar K, Srinivas K, Chauhan S, Chauhan S*. IRGM Links Autoimmunity to Autophagy. Autophagy. 2020 Aug 19. doi: 10.1080/15548627.2020.1810920. PMID: 32813580. Corresponding author

2019

1. ​Mehto S, Jena KK, Nath P, Chauhan S, Kolapalli SP, Das SK, Sahoo PK, Jain A, Taylor GA, Chauhan S*. The Crohn’s disease risk factor IRGM limits NLRP3 inflammasome activation by impeding its assembly and by mediating its selective autophagy.  Molecular Cell. 2019 Feb 7;73(3):429-445.e7.                                                                                                            Preview: Nabar NR, Kehrl JH. Inflammasome Inhibition Links IRGM to Innate Immunity. Mol Cell. 2019 Feb 7;73(3):391-392.
2. Mehto S, Chauhan S, Jena KK, Chauhan NR, Nath P, Sahu R, Dhar K, Das SK, Chauhan S*. IRGM restrains NLRP3 inflammasome activation by mediating its SQSTM1/p62-dependent selective autophagy. Autophagy. 2019 Jun 20:1-3.
3. Jena KK, Mehto S, Kolapalli SP, Nath P, Sahu R, Chauhan NR, Sahoo PK, Dhar K, Das SK, Chauhan S, Chauhan S*. TRIM16 governs the biogenesis and disposal of stress-induced protein aggregates to evade cytotoxicity: implication for neurodegeneration and cancer. Autophagy. 2019 May;15(5):924-926. 
4. Jena KK, Mehto S, Kolapalli SP, Nath P, Chauhan S, Chauhan S*. TRIM16 employs NRF2, ubiquitin system and aggrephagy for safe disposal of stress-induced misfolded proteins. Cell Stress. 2018 Nov 16;2(12):365-367. 
5. Saha S, Murmu KC, Biswas M, Chakraborty S, Basu J, Madhulika S, Kolapalli SP, Chauhan S, Sengupta A, Prasad P. Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia. Front Oncol. 2019 Aug 6;9:692.

2018

1. Jena KK, Kolapalli SP, Mehto S, Nath P, Das B, Sahoo PK, Ahad A, Syed GH, Raghav SK, Senapati S, Chauhan S, Chauhan S. TRIM16 controls assembly and degradation of protein aggregates by modulating the p62-NRF2 axis and autophagy. EMBO J. 2018 Sep 14;37(18).
2. Jena KK, Kolapalli SP, Mehto S, Chauhan S, Chauhan S. TRIM16 controls turnover of protein aggregates by modulating NRF2, ubiquitin system, and autophagy: implication for tumorigenesis.  22 Oct 2018, Molecular & Cellular Oncology. 2018 Oct 22;5(6):e1532251
3. Jena KK, Mehto S, Kolapalli SP, Nath P, Sahu R, Chauhan NR, Sahoo PK, Dhar K, Das SK, Chauhan S, Chauhan S. TRIM16 governs the biogenesis and disposal of stress-induced proteins aggregates to evade cytotoxicity: implication in neurodegeneration and cancer. Autophagy. 2019 Feb 26:1-3.
4. Jena KK, Mehto S, Kolapalli SP, Nath P, Chauhan S, Chauhan S. TRIM16 employs NRF2, ubiquitin system and aggrephagy for safe disposal of stress-induced misfolded protein, Cell Stress, 2, No. 12, pp. 365 – 367.

2017

1. Kumar S, Chauhan S, Jain A, Ponpuak M, Choi SW, Mudd M, Peters R, Mandell MA, Johansen T, Deretic V. Galectins and TRIMs directly interact and orchestrate autophagic response to endomembrane damage. Autophagy. 2017 Jun 3;13(6):1086-1087. doi: 10.1080/15548627.2017.1307487. Epub 2017 Apr 3. 1.

