PhD Student position in Sandro Banfi's lab (ProgRET-Marie Skłodowska-Curie Doctoral Network)

 PhDs on vision research to address the knowledge gaps to understanding, diagnosing and treating Inherited Retinal Diseases.

 ProgRET is a Marie Skłodowska-Curie Doctoral Network (2024-2027), offering 10 PhD positions. The objective of ProgRET is to train a new generation of vision researchers specialising in inherited retinal diseases (IRD).

 Eye diseases are among the most common inherited human disorders. Vision research has often blazed a trail for many disciplines to follow, giving a lead in multi-omics, stem cell biology, genome editing, animal models of disease, and the development of novel therapeutic approaches such as gene therapy. In recent years, human geneticists, have identified a large proportion of the genes implicated in IRD. Despite this progress the most important challenges in the IRD field relate to the diagnosis, understanding as well as therapy development of autosomal dominant IRD (adIRD). There are an estimated 925,000 affected individuals worldwide, representing 25%–40% of IRD. As we have demonstrated an emerging role for complex structural variants (SVs) and defects in non-coding regions such as non-coding RNAs and cis-regulatory elements in adIRD, we hypothesize that these may explain unsolved IRD cases and may represent novel targets for intervention.

 The objective of ProgRET is to conduct advanced vision research that addresses the knowledge gaps to understanding, diagnosing and treating autosomal dominant inherited retinal disease (adIRD), using innovative approaches related to genomics, transcriptomics, epigenomics, multi-omics, bioinformatics, gene regulation, retinal stem cell models, organoids, aquatic animal disease models, and therapy development.

We will pursue the following specific research objectives: 1. To understand mechanisms of adIRD using retinal stem cell and aquatic animal models; 2. To advance diagnostics in adIRD using a single-molecule multi-omics framework; 3. To develop novel therapeutics for adIRD using RNA therapy and genome editing.

 Application Deadline: 15 Mar 2024 - 23:59 (Europe/Paris)

Researcher Profile: First Stage Researcher (R1)

Research Field: ’(Human) Genetics’ ’Molecular Biology’ ’Biomedical research’ ’translational research’ ’integrative omics’ ’(Applied) Bioinformatics’ ‘Neurosciences’ ‘Gene therapy’

Type of Contract: Temporary

Job Status: Full-time

Anticipated starting date: October 1, 2024

 Supervisor: Prof. S. Banfi

Host institute: Telethon Institute of Genetics and Medicine, Italy

Secondments planned: Phenopolis, UK (virtual); Ghent University, Belgium; Radboud University Medical Center Nijmegen, The Netherlands

Doctoral program: Biomolecular Sciences at University of Campania “Luigi Vanvitelli”

Project description
DC4@TIGEM:DC4: Definition of transcriptional units of adIRD genes in human retina, RPE, PPCs and retinal organoids using long-read sequencing
We have significantly contributed to the initial reconstruction of the architecture of the human retinal transcriptome and miRNome, in physiological conditions. By capitalizing on the above resources and competence, DC4 will characterize the transcriptional units of Inherited Retinal Disease (IRD) genes in the human retina using an integrated approach, including both meta-analysis of already available data and generation of new transcriptome datasets from retina

samples of both unaffected donors and retinal organoids generated from patient-derived iPSCs. Furthermore, DC4 will carry out co-expression analysis efforts using bioinformatic tools to reconstruct the gene networks that underlie the expression of IRD genes. Particular attention will be given to the identification and characterization of noncoding RNAs such as microRNAs and long noncoding RNAs that are significantly co-expressed with IRD genes. The activities of DC4 will aim at enhancing our understanding of the molecular basis of IRDs and at providing novel insights into the composition of the integrated gene networks that control retinal function.

Requirements

At the date of recruitment have a Masters’ Degree (or equivalent) in one of the following research fields: ’(Human) Genetics’, ’Molecular Biology’, ’Biomedical research’, ’translational research’, ’integrative omics’, ’(Applied) Bioinformatics’, ‘Neurosciences’, ‘Gene therapy’.

Languages: ENGLISH

Level: Excellent

 Benefits

Marie Sklodowska-Curie PhDs are paid a competitive gross salary of 3,400 €/month, adjusted for their host country, a Mobility Allowance of 600 €/month and, for researchers who have a family, a Family Allowance of 660 €/month. All amounts are subject to deductions and taxes. Family is defined as persons linked to the researcher by (i) marriage, or (ii) a relationship with equivalent status to a marriage recognised by the national legislation of the country of the beneficiary or of nationality of the researcher, or (iii) dependent children who are actually being maintained by the researcher.

 
Eligibility criteria

To apply for one of these PhD positions, the applicant must fulfil the following conditions:

Have — at the date of recruitment — a Master’s degree in Life Sciences, Biomedical Sciences, Biotechnology, Biochemistry, Biology, Bioinformatics, Systems Biology (or an equivalent diploma), Bioengineering.

Trans-national mobility: The applicant — at the date of recruitment — should not have resided in the country where the research training takes place for more than 12 months in the 3 years immediately prior to recruitment, and not have carried out their main activity (work, studies, etc.) in that country. For refugees under the Geneva Convention (1951 Refugee Convention and the 1967 Protocol), the refugee procedure (i.e. before refugee status is conferred) will not be counted as ‘period of residence/activity in the country of the beneficiary’.

Be able to communicate fluently in English (at least B2-level speaking and writing).

 How to apply:

To apply for one of these positions, submit to simone.dusseljee@radboudumc.nl a single pdf document containing:

• _a detailed CV in EU format, including education, work experience, skills, dissertations, research interests, career objectives, and names and contact details of two referees, that can include the supervisor of the master thesis, willing to provide confidential letters of recommendation;
• _a max. 1-page letter of motivation regarding the position(s) as well as the ProgRET network;
• _a transcript of the master studies’ grades (including the overall grade and an explanation of the grading system) and the master’s thesis if available;

 and indicate as TITLE your full name, add 3 KEYWORDS, and mention the PROJECT(S) you are interested in (max 3; DC4).

Additional comments

For more information on ProgRET and additional job details see http://progret.eu/

Where to submit your application: simone.dusseljee@radboudumc.nl

Deadline: March 15, 2024, after which we will review applications and interview candidates.

All questions about the vacancies and submission should be emailed to the project manager of ProgRet: simone.dusseljee@radboudumc.nl