PhD project proposal: Predicting response and non-response to medical treatment of infl...

Aim of the Ph.D. Today, the most wide-spread used targeted drug in chronic inflammatory diseases (CIDs) such as Inflammatory Bowel Disease (IBD) and Rheumatoid arthritis (RA) is a TNF inhibitor (TNFi). TNFi is effective in 1/3 to 2/3 of the cases. Therefore, being able to predict who will respond to the treatment will help select the best treatment to the individual patient. Based on the idea that the gut mucosa is the key organ for the disease process, single-cell transcriptomics, proteomics, PTMomics (the study of post-translational modifications such as phosphorylation and glycosylation), and metabolomics will be applied to patient intestinal biopsies. Results will be evaluated biologically, i.e. whether high-level mRNAs identified by transcriptomics lead to higher protein levels in the intestine (identified by proteomics), etc. In addition, we will perform an integrated analysis of the multi-omics data using a variety of freely available software. From this integration of data, we will perform various analyses, both data-driven and hypothesis-driven. By combining the different results, promising biomarkers will be selected for evaluation in blood from the Danish cohort. Biomarkers passing this first step will be further evaluated in Canadian, Swedish, and Norwegian cohorts. Finally, we will integrate the information in a model for further evaluation and optimization in future clinical studies before being implemented in clinical practice.

This Ph.D. project aims to identify biomarkers associated with response to targeted treatment by applying single-cell transcriptomics on biopsies from IBD patients treated with TNFi.

First, the PhD student will perform a literature review to use all available, updated, information on clinical factors and multi-omics biomarkers associated with treatment response in IBD. The PhD student will under supervision be involved in the clinical data administration and in performing the transcriptomics and data analysis.

The research team. You will member of a small, ambitious research team with various backgrounds (molecular biology, doctor, nurse, health research). You will be in close contact with other Ph.D. students.

Mentors. Contact: Signe Bek Sørensen, postdoc, [email protected], +45 2938 5683 (study coordinator). Vibeke Andersen, professor, Focused Research Unit for Molecular Diagnostics and Clinical Research (MOK), University Hospital of Southern Jutland, Åbenrå, +45 2115 7790, [email protected] (main supervisor), Mads Thomassen, [email protected], Clinical Genome Center, Odense University Hospital.

Practical Information. A student with interest in biomedical research is preferred (e.g. Molecular Science, Medicine or Human Biology). You will be involved in writing the protocol, applying for the economy. One year wage is already paid by H2020. The study will be performed at the Clinical Genome Center, Odense University Hospital and MOK, University Hospital of Southern Denmark, in close contact with SDU. Only applicants with at least one published work are accepted as Ph.D. students. Deadline for the application: the 25th of May 2020. The interview will take place the 28th of May 2020

Salary. The PhD programme will be carried out in accordance with Faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order). The terms of employment as a salaried PhD Research Fellow are stated in the Agreement between the Ministry of Finance and the Danish Confederation of Professional Associations (AC).

Applications must include:

• A letter stating the interest, motivation and qualifications for the project (max. 2 pages),
• Detailed CV, including personal contact information,
• Certified copy of diploma (Master’s degree in a relevant field).

Additional information may be requested and the application process may include an interview before a final decision is made. Successful candidates will be asked to send an application to the PhD Secretariat, Faculty of Health Sciences, to be enrolled as PhD students. Incomplete applications and applications received after the deadline will not be considered. All interested and qualified persons are encouraged to apply, regardless of age, gender, religious affiliation or ethnic background.

1. Christensen R, Heitmann BL, Andersen KW, et al. Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases: protocol for a prospective cohort study of prognostic factors and personalised medicine. BMJ Open. 2018;8(2):e018166.

Kilde: Jobnet.dk