CALL FOR 12 PhD students
General description of the Network
The Tripartite motif (TRIM) family of Ubiquitin E3 ligases plays an important role in many physiological processes and in many diseases including cancer, neurodegenerative and neuro-muscular disorders and rare genetic diseases. As such, they are excellent targets for therapeutic manipulation. TRIM-NET is a training programme for Early-Stage Researchers to identify novel therapeutic targets and to develop the strategies to validate them in preclinical studies. The TRIM-NET network will integrate complementary expertise and multidisciplinary approaches to exploit common targeting strategies for translational applications. The consortium will train a cohort of young researchers in skills and expertise essential for biomedical research focusing on:
- determining how TRIM proteins contribute to disease;
- developing strategies to modulate TRIM protein activity;
- designing high throughput screening assays for drug discovery.
The project consists of 12 individual research projects.
As the scientific work packages are highly integrated, recruited students will avail of techniques and training opportunities, including secondments, across the work packages. Through a unique international partnership between academic and non-academic partners the TRIM-NET training programme will provide young researchers with skills required for biomedical research in industry and academia.
Eligibility and Requirements
- Not having a doctoral degree yet
- Less than 4 years full-time research experience
- A degree which entitles to embark on a doctorate in the host countries
- Less than 12 months spent in the host country in the 3 years prior to the recruitment
- A strong background in Biology, Biochemistry, Chemistry, Medicine or related fields according to the individual research projects
- The relevant PhD accession title should be achieved by June 2019 through September 2019 according to the specific PhD programmes and countries
- Attractive salary
- 3-year full-time employment contract in accordance with the Marie Skłodowska-Curie Action regulations for Early Stage Researchers;
- Enrollment in a PhD programme at the local partner’s institution. In case the student is enrolled in a doctoral programme in a country where the duration of the PhD study is beyond the 3-year- MSCA contract, additional funding for the additional year(s) will be provided by the host group
- Access to state-of-the-art research and supervision by recognized experts
- Participation in network-wide training activities, schools and conferences
- Secondments periods at other network partners’ labs.
Applications in English should include:
- A cover letter indicating the top three projects of election in the order of preference (see below) and the indication of the countries of residence during the last 3 years;
- CV (contact details, education, work experience, list of publications, prizes/awards, language skills, etc....);
- A motivation letter;
- A digital copy of the degree certificate and official academic transcripts of Bsc and Msc studies (Master diploma/certificate or equivalent qualification giving access to the Doctoral Programme + Transcript of Records including examinations and scores obtained. If the documents are issued in a language other than English, a translation must be included, along with the original document);
- A documentation of English language qualifications;
- Two recommendation letters sent directly by the referees to firstname.lastname@example.org with the subject:
“Letter concerning - Surname Name”
and full contact details of the reference persons;
- Application in a single pdf file should be sent by e-mail to email@example.com with indication of “TRIM-NET application” in the subject line. Equal consideration will be given to female and male applicants.
Deadlines of Application, Evaluation process and Starting date
- Deadline for Application: April 24, 2019.
- The merit-based recruitment process will be on a competitive basis across all applicants for each project.
- Short-listed students will be interviewed via Skype on May 9-10, 2019.
- Students are expected to initiate their contracts between June 1st, 2019 and November 1st, 2019 depending on the PhD enrollment rules of the different countries.
Vacancies - Overview of the 12 vacant ESR positions
TRIM17 increases α-synuclein expression by inhibiting ubiquitination/degradation of the transcription factor ZSCAN21 mediated by TRIM41.
The aim is to assess:
- The role of this pathway in Parkinson’s disease models;
- The impact of TRIM41 and ZSCAN21 mutations identified in patients;
- The molecular mechanisms of TRIM41 inhibition by TRIM17.
Lafora progressive myoclonus epilepsy is caused by mutations in the TRIM-like E3-ubiquitin ligase malin. This study will identify the role of malin in pathophysiology. Interactomics and proteomic techniques will be used to identify substrates of malin. We will also pay attention to the deubiquitinases that accompany malin in its action.
