National Centre for Cell Science

Deepa Subramanyam, Ph.D.

Email

deepa@nccs.res.in

Research Areas

Cell Organization and Function, Stem Cells and Regeneration

Education and Experience

Education

Phd : National Centre for Biological Sciences,TIFR, Bangalore - 2006.

BSc : PSG College of Arts and Science, Coimbatore - 1999.

Research Experience

Scientist E - National Centre for Cell Science, Pune - 2022 to present

Scientist E - National Centre for Cell Science, Pune - 2017 to 2022

Scientist D - National Centre for Cell Science, Pune - 2012 November to 2017

Postdoctoral Fellow - University of California at San Francisco - 2006 - 2012.

Lab webpage

Deepa Laboratory

Research

Our lab is interested in aspects of cellular trafficking that differ between embryonic stem cells and differentiated cells. We are primarily focusing on the role of endocytosis in cell fate determination. This work is important in embryonic stem cell development and for understanding early mammalian development.

Publications

Selected Publications All Publications

Selected publications

Sinjini Bhattacharyya, Ridim D. Mote, Jacob W. Freimer, Surya Bansi Singh, Sandhya Arumugam, Yadavalli V. Narayana, Raghav Rajan and Deepa Subramanyam*. Cell–cell adhesions in embryonic stem cells regulate the stability and transcriptional activity of β-catenin. FEBS Lett.; 2022, https://doi.org/10.1002/1873-3468.14341
Jyoti Das, Mahak Tiwari and Deepa Subramanyam*. Clathrin light chains – not to be taken so lightly. Front. Cell Dev. Biol., 14 December 2021 https://doi.org/10.3389/fcell.2021.774587
Ridim D Mote, Jyoti Yadav, Surya Bansi Singh, Mahak Tiwari, Laxmikant Shinde V, Shivprasad Patil and Deepa Subramanyam*. Pluripotency of embryonic stem cells lacking clathrin mediated endocytosis cannot be rescued by restoring cellular stiffness. J. Biol. Chem. 2020; 295(49): 16888-16896.
Yadavalli V Narayana, Chetan Gadgil, Ridim D. Mote, Raghav Rajan and Deepa Subramanyam*. Clathrin-mediated endocytosis regulates a balance between opposing signals to maintain the pluripotent state of embryonic stem cells. Stem Cell Reports. 2019; 12(1): 152-164.
Ridim D. Mote, Gaurang Mahajan, Anup Padmanabhan, Ramaraju Ambati and Deepa Subramanyam*. Dual repression of endocytic players by ESCC microRNAs and the Polycomb complex regulates mouse embryonic stem cell pluripotency. Scientific Reports. 2017; 7(1): 17572.

Sinjini Bhattacharyya, Ridim D. Mote, Jacob W. Freimer, Surya Bansi Singh, Sandhya Arumugam, Yadavalli V. Narayana, Raghav Rajan and Deepa Subramanyam*. Cell–cell adhesions in embryonic stem cells regulate the stability and transcriptional activity of β-catenin. FEBS Lett.; 2022, https://doi.org/10.1002/1873-3468.14341

Jyoti Das, Mahak Tiwari and Deepa Subramanyam*. Clathrin light chains – not to be taken so lightly. Front. Cell Dev. Biol., 14 December 2021 https://doi.org/10.3389/fcell.2021.774587

Ridim D Mote, Jyoti Yadav, Surya Bansi Singh, Mahak Tiwari, Laxmikant Shinde V, Shivprasad Patil and Deepa Subramanyam*. Pluripotency of embryonic stem cells lacking clathrin mediated endocytosis cannot be rescued by restoring cellular stiffness. J. Biol. Chem. 2020; 295(49): 16888-16896.

Yadavalli V Narayana, Chetan Gadgil, Ridim D. Mote, Raghav Rajan and Deepa Subramanyam*. Clathrin-mediated endocytosis regulates a balance between opposing signals to maintain the pluripotent state of embryonic stem cells. Stem Cell Reports. 2019; 12(1): 152-164.