2016

1. Santosh Chauhan*, Suresh Kumar*, Ashish Jain*, Marisa Ponpuak*, Michal H. Mudd, Tomonori Kimura,Seong Won Choi, Ryan Peters, Michael Mandell, Terje Johansen, and Vojo Deretic. TRIMs and Galectins globally cooperate and TRIM16 and Galectin-3 codirect autophagy in endomembrane damage homeostasis. * Equal authorships. Developmental Cell.
   DOI: http://dx.doi.org/10.1016/j.devcel.2016.08.003
2. Klionsky DJ et al.,. Guidelines for the use and interpretation of assays for   monitoring autophagy (3rd edition).  Autophagy Jan 2;12(1):1-222, 2016

2015

1. Santosh Chauhan*, Zahra Ahmed*, Steven B. Bradfute,….Vincent Piguet, and Vojo Deretic. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential. * Equal authorship. Nature Communication. 2015 Oct 27;6:8620. doi: 10.1038/ncomms9620.
2. Chauhan, S.*, Mandell, M. and Deretic, V.*. IRGM governs the core autophagy machinery to conduct antimicrobial defense. Volume 58, Issue 3, p507–521, 7 May, Molecular Cell. * Corresponding author.
3. Chauhan S, Mandell MA, Deretic V. Mechanism of action of the tuberculosis and Crohn disease risk factor IRGM in autophagy. Autophagy. 2015 Aug 27:0. PMID: 26313894.
4. Ponpuak M, Mandell MA, Kimura T, Chauhan S, Cleyrat C, Deretic V. Secretory autophagy. Curr Opin Cell Biol. 2015 May 16;35:106-116. doi: 10.1016/j.ceb.2015.04.016.
5. Deretic V, Kimura T, Timmins G, Moseley P, Chauhan S, Mandell M. Immunological manifestations of autophagy. J Clin Invest. 2015 Jan;125(1):75-84. doi: 10.1172/JCI73945.

2014

1. Mandell MA, Jain A, Arko-Mensah J, Chauhan S, Kimura T, Dinkins C, Silvestri G, Münch J, Kirchhoff F, Simonsen A, Wei Y, Levine B, Johansen T, Deretic V. TRIM proteins   regulate autophagy and can target autophagic substrates by direct recognition. Developmental Cell. 2014 Aug 25; 30(4):394-409.
2. Dupont N, Chauhan S, Arko-Mensah J, Castillo EF, Masedunskas A, Weigert R, Robenek H, Proikas-Cezanne T, Deretic V. Neutral lipid stores and lipase PNPLA5 contribute to autophagosome biogenesis. Current Biology. 2014 Mar 17;24 (6):609-20.

2013

1.  Chauhan, S., Goodwin, J.G., Chauhan, S., Manyam, G., Wang, J., Kamat, A.M., and Boyd, D.D. (2013). ZKSCAN3 Is a Master Transcriptional Repressor of Autophagy. Molecular Cell. Apr 11;50(1):16-28. Highlighted in Cancer Discovery (AACR) journal, February 28, 2013; doi:10.1158/2159-8290.CD-RW2013-046. Recommended by Faculty of 1000 (http://f1000.com/prime/717980675)
2.  Bradfute SB, Castillo EF, Arko-Mensah J, Chauhan S, Jiang S, Mandell M, Deretic V. Autophagy as an immune effector against tuberculosis. Curr Opin Microbiol. 2013 Jun 18. pii: S1369-5274(13)00070-2. doi: 10.1016/j.mib.2013.05.003.

2012

1.  Chauhan, S., and Boyd DD. Regulation of u-PAR gene expression by H2A.Z is modulated by the MEK-ERK/AP-1 pathway. Nucleic Acids Research. 2012 Jan; 40 (2):600-13.
2.  Chauhan, S, Sharma, D., Singh, A., Surolia, A. and Tyagi, J.S. Comprehensive insights into Mycobacterium tuberculosis DevR (DosR) regulon activation switch. Nucleic Acids Research. 2011 Sep 1;39(17):7400-14.

 2011

1. Chauhan, S and Tyagi, J.S. (2011) Analysis of transcription at the oriC locus in Mycobacterium tuberculosis. Microbiol Res. 2011 Sep 20;166(6):508-14.
2. Avila H, Wang H, Chauhan S, Hartig S, Boyd DD. Accelerated urokinase-receptor protein turnover triggered by interference with the addition of the glycolipid anchor. Biochem J. 2011 Mar 1;434(2):233-42.
3. Gupta, R.K., Chauhan, S. and Tyagi, J.S. K182G substitution in DevR or C(8) G mutation in the Dev box impairs protein-DNA interaction and abrogates DevR-mediated gene induction in Mycobacterium tuberculosis. FEBS J. 2011 Jun; 278(12):2131-9.
4. Gautam, U.S., Chauhan, S. and Tyagi, J.S. Determinants outside the DevR C-terminal domain are essential for cooperativity and robust activation of dormancy genes in Mycobacterium tuberculosis. PLoS One. 2011 Jan 27;6(1):e16500.

