Sanjay Ghosh

Research Focus Key Words

Synthetic biology, Genome engineering technologies, Functional genomics, Metabolic engineering, Host-virus interactions

Background

Dr. Ghosh completed his Masters in Zoology from Banaras Hindu University and received his PhD degree from Jadavpur University working at CSIR-IICB, Kolkata. Subsequently, he joined BIT Mesra as Lecturer in Department of Biotechnology. For his postdoctoral training, Dr. Ghosh worked at European Molecular Biology Laboratory, Germany, and McGill University, Canada, on intracellular RNA transport and translation control mechanisms during Drosophila development. Thereafter, he worked on the CRISPR-based gene editing technologies at the University of Oxford, UK, and demonstrated the use of CRISPR interference method to knock down long non-coding RNAs. He also worked at the Department of Biochemistry, University of Cambridge, UK, on genome-wide stress-dependent translation response in yeast using ribosome profiling method. He is the recipient of DBT-Ramalingaswami re-entry fellowship for the year 2016-2017.

Education

1. PhD, CSIR-Indian Institute of Chemical Biology (Jadavpur University), Kolkata
2. Postdoctoral training at EMBL Heidelberg, McGill University, University of Oxford and University of Cambridge

Professional experience

1. Lecturer, Birla Institute of Technology Mesra, Ranchi
2. Faculty at IBAB since 2017

Research Goal:

We are primarily interested in developing translatable technologies and products using synthetic biology approaches. We utilize latest genome editing technologies and DNA assembly methods to engineer microorganisms, mosquito and human cells.

Research Projects:

1. Developing robust yeast gene expression system using synthetic promoters and gene editing technology
   Distinct biotechnological applications require different promoter properties in terms of expression range and inducibility. Currently promoter discovery is focused largely on manipulating native promoters which are large DNA sequences and are regulated in a complex fashion. We are developing expression systems using synthetic promoters and genetic elements for enhanced expression of biomolecules over a broad dynamic range. In addition, a library of yeast cells containing distinct promoter activities will be created which will be useful for customized production of proteins and metabolites in a high throughput format.
2. Metabolic engineering of yeast cells for biotechnological applications
   Yeast is recognized as GRAS organism and used extensively for industrial production of valuable molecules. We are generating value-added yeast strains that overexpress phytochemicals, food supplements, human metabolic enzymes and nutraceuticals. This is achieved by rational engineering of the endogenous metabolic genes and pathways using genetic switches and circuits as well as transplanting genes from heterologous sources by using recombinant DNA methods. Using gene editing technologies we also seek to modify metabolic pathways in yeast cells to generate “humanised yeast stains” for production of human therapeutic proteins and biologics.
3. Engineering human cells for therapeutic applications
   We are establishing robust protocols and platform for precise customized gene editing of human cells for various therapeutic purposes including cell lines (a) to develop gene editing strategies for gene correction and functional genomics studies, (b) to improve existing therapeutic approaches to autoimmune diseases, cancers and rare genetic disorders, and (c) that mirror disease-causing mutations for drug resistance studies and screening purposes.
4. Functional genomic approaches to combat vector-borne diseases
   Viruses belonging to the family Flaviviridae is a major public health problem worldwide including India. Using the Aedes-dengue virus infection model, we aim to identify key factors controlling virus multiplication in the mosquito using genome wide approaches and characterize their function using gene editing technologies. In addition, gene interaction networks will be used to generate models of infection. Subsequently we will be translating this knowledge to design effective disease transmission blocking strategies for dengue and other viral infections.slating this knowledge to design effective disease transmission blocking strategies for Dengue and other viral infections.

Group members

Shikha Kumari (Senior Research Fellow)
Shikha completed Master’s degree in Biotechnology from Hemvati Nandan Bahuguna Garhwal University, Uttarakhand. She worked at Syngene International Ltd., Bengaluru as a Research Associate before joining the group in 2019. Her area of expertise is optimization, development and validation of cell-based assays. Shikha’s research interest lies in the development of antibodies for immunotherapy.

Arti Rani (Research Scientist)
Arti completed her PhD at CSIR-IHBT in plant biotechnology. She worked at Vittal Mallya Scientific Research Foundation as DST-Women Scientist Fellow in the areas of functional genomics, proteomics and metabolomics. Arti joined the group in 2022 as Post-Doctoral Fellow and is working on metabolic engineering of yeast cells for enhanced production of high-value products.