Ridim D. Mote, Gaurang Mahajan, Anup Padmanabhan, Ramaraju Ambati and Deepa Subramanyam*. Dual repression of endocytic players by ESCC microRNAs and the Polycomb complex regulates mouse embryonic stem cell pluripotency. Scientific Reports. 2017; 7(1): 17572.

All Publications: Deepa Subramanyam:

Deepika Puri, Aparna Kelkar, Bhaskar Gauri Shankar and Deepa Subramanyam. Autophagy-cell death balance is maintained by Polycomb-mediated regulation during stem cell differentiation. bioRxiv 2022.03.29.486206; doi: https://doi.org/10.1101/2022.03.29.486206.
Sinjini Bhattacharyya, Ridim D. Mote, Jacob W. Freimer, Surya Bansi Singh, Sandhya Arumugam, Yadavalli V. Narayana, Raghav Rajan and Deepa Subramanyam*. 2022), Cell–cell adhesions in embryonic stem cells regulate the stability and transcriptional activity of β-catenin. FEBS Lett.; 2022, https://doi.org/10.1002/1873-3468.14341
Jyoti Das, Mahak Tiwari and Deepa Subramanyam*. Clathrin light chains – not to be taken so lightly. Front. Cell Dev. Biol., 14 December 2021, https://doi.org/10.3389/fcell.2021.774587
Ridim D. Mote, Laxmikant Shinde V, Surya Bansi Singh, Mahak Tiwari, Hemant, Juhi Srivastava, Vidisha Tripathi, Vasudevan Seshadri, Amitabha Majumdar and Deepa Subramanyam*. A cost-effective and efficient approach for generating and assembling reagents for conducting real-time PCR. 2021, J. Biosciences, 46:109
Shalmali Bivalkar-Mehla, Deepika Puri, Surya Bansi Singh and Deepa Subramanyam*. Understanding the role of Beclin1 in mouse embryonic stem cell differentiation through CRISPR-Cas9-mediated gene editing. J. Biosciences; 2021; 46:18.
Ridim D Mote, Jyoti Yadav, Surya Bansi Singh, Mahak Tiwari, Laxmikant Shinde V, Shivprasad Patil and Deepa Subramanyam*. Pluripotency of embryonic stem cells lacking clathrin mediated endocytosis cannot be rescued by restoring cellular stiffness. J. Biol. Chem. 2020; 295(49): 16888-16896.
Deepika Puri* and Deepa Subramanyam*. Stress – (self) eating: Epigenetic regulation of autophagy in response to psychological stress. The FEBS Journal. 2019; doi: 10.1111/febs.14826.
Yadavalli V Narayana, Chetan Gadgil, Ridim D. Mote, Raghav Rajan and Deepa Subramanyam*. Clathrin-mediated endocytosis regulates a balance between opposing signals to maintain the pluripotent state of embryonic stem cells. Stem Cell Reports. 2019; 12(1): 152-164.
Sonam Kumari, Apurv Solanki, Saptarshi Mandal, Deepa Subramanyam and Prolay Das. Creation of Linear Carbon dot array with improved optical properties through controlled covalent conjugation with DNA. Bioconjugate Chemistry. 2018; 29(5): 1500-1504.
Sarita Kumari, Steven Vermeulen, Ben van der Veer, Aurelie Carlier, Jan de Boer and Deepa Subramanyam*. Shaping cell fate: influence of topographical substratum properties on embryonic stem cells. Tissue Engineering Part B. 2018; doi: 10.1089/ten.TEB.2017.0468.
Ridim D. Mote, Gaurang Mahajan, Anup Padmanabhan, Ramaraju Ambati and Deepa Subramanyam*. Dual repression of endocytic players by ESCC microRNAs and the Polycomb complex regulates mouse embryonic stem cell pluripotency. Scientific Reports. 2017; 7(1): 17572.
Nayoung Suh, Deepa Subramanyam and Mi-Young Lee. Molecular signatures of secretomes from mesenchymal stem cells: therapeutic benefits. Molecular and Cellular Toxicology. 2017; 13(2): 133-141.