TRIM32 is the gene responsible for Limb Girdle Muscular Dystrophy type 2H and Sarcotubular Myopathy. The TRIM32 gene product is an E3 ubiquitin ligase for which many substrates have been reported. To unravel its function in muscular dystrophy, it is important to understand how TRIM32 pleiotropy is achieved. TRIM32 ability to homo-interact, thus offering several RING moieties to E2 binding, and to interact with different E2 enzymes can underlie TRIM32 potential to form different complex combinations. As E3-E2 pairs determine the type of ubiquitin modification, this may result in the amplification of TRIM32 spectrum of action in regulating the fate of several targets and implication in diverse pathological conditions.
The objective of this project is to thoroughly define TRIM32 ubiquitin E3 ligase activity by assessing the specific TRIM32-E2 complexes and the ubiquitin chains formed for the control of specific muscular targets, combining biochemical, biophysical and cell biology approaches.
ESR3 will investigate TRIM32 role and biochemistry, self-interaction requirements, and potential to catalyse different ubiquitin chain topologies, dissecting in vitro its E3 activity with different E2 enzyme combinations. These features will be then validated on TRIM32 natural substrates in normal and pathological cellular systems. C2C12 cells induced to differentiate into myofibers and fibroblasts from LGMD2H patients differentiated towards a muscular phenotype by MyoD transduction will be employed for these studies. The accomplishment of the proposed experiments will elucidate the ability of TRIM32 to use different partners within the ubiquitination machinery to produce specific ubiquitin modifications of muscular substrates. These data will be important for the design of muscular dystrophy therapies without interfering with non-muscular pathways.
Institution information: University Clermont-Auvergne (UCA) and INRA, Clermont-Ferrand, France. Clermont-Ferrand is a vibrant student city and UCA is committed to developing educational programs for an international public (dual-award programs) and to enhancing its research at an international level. Since its creation, UCA has embraced the two main European political roadmaps for 2014-2020 through the Erasmus+ and Horizon 2020 programs.
Context: This position is part of a European Marie Skłodowska-Curie Action (see details in the joined PDF). This job includes an attractive 3-year full-time employment contract Enrolment in a PhD programme, supervision by recognized experts and access to state-of-the-art research, network-wide training activities, participation at workshops, on-line courses, schools and conferences in addition to local training activities in host labs.
Background: Protein degradation is the main determinant of muscle wasting and the ubiquitin proteasome proteolytic system (UPS) is a key player. Only specific E2-E3 combinations will lead to the degradation of specific substrates, e.g. contractile proteins.
We previously showed that the muscle specific Trim63/MuRF1 is the main UPS actor targeting muscle contractile protein for degradation in catabolic states [1, 2]. Trim63/MuRF1 E3 enzyme is a good candidate for pharmacological treatment; however, it can target substrates from several metabolic pathways. We recently identified 5 E2 enzymes that interact with Trim63/MuRF1 [3-6]. The Ph.D. student objectives will be (i) to identify the muscle specific E2-E3 couple(s) implicated in muscle atrophy and (ii) to elaborate a pharmacological drug for inhibiting the implicated couple for fighting against patient’s weakness. We will first determine which E2-MuRF1 couple(s) specifically lead to contractile protein degradation in cellulo and in vivo. We will knockdown or overexpress (electroporation) the 5 E2-MuRF1 couples already identified and will address their impact on muscle structure (histological immunostaining and immunoblots) and function.
As a second step, the goal will be to search for pharmacological inhibitors to impede MuRF1-E2 interaction. Inhibitor screening will be performed by identifying amino acids residues involved in MuRF1-E2 interactions (hot spots approach, collaboration with chemists). E2s hot spots are already known and the ESR will identify their counterparts in Trim63/MuRF1. Identification of these residues will allow chemical synthesis of inhibitors. The inhibitory capacity to block specific MuRF1-E2 interactions will be performed in cultured cells using a split-GFP assay. Finally, the safety and the efficiency of inhibitors to block MuRF1-dependent degradation will be addressed by determining MuRF1 targets levels in skeletal muscle from catabolic mice.
