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Regulation of autophagy in human embryonic stem cells and its therapeutic application in induced pluripotent stem cell-based disease models

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

About This PhD Project

Project Description

Project background: Regulation of proteostasis is critical for maintaining tissue homeostasis. Autophagy, a major intracellular degradation pathway essential for cellular and energy homeostasis, functions in the clearance of aggregation-prone proteins and damaged organelles. It acts primarily as a cell survival process. This process is regulated by mammalian target of rapamycin (mTOR) and mTOR-independent pathways that are amenable to chemical perturbations. Several small molecules modulating autophagy have been identified that have potential therapeutic application in diverse human diseases, including neurodegeneration. Neurodegeneration-associated aggregation-prone proteins are predominantly degraded by autophagy, and therefore, stimulating this process with chemical inducers is beneficial in several transgenic disease models. Compromised autophagy contributes to the pathology of various neurodegenerative diseases by causing accumulation of mutant proteins and cellular toxicity. Moreover, autophagy has been implicated in various human physiological and pathological conditions, including development, immunity, cancer, neurodegeneration and longevity. Although autophagy is evolutionarily conserved and is well characterized in yeasts, its regulation in the human system is not completely understood. Combining the knowledge of autophagy dysfunction and mechanism of drug action in human disease-relevant cellular contexts may be rational for designing targeted therapy. Dr Sovan Sarkar’s laboratory is working on the regulation and therapeutic application of autophagy in the human system using human embryonic stem cells (hESCs) and disease-specific human induced pluripotent stem cells (hiPSCs).

Research topics: These include:
(i) Role and regulation of autophagy in hESCs and in hESC-derived human disease-relevant cell-types.
(ii) Molecular mechanisms of autophagy in its role in cellular homeostasis and neurodegeneration.
(iii) Mechanisms of cellular degeneration and proteostasis in disease-specific hiPSCs.
(iv) Drug discovery for autophagy modulators using human stem cell models.

Methodology: The project will involve cell biology, biochemistry, high-content and confocal microscopy, mass spectrometry, generation of hiPSCs by reprogramming, genome engineering by CRISPR/Cas9, differentiation of hESCs/hiPSCs into adult cell-types, and compound screening, amongst others. For further details, visit

Person Specification
Applicants should have a strong background in cell and molecular biology, and ideally a background in stem cells. They should have a commitment to research in Biological Sciences and hold or realistically expect to obtain at least an Upper Second Class Honours Degree in a relevant Biology subject.

How to apply
Informal enquiries should be directed to Dr Sovan Sarkar by e-mail at

Applications should be directed to Dr Sovan Sarkar (e-mail: ). To apply, please send:
• A detailed CV, including your nationality and country of birth;
• Names and addresses of two referees;
• A covering letter highlighting your research experience/capabilities;
• Copies of your degree certificates with transcripts;
• Evidence of your proficiency in the English language, if applicable.


1. Carroll, B., Maetzel, D., Maddocks, O.D.K., Otten, G., Ratcliff, M., Smith, G.R., Dunlop, E.A., Passos, J.F., Davies, O.R., Jaenisch, R., Tee, A.R., Sarkar, S. and Korolchuk, V.I. (2016) Control of TSC2-Rheb signaling axis by arginine regulates mTORC1 activity. eLife 5: e11058.
2. Kuo, S.Y., Castoreno, A.B., Aldrich, L.N., Lassen, K.G., Goel, G., Dančík, V., Kuballa, P., Latorre, I., Conway, K.L., Sarkar, S., Maetzel, D., Jaenisch, R., Clemons, P.A., Schreiber, S.L.,Shamji, A.F. and Xavier, R.J. (2015) Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics. PNAS 112(31): E4281-E4287.
3. Maetzel M.*, Sarkar S.*, Wang H.*, Abi-Mosleh L., Xu P., Cheng A.W., Gao Q., Mitalipova M. and Jaenisch R. (2014) Genetic and chemical correction of cholesterol accumulation and impaired autophagy in hepatic and neural cells derived from Niemann-Pick type C patient-specific iPS cells. Stem Cell Reports 2(6): 866-880. *Equal contribution
4. Sarkar S. (2013) Regulation of autophagy by mTOR-dependent and mTOR-independent pathways: Autophagy dysfunction in neurodegenerative diseases and therapeutic application of autophagy enhancers. Biochemical Society Transactions 41(5): 1103-1130.
5. Sarkar S., Carroll B., Buganim Y., Maetzel D., Ng A.H.M., Cassady J.P., Cohen M.A., Chakraborty S., Wang H., Spooner E., Ploegh H., Gsponer J., Korolchuk V.I. and Jaenisch R. (2013) Impaired autophagy in the lipid storage disorder Niemann-Pick type C1 disease. Cell Reports 5(5): 1302-1315.
6. Sahay, G., Querbes, W., Alabi, C., Eltoukhy, A., Sarkar, S., Zurenko, C., Karagiannis, E., Love, K., Chen, D., Zoncu, R., Buganim, Y., Schroeder, A., Langer, R. and Anderson, D.G. (2013) Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling. Nature Biotechnology 31(7): 653-658.
7. Buganim, Y., Itskovich, E., Hu, Y.C., Cheng, A.W., Ganz, K., Sarkar, S., Fu, D., Welstead, G.G.,Page, D.C. and Jaenisch, R. (2012) Direct reprogramming of fibroblasts into embryonic Sertoli-like cells by defined factors. Cell Stem Cell 11(3): 373-386.
8. Sarkar S., Korolchuk V.I., Renna M., Imarisio S., Fleming A., Williams A., Garcia-Arencibia M., Rose C., Luo S., Underwood B.R., Kroemer G., O’Kane C.J. and Rubinsztein D.C. (2011) Complex inhibitory effects of nitric oxide on autophagy. Molecular Cell 43(1): 19-32.

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