Rajesh Kumar Manne, Yashika Agrawal, Anil Bargale, Asha Patel, Debasish Paul, Neha Anilkumar Gupta, Srikanth Rapole, Vasudevan Seshadri, Deepa Subramanyam, Praveenkumar Shetty, and Manas Santra. A microRNA/Ubiquitin Ligase feedback loop regulates Slug-mediated invasion in breast cancer. Neoplasia. 2017; 19(6): 483-495.
Surya Bansi Singh and Deepa Subramanyam*. CRISPR/ Cas9: A toolbox with clinical potential. Int J of Cell Science and Mol Bio. 2016, 1(1) : 555554.
Nam D Tran, Michael Kissner, Deepa Subramanyam, Ron J Parchem, Diana J Laird, Robert H Blelloch. A miR-372/let-7 Axis Regulates Human Germ versus Somatic Cell Fates. Stem Cells. 2016; 34(7): 1985-91.
Deepa Subramanyam*. Cellular reprogramming – Turning the clock back. Resonance, June 2013; 514-521.
Yangming Wang, Collin Melton, Ya-Pu Li, Archana Shenoy, Xin-Xin Zhang, Deepa Subramanyam and Robert Blelloch. MiR-294/miR-302 family promotes proliferation, suppresses the G1-S restriction point, and inhibits embryonic stem cell differentiation through separable mechanisms. Cell Reports, 2013; 4(1): 99-109.
Samy Lamouille, Deepa Subramanyam, Rik Derynck and Robert Blelloch. Regulation of epithelial–mesenchymal and mesenchymal–epithelial transitions by microRNAs. Current Opinion in Cell Biology, 2013; 25(2) : 200-7.
Devanand S. Manoli, Deepa Subramanyam, Catriona Carey, Julie A. Van Westerhuyzen, Karen L. Bales, Robert Blelloch and Nirao M. Shah. Generation of induced pluripotent stem cells from the Prairie vole. PLoS One, 2012; 7(5):e38119.
Deepa Subramanyam, Samy Lamouille, Robert L. Judson, Jason Y. Liu, Nathan Bucay, Rik Derynck and Robert Blelloch. Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nature Biotechnology, 2011 May;29(5):443-8.
Deepa Subramanyam and Robert Blelloch. From microRNAs to targets: pathway discovery in cell fate transitions. Review. Current Opinion in Genetics and Development, 2011 Aug; 21(4):498-503.
Jeevisha Bajaj, Tessy T. Maliekal, Eric Vivien, Chitra Pattabiraman, Sweta Srivastava, H. Krishnamurthy, G. V. Giri, Deepa Subramanyam and Sudhir Krishna. Notch signaling in CD66+ cells drives the progression of human cervical cancers. Cancer Research, 2011; 71 (14), 4888-4897.
Hamed Al-Hussaini, Deepa Subramanyam, Michael Reedijk and Srikala Sridhar. Notch Signaling Pathway as a Therapeutic Target in Breast Cancer. Molecular Cancer Therapeutics, 2011 Jan;10(1):9-15.
Deepa Subramanyam, Cassandra D. Belair, Keegan Q. Barry-Holson, Haijiang Lin, Scott C. Kogan, Emmanuelle Passegué, and Robert Blelloch. PML-RARα and Dnmt3a1 cooperate in vivo to promote acute promyelocytic leukemia. Cancer Research, 2010; Nov 1;70(21):8792-801.
Deepa Subramanyam and Robert Blelloch. Watching reprogramming in real time. Nature Biotechnology, 2009, Nov;27(11):997-8.
Tessy T. Maliekal, Jeevisha Bajaj, V. Giri, Deepa Subramanyam, Sudhir Krishna.The role of Notch signaling in human cervical cancer: implications for solid tumors. Oncogene, 2008 Sep 1;27(38):5110-4.
Deepa Subramanyam* and Sudhir Krishna. c-Myc substitutes for Notch1-CBF1 functions in cooperative transformation with papillomavirus oncogenes. Virology, 2006 Mar 30;347(1):191-8.
Deepa Subramanyam*. Asymmetry Pins Inscuteable. Current Science, 2000 August 10; 79(3): 271-3.