Ranu Deka (Junior Research Fellow)
Ranu completed her M.Tech in Biotechnology from West Bengal University of Technology, Kolkata. She has industrial research experience working at Syngene International Ltd, Reliance Industries Ltd and Biocon Biologics. Ranu joined the group in 2021 as Junior Research Fellow and is working on developing synthetic genetic elements and gene expression systems in yeast cells for biotechnological applications.

Madhushruti Borah (Junior Research Fellow)
Madhushruti completed her Master’s degree in Biotechnology & Bioinformatics from IBAB. She joined the group in 2022 and is working on genome integration strategies and engineering yeast metabolic pathway to produce high-value products using CRISPR-based approaches.

Subhash Chaithanya K (Junior Research Fellow)
Subhash completed his Master’s degree in Molecular Biology from Yuvaraja’s College, University of Mysore. He joined the group in 2022 and is working on generating yeast strains producing high-value biologics using biowaste.

Sutripto Ghosh (Project Assistant)

Sutripto completed his Master’s in Biotechnology from Maulana Abul Kalam Azad University of Technology (formerly West Bengal University of Technology), Kolkata. He joined the group in 2023 and is working on understanding the molecular mechanism of flavivirus infection using CRISPR-Cas systems.

Roseanne Mascarenhas (Project Assistant)

Roseanne completed her Master’s degree in Biotechnology from CHRIST (Deemed to be University), Bengaluru. She joined the group in 2023 and is working on functional characterization of host factors in dengue infection using cell-based assays and CRISPR technology.

Barathvaj Renganathan (Senior Research Fellow)

Barathvaj completed his Master’s in Biotechnology from the Bharathidasan University, Tiruchirappalli, Tamil Nadu. Prior to joining IBAB, he worked as a Project Associate at CFTRI, Mysore and Project Fellow in ICAR-NRCB, Tamil Nadu. He joined the group in 2023 and is developing CRISPR-based strategies to control human arbovirus transmission by Aedes mosquito.

Alumni:

1. Poornima R (Project Assistant)
2. Anusha KR (Project Assistant)
3. Deepthi Menon (Postdoctoral Fellow)
4. T Sai Kavya Rao (Project Trainee)
5. Anjitha P (Project Trainee)
6. Bilal M Akhtar (Intern, MSc06 IBAB)
7. Mansi Srivastava (Intern, MSc06 IBAB)
8. Pritha Dey (Intern, MSc06 IBAB)
9. Tanisha Gupta (Intern, MSc06 IBAB)
10. Tanushree Sengupta (Intern, MSc06 IBAB)
11. Sneha Lahorani (Intern, MSc07 IBAB)
12. Harini N Pillai S (Intern, MSc07 IBAB)
13. Rashmi Gurudatta Sardessai (Intern, MSc07 IBAB)
14. Usha TM (Intern, MSc Bangalore University)
15. Samantha J Coelho (Project Assistant)
16. Snigdha N Rao (Junior Research Fellow)
17. Sneha C Antony (Project Assistant)
18. Yamini Vadapalli (Project Assistant)
19. Shubham Dixit (Postdoctoral Fellow)
20. Aparna MS (Senior Research Fellow)
21. Tanvi Kale (Intern, MSc08 IBAB)
22. Mithun P Murlidharan (Intern, MSc08 IBAB)
23. Bidisha Roy (Intern, MSc08 IBAB)
24. Prakriti Kalra (Intern, MSc08 IBAB)
25. Sara Ashok Varghese (Junior Research Fellow)
26. Priyanka Sasmal (Project Assistant)
27. Gnanesh Rao (Project Assistant)
28. Shivani Gidla (Project Assistant)
29. Ajay Extross (Intern, MIT-ADT University, Pune)
30. Rani Bajaj (Postdoctoral Fellow)
31. Neha Rao (Intern, MS Ramaiah University, Bengaluru)
32. Mariet Mathew Stephen (Project Assistant)
33. Ambily Nath IV (Postdoctoral Fellow)
34. Venitha Bernard (Project Assistant)
35. Kasturi Bhamidipati (Intern, PES University, Bengaluru)
36. Arpita Biswas (Intern, KIIT University, Bhubaneswar)
37. Simarpreet Kaur (Intern, IISER Thiruvananthapuram)
38. Arufi Singh (Intern, MSc10 IBAB)
39. Akshaya Kailasnathan (Junior Research Fellow)
40. Vijeta Jaiswal (Senior Research Fellow)
41. Nabodit Bhattacharya (Intern, MSc10 IBAB, Project Assistant)
42. Sushma Hegde (Intern, MSc10 IBAB, Project Assistant)
43. Karishma Murugesh (Intern, Vellore Institute of Technology)
44. Albert Paul (Intern, Amrita Vishwa Vidyapeetham)
45. Priya Bhatia (Intern, MSc11 IBAB)
46. Sukanya Sahoo (Intern, MSc11 IBAB)
47. Aratrika Ghoshal (Intern, MSc11 IBAB)
48. Sneha Shah (Junior Research Fellow)
49. Akshay Kumar (Project Assistant)
50. Dinakar HL (Intern, Yuvaraja College Mysuru)