For more information: firstname.lastname@example.org
References 1. Polge, C., et al. (2011) Muscle actin is polyubiquitinylated in vitro and in vivo and targeted for breakdown by the E3 ligase MuRF1. FASEB J. 25, 3790–3802. 2. Aniort, J., et al. (2016). Upregulation of MuRF1 and MAFbx participates to muscle wasting upon gentamicin-induced acute kidney injury. Int J Biochem Cell Biol, 79, 505-516. 3. Polge, C., et al. (2018). A muscle-specific MuRF1-E2 network requires stabilization of MuRF1-E2 complexes by telethonin, a newly identified substrate. J Cachexia Sarcopenia Muscle, 9(1), 129-145. 4. Polge, C., et al. (2018). UBE2E1 Is Preferentially Expressed in the Cytoplasm of Slow-Twitch Fibers and Protects Skeletal Muscles from Exacerbated Atrophy upon Dexamethasone Treatment. Cells, 7(11). 5. Polge, C., et al. (2016). UBE2D2 is not involved in MuRF1-dependent muscle wasting during hindlimb suspension. Int J Biochem Cell Biol, 79, 488-493. 6. Polge, C., et al. (2016). UBE2B is implicated in myofibrillar protein loss in catabolic C2C12 myotubes. J Cachexia, Sarcopenia Muscle, 7(3), 377-87.
Prostate cancer is one of the leading cancer deaths for men. By applying state-of-the-art techniques in molecular biology and biochemistry, we will investigate how TRIM25 controls androgen receptor activity and proliferation and migration of prostate cancer cells and elucidate its suitability as a target for drug development.
Around 75% of all breast cancers are positive for the Estrogen Receptor (ER), which is considered the main driver of the disease. In a siRNA screen targeting all 781 E1, E2 and E3 ligases throughout the human genome, we set out to discover novel regulators of ER stability. We identified TRIM33 as a crucial factor to regulate ER levels and activity. We aim to unravel the biological interplay between ER function and TRIM33, and explore how this interaction can be therapeutically exploited using novel inhibitors.
We previously identified TRIM28 as a direct interactor of the Androgen Receptor in prostate cancer cells, critically involved in prostate cancer cell proliferation. This study will: 1. identify the functional contribution of TRIM28 on Androgen Receptor function in prostate cancer cells, 2. Unravel the underlying basis of the observed genomic selectivity, 3. Reveal the clinical implications of TRIM28 on prostate cancer patient outcome and response to therapy, and 4. Expose how this TRIM28/AR interaction could be therapeutically exploited in the treatment of prostate cancer patients.
Reduced E3 ubiquitin ligase activity of TRIM8 contributes to the glioma pathogenesis.
This study aims to identify TRIM8-partners and TRIM8 glioma-related functions. Transcriptomic, proteomic, and bioinformatics will be exploited to identify TRIM8- related glioma signatures, identify novel pathways that correlate with the pathophysiology of this tumour, and ultimately indicate therapeutic avenues
Arsenic is used therapeutically to treat Acute Promyelocytic Leukaemia by inducing SUMO- dependent, ubiquitin-mediated degradation of the PML- RAR oncoprotein. The objective of the work will be to define the mechanism by which arsenic induces SUMO modification of PML (TRIM19) and will involve a combination of biochemical, proteomic and structural biology approaches.
One of the specific requirements for an E3 ligase is the interaction with the ubiquitin-charged E2. The important role of E2 enzymes in determining ubiquitin chain length and topology, hence the final fate of the modified substrates, is nowadays well accepted.
The objective of this project is to understand E3-E2 pair selection and its determinants for the TRIM proteins studied within this network (TRIM8, 17, 19, 25, 28, 32, 33, 41, 63 and Malin). The ultimate goal is to explore novel strategies of drug design and screening to interfere with specific E3 activities.
ESR10 will test functional interactions of the above TRIM proteins and E2 enzymes using autoubiquitination assays with panels of E2s provided by PO2 (Ubiquigent) and test physical interactions by performing MBP pull-down assays. To define the RING domain-E2 interaction surfaces, he/she will use modelling analyses combining alignment of RING primary sequences and threading on solved structures of isolated RING fingers and/or RING-E2 complexes to predict the residues responsible for the specific binding. Site-specific mutagenesis coupled with the above assays to reveal either loss or specificity alteration of the binding will be also employed. Structural information will be essential in understanding the manner in which potential small molecules inhibitors might mimic the most important binding elements of the native ligands guiding the strategies for class selection and optimization of compounds.
As a further objective, the ESR will also employ mid-throughput screening assays to identify the DUBs implicated in the TRIM-associated disease pathways under study within the consortium. Using the cellular system developed by the other beneficiaries siRNA DUBs libraries will be tested for destabilization of the disease-relevant TRIM protein substrates. Identified DUBs will be validated with in vitro and in the above mentioned cellular systems.