Deepika Puri*, Aparna Kelkar, Bhaskar Gauri Shankar and Deepa Subramanyam*. Autophagy-cell death balance is maintained by Polycomb-mediated regulation during stem cell differentiation. bioRxiv 2022.03.29.486206; doi: https://doi.org/10.1101/2022.03.29.486206.

Sinjini Bhattacharyya, Ridim D. Mote, Jacob W. Freimer, Surya Bansi Singh, Sandhya Arumugam, Yadavalli V. Narayana, Raghav Rajan and Deepa Subramanyam*. 2022), Cell–cell adhesions in embryonic stem cells regulate the stability and transcriptional activity of β-catenin. FEBS Lett.; 2022, https://doi.org/10.1002/1873-3468.14341

Jyoti Das, Mahak Tiwari and Deepa Subramanyam*. Clathrin light chains – not to be taken so lightly. Front. Cell Dev. Biol., 14 December 2021, https://doi.org/10.3389/fcell.2021.774587

Ridim D. Mote, Laxmikant Shinde V, Surya Bansi Singh, Mahak Tiwari, Hemant, Juhi Srivastava, Vidisha Tripathi, Vasudevan Seshadri, Amitabha Majumdar and Deepa Subramanyam*. A cost-effective and efficient approach for generating and assembling reagents for conducting real-time PCR. 2021, J. Biosciences, 46:109

Shalmali Bivalkar-Mehla, Deepika Puri, Surya Bansi Singh and Deepa Subramanyam*. Understanding the role of Beclin1 in mouse embryonic stem cell differentiation through CRISPR-Cas9-mediated gene editing. J. Biosciences; 2021; 46:18.

Deepika Puri* and Deepa Subramanyam*. Stress – (self) eating: Epigenetic regulation of autophagy in response to psychological stress. The FEBS Journal. 2019; doi: 10.1111/febs.14826.

Sonam Kumari, Apurv Solanki, Saptarshi Mandal, Deepa Subramanyam and Prolay Das. Creation of Linear Carbon dot array with improved optical properties through controlled covalent conjugation with DNA. Bioconjugate Chemistry. 2018; 29(5): 1500-1504.

Sarita Kumari, Steven Vermeulen, Ben van der Veer, Aurelie Carlier, Jan de Boer and Deepa Subramanyam*. Shaping cell fate: influence of topographical substratum properties on embryonic stem cells. Tissue Engineering Part B. 2018; doi: 10.1089/ten.TEB.2017.0468.

Ridim D. Mote, Gaurang Mahajan, Anup Padmanabhan, Ramaraju Ambati and Deepa Subramanyam*. Dual repression of endocytic players by ESCC microRNAs and the Polycomb complex regulates mouse embryonic stem cell pluripotency. Scientific Reports. 2017; 7(1): 17572.

Nayoung Suh, Deepa Subramanyam and Mi-Young Lee. Molecular signatures of secretomes from mesenchymal stem cells: therapeutic benefits. Molecular and Cellular Toxicology. 2017; 13(2): 133-141.

Rajesh Kumar Manne, Yashika Agrawal, Anil Bargale, Asha Patel, Debasish Paul, Neha Anilkumar Gupta, Srikanth Rapole, Vasudevan Seshadri, Deepa Subramanyam, Praveenkumar Shetty, and Manas Santra. A microRNA/Ubiquitin Ligase feedback loop regulates Slug-mediated invasion in breast cancer. Neoplasia. 2017; 19(6): 483-495.

Surya Bansi Singh and Deepa Subramanyam*. CRISPR/ Cas9: A toolbox with clinical potential. Int J of Cell Science and Mol Bio. 2016, 1(1) : 555554.

Nam D Tran, Michael Kissner, Deepa Subramanyam, Ron J Parchem, Diana J Laird, Robert H Blelloch. A miR-372/let-7 Axis Regulates Human Germ versus Somatic Cell Fates. Stem Cells. 2016; 34(7): 1985-91.

Deepa Subramanyam*. Cellular reprogramming – Turning the clock back. Resonance, June 2013; 514-521.