Collaborators:

1. Dr. S Thiyagarajan, IBAB, Bengaluru
2. Dr. Shruthi Vembar, IBAB, Bengaluru
3. Dr. Shubhada Hegde, IBAB, Bengaluru
4. Dr. Swathi Alagesan, IBAB, Bengaluru
5. Dr. Shashank Tripathi, IISc, Bengaluru
6. Dr. Kartik Sunagar, IISc, Bengaluru
7. Dr. Baskar Bakthavachalu, IIT, Mandi
8. Dr. Ishaan Gupta, IIT, Delhi
9. Dr. Daniel Reegan, NCDC, Bengaluru
10. Jananom Private Limited, Bengaluru
11. Syngene International Limited, Bengaluru
12. Merck Healthcare KGaA, Germany

Publications and Patents:

1. Samuel J, Ghosh S* and Thiyagarajan S* (2024)
   Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods.
   Journal of Biomolecular Structure and Dynamics https://doi.org/10.1080/07391102.2024.2313161.
2. Jaiswal V, Varghese SA, Ghosh S* (2023)
   Validation of CRISPR activation system in Aedes cells using multicistroic plasmid vectors.
   Frontiers in Bioengineering and  Biotechnology,https://doi.org/10.3389/fbioe.2023.1142415.
3. Rubio, A., Ghosh S.,  Mülleder, M., Ralser, M. and Mata, J. (2020)
   Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
   Nucleic Acids Research, gkaa1180, https://doi.org/10.1093/nar/gkaa1180
4. de la Roche, M., Hamilton, C., Mortensen, R., Jeyaprakash, A.A., Ghosh, S. and Anand P.K. (2018)
   Trafficking of cholesterol to the ER is required for NLRP3 inflammasome activation.
   Journal of Cell Biology, doi:10.1083/jcb.201709057.
5. Ghosh, S.* and Liu, J.L.* (2018)
   Genomic Tagging of AGO1 using CRISPR/Cas9-mediated Homologous Recombination.
   Methods in Molecular Biology, 1680: 217-235.  *corresponding authors
6. Yong, H., Wang, J.J., Ghosh, S.* and Liu, J.L.* (2017)
   Critical roles of CTP synthase N-terminal in cytoophidium assembly.
   Experimental Cell Research 354(2):122-133. *corresponding authors
7. Ghosh, S. *, Tibbit, C., and Liu, J.L.* (2016)
   Efficient knockdown of Drosophila long non-coding RNAs by CRISPR interference.
   Nucleic Acids Research, 44(9): e84. *corresponding authors
8. Ghosh, S.* and Lasko, P.* (2015)
   Loss-of-function analysis reveals distinct requirements  of the translation initiation factors eIF4E, eIF4E-3, eIF4G and eIF4G2 in Drosophila spermatogenesis.
   PLOS One 10(4): e0122519. *corresponding authors
9. Ghosh, S., Obrdlik, A., Marchand, V. and Ephrussi, A. (2014)
   The EJC binding and dissociation activity of PYM is regulated in Drosophila.
   PLOS Genetics 10(6):e1004455.
10. Ghosh, S.*, Marchand, V.*, Gaspar, I. and Ephrussi, A. (2012)
    Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA.
    Nature Structural Molecular Biology 19(4), 441-449. *equal contribution
11. Ghosh, S., Goswami, S. and Adhya, S. (2003)
    Role of superoxide dismutase in survival of Leishmania within the macrophage.
    Biochemical Journal 369(Pt.3), 447-452.
12. Adhya, S., Basu, S., Bhattacharyya, S.N., Chatterjee, S., Dhar, G., Goswami, S., Ghosh, S., Home, P., Mahata, B. and Tripathi, G. (2003)
    Mitochondrial differentiation in Kinetoplastidprotozoa: a plethora of RNA controls.
    Differentiation 71, 549–556.

Funding:

1. KITS, Department of IT, BT and S&T, Government of Karnataka
2. Department of Biotechnology, Government of India (Ramalingaswami Re-entry Fellowship & Genome Engineering Technologies)
3. Biotechnology Industry Research Assistance Council (BIRAC), Government of India
4. Science and Engineering Research Board, Department of Science and Technology, Government of India (Core Research Grant)