2 PhD projects offered in the IPP summer call 2021
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are progressive age-related neurodegenerative diseases for which currently no therapies are available. A molecular hallmark of both disorders is mislocalization and cytosolic aggregation of the RNA-binding proteins TDP-43 (TAR DNA binding protein of 43 kDa) or FUS (Fused in sarcoma). The molecular mechanisms leading to RNA-binding protein pathology in these disorders and how it could potentially be prevented or reversed is currently not well understood.
Recently, we found that nuclear import receptors (importins) and post-translational modifications (e.g. arginine methylation or phosphorylation) can protect against aberrant phase separation and aggregation of disease-linked RNA-binding proteins. We aim to better understand these quality control mechanisms, their general relevance for aggregation-prone proteins, under what conditions they operate in cells, how their failure contributes to ageing or disease and whether we can harness them in new therapeutic approaches.
PhD project 1: Role of TNPO1 in cytoplasmic chaperoning and RNP granule dynamics
Importins not only chaperone aggregation-prone RNA-binding proteins, they were also shown to chaperone ribosomal proteins, histones and FG-rich nucleoporins, suggesting that diverse proteins might require chaperoning by importins in the cytoplasm. TNPO1 and other importins are also found in cytoplasmic membrane-less organelles, e.g. stress granules, implying that importins may regulate the dynamics and function of these compartments. In this project, we will explore the cytosolic functions of TNPO1, by identifying cellular cargoes that aggregate upon acute depletion of TNPO1 and by examining whether the dynamics and functions of stress granules or other cytosolic RNP granules depend on TNPO1 or other importins. The project will involve establishing a new method to acutely deplete TNPO1 from cells, as well as proteomics and live cell imaging techniques. Candidates with a strong background in cell biology or biochemistry are encouraged to apply.
PhD Project 2: Role of disease-linked phosphorylation in TDP-43 proteinopathies
Abnormal post-translational modifications (PTMs) have been identified in several neurodegenerative diseases, e.g. FUS is hypomethylated in FTD patients, and TDP-43 is hyperphosphorylated and polyubiquitinated in ALS and FTD. Aberrant PTMs could play an important pathological role in neurodegeneration and contribute to protein mislocalization, aggregation and/or functional impairment, eventually leading to neuronal dysfunction. Alternatively, disease-linked PTMs may have a protective role and counteract these pathological changes. We have recently shown that C-terminal hyperphosphorylation of TDP-43, which occurs in ALS and FTD patients, might be such a protective mechanism, as it suppresses aberrant phase separation and solidification of TDP-43. In this project, we will explore under which cellular conditions phosphorylation arises on TDP-43, which kinases are relevant for C-terminal TDP-43 hyperphosphorylation and how it affects the cellular behavior of TDP-43, e.g. its protein-protein-interactions, turnover or modification with other PTMs. The project will involve the screening of kinase inhibitor or CRISPR libraries to identify relevant kinases and proteomics to identify protein-protein interactions or map PTM sites. Candidates with a strong background in cell biology or biochemistry are encouraged to apply.
Publications relevant to the project
Gruijs da Silva L, Simonetti F, Hutten S, Riemenschneider R, Sternburg EL, Pietrek LM, Gebel J, Doetsch V, Edbauer D, Hummer G, Stelzl LS, Dormann D. Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation, submitted
Hutten S, Usluer S, Bourgeois B, Simonetti F, Odeh HM, Fare CM, Czuppa M, Hruska-Plochan M, Hofweber M, Polymenidou M, Shorter J, Edbauer D, Madl T and Dormann D (2020) Nuclear import receptors directly bind to arginine-rich dipeptide repeat proteins and suppress their pathological interactions. Cell Rep, 33:108538 Link
Alberti S and Dormann D (2019) Liquid-liquid phase separation in disease. Annu Rev Genet, 53:171–194 Link
Hofweber M and Dormann D (2019) Friend or foe-post-translational modifications as regulators of phase separation and RNP granule dynamics. J Biol Chem, 294:7137–7150 Link
Hofweber M, Hutten S, Bourgeois B, Spreitzer E, Niedner-Boblenz A, Schifferer M, Ruepp MD, Simons M, Niessing D, Madl T and Dormann D (2018) Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation. Cell, 173:706-719.e13 Link