Yangming Wang, Collin Melton, Ya-Pu Li, Archana Shenoy, Xin-Xin Zhang, Deepa Subramanyam and Robert Blelloch. MiR-294/miR-302 family promotes proliferation, suppresses the G1-S restriction point, and inhibits embryonic stem cell differentiation through separable mechanisms. Cell Reports, 2013; 4(1): 99-109.

Samy Lamouille, Deepa Subramanyam, Rik Derynck and Robert Blelloch. Regulation of epithelial–mesenchymal and mesenchymal–epithelial transitions by microRNAs. Current Opinion in Cell Biology, 2013; 25(2) : 200-7.

Devanand S. Manoli, Deepa Subramanyam, Catriona Carey, Julie A. Van Westerhuyzen, Karen L. Bales, Robert Blelloch and Nirao M. Shah. Generation of induced pluripotent stem cells from the Prairie vole. PLoS One, 2012; 7(5):e38119.

Deepa Subramanyam, Samy Lamouille, Robert L. Judson, Jason Y. Liu, Nathan Bucay, Rik Derynck and Robert Blelloch. Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nature Biotechnology, 2011 May;29(5):443-8.

Deepa Subramanyam and Robert Blelloch. From microRNAs to targets: pathway discovery in cell fate transitions. Review. Current Opinion in Genetics and Development, 2011 Aug; 21(4):498-503.

Jeevisha Bajaj, Tessy T. Maliekal, Eric Vivien, Chitra Pattabiraman, Sweta Srivastava, H. Krishnamurthy, G. V. Giri, Deepa Subramanyam and Sudhir Krishna. Notch signaling in CD66+ cells drives the progression of human cervical cancers. Cancer Research, 2011; 71 (14), 4888-4897.

Hamed Al-Hussaini, Deepa Subramanyam, Michael Reedijk and Srikala Sridhar. Notch Signaling Pathway as a Therapeutic Target in Breast Cancer. Molecular Cancer Therapeutics, 2011 Jan;10(1):9-15.

Deepa Subramanyam, Cassandra D. Belair, Keegan Q. Barry-Holson, Haijiang Lin, Scott C. Kogan, Emmanuelle Passegué, and Robert Blelloch. PML-RARα and Dnmt3a1 cooperate in vivo to promote acute promyelocytic leukemia. Cancer Research, 2010; Nov 1;70(21):8792-801.

Deepa Subramanyam and Robert Blelloch. Watching reprogramming in real time. Nature Biotechnology, 2009, Nov;27(11):997-8.

Tessy T. Maliekal, Jeevisha Bajaj, V. Giri, Deepa Subramanyam, Sudhir Krishna.The role of Notch signaling in human cervical cancer: implications for solid tumors. Oncogene, 2008 Sep 1;27(38):5110-4.

Deepa Subramanyam* and Sudhir Krishna. c-Myc substitutes for Notch1-CBF1 functions in cooperative transformation with papillomavirus oncogenes. Virology, 2006 Mar 30;347(1):191-8.

Deepa Subramanyam*. Asymmetry Pins Inscuteable. Current Science, 2000 August 10; 79(3): 271-3.

*Corresponding author.
For a complete list of publications go to: http://www.ncbi.nlm.nih.gov/pubmed/?term=Deepa+Subramanyam

Funding

Department of Biotechnology, Govt. of India (ongoing)
Department of Science and Technology, Govt. of India (ongoing)
Indian Council for Medical Research (ongoing)
Wellcome Trust –DBT India Alliance Intermediate Fellowship (2013-2020)
NCCS Intramural funds

Collaborations

We have ongoing collaborations with:
Dr. Raghav Rajan, IISER Pune
Dr. Amitabha Majumdar, NCCS, Pune
Dr. Shivprasad Patil, IISER Pune
Dr. Amitabha Nandi, IIT Bombay

Opportunities

We are looking for highly motivated individuals interested in stem cell biology and early development. If you feel our science excites you, please send an email to deepa@nccs.res.in with your updated CV containing the names of three references along with a statement of purpose. We have a number of vacant positions for graduate students who have their own fellowships. Posts are also available for individuals interested in pursuing their postdoctoral training, who have their own source of funding.

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Last updated On : 10 January 2023 11:27

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