2010

1. Majumdar, S.D., Sharma, D., Vashist, A., Kaur, K., Taneja, N.K., Chauhan, S., Challu, V.K., Ramanathan, V.D., Balasangameshwara, V., Kumar, P. et al. Co-expression of DevR and DevR(N)-Aph proteins is associated with hypoxic adaptation defect and virulence attenuation of Mycobacterium tuberculosis. PLoS One. 2010, Feb 26;5(2):e9448.
2. Chauhan S, Singh A, Tyagi JS. A single-nucleotide mutation in the -10 promoter region inactivates the narK2X promoter in Mycobacterium bovis and Mycobacterium bovis BCG and has an application in diagnosis. FEMS Microbiol Lett. 2010, Feb;303(2):190-6.

 2009

1.  Chauhan S, Tyagi JS. Powerful induction of divergent tgs1-Rv3131 genes in Mycobacterium tuberculosis is mediated by DevR interaction with a high-affinity site and an adjacent cryptic low-affinity site. Journal of Bacteriology. 2009, Oct;191(19):6075-81.
2. Chauhan S, Kumar A, Singhal A, Tyagi JS, Krishna Prasad H. CmtR, a cadmium-sensing ArsR-SmtB repressor, cooperatively interacts with multiple operator sites to autorepress its transcription in Mycobacterium tuberculosis. FEBS J. 2009, Jul; 276(13):3428-39.

2008

1.  Chauhan S, Tyagi JS. Interaction of DevR with Multiple Binding Sites Synergistically Activates Divergent Transcription of narK2-Rv1738 Genes in Mycobacterium tuberculosis. Journal of Bacteriology. Aug 2008, p. 5394–5403, 190, No. 15.
2.  Chauhan S, Tyagi JS. Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: Implication in the induction of DevR target genes. Journal of Bacteriology, June 2008, p. 4301–4312, 190, No.12.

2005

1. Bagchi G^Y, Chauhan S^Y, Sharma D, Tyagi JS. Transcription and autoregulation of Rv3134c-devR-devS operon of Mycobacterium tuberculosis. Microbiology (2005), 151, 4045-4053.^Y Equal contribution to work.

Current Lab Members

1. Kshitish Kumar Rout -Lab Technician
2. Ramya Bal- Project Assistant
3. Kautilya Kumar Jena- Ph.D. student
4. Parej Nath- Ph.D. student
5. Rinku Sahu- Ph.D. student
6. Kollori Dhar- Ph.D. student
7. Reena Yadav- JRF
8. Shivram Krishan- Ph.D. student
9. Dr. Subhash Mehto- Inspire Faculty
10. Dr. Nishant Ranjan Chauhan- RA
11. Dr. Nuzhat Ahsan- WOS (A)

The lab is currently open for research scholars (at all levels, Postdocs, JRF, SRF..etc). The only criteria here are, hardworking and interest in the field of mainly Cell Biology, Autophagy, Innate immunity, Inflammation.

I will be more than happy to assist in writing and submitting the postdoctoral grant proposals (based on my lab interest) to the candidate scholars who have completed their Ph.D. or at later stages of  Ph.D. completion.  Following are the opportunities where I may be of help:

1. The SERB-National Post Doctoral Fellowship ( N-PDF)– details at https://indiabioscience.org/grants/the-serb-national-post-doctoral-fellowship-n-pdf
2. The Innovative Young Biotechnologist Award (IYBA)- details at https://indiabioscience.org/grants/the-innovative-young-biotechnologist-award-iyba
3. DBT Research Associateship- details at http://biochem.iisc.ernet.in/dbtra.html
4. INSPIRE Fellowship- details at http://www.inspire-dst.gov.in/faculty_scheme.html
5. Wellcome-DBT early career fellowship- http://www.wellcomedbt.org/fellowships/early-career-fellowships
6. OR Any other RA or SRF programme

If interested, please send me an e-mail with your detailed CV. Please visit http://autophagylab.com for more details.

E-mail us at: schauhan@ils.res.in; chauhan2010santosh@gmail.com

1. Wellcome-DBT intermediate fellowship: This scheme supports excellent scientists who wish to undertake high-quality research and to establish themselves as independent researchers in an academic institution in India. The fellowship is for five years  and provides research expenses, including two research staff. The total amount of award is up to 3.6 crores (http://www.wellcomedbt.org/fellowships/intermediate-fellowships).
2. ILS intramural start-up support:  ILS provide very generous support to new faculties for starting up a new lab.

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