Projects
Name
Natural variants in BK Polyomavirus and cytidine/uridine monophosphate kinase (CMPK) genes may impact on viral pathogenicity and clearance
University
Belgium (BeMSA) - KU Leuven, Leuven
Domain
Immunology
Departement
Department of Immunology and microbiology, Rega Institute for medical research
Head
Robert Snoeck
Tutor
Dimitrios Topalis & Olga Mineeva-Sangwo
Languages
English
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No No Yes No No No No No
Type of Research Project
- Clinical Project with Laboratory work
What is the background of the project?
BK polyomavirus (BKPyV) is the first human polyomavirus discovered in the early 70s in a kidney transplant patient. The immunosuppression state of the patient allows the reactivation of the virus, leading in 30% of the cases to graft loss. Up to now, no protocol for the management of BKPyV associated nephropathy have been established. The combination of immunomodulatory drugs and cidofovir (an anti- deoxyribonucleic acid (DNA) virus agent) permits in many cases to control the viral replication and the integrity of the graft. However, in some patients, this therapeutic strategy does not result in the control of the viral infection and might lead to graft loss.
What is the aim of the project?
In this project, we plan to analyze the genomic variation of BKPyV isolated from kidney-transplant patients that respond successfully to the combination therapy (immunomodulation + antiviral) and from patients in therapeutic failure. In parallel, in a recent study from our laboratory, we have identified mutations in one of the cellular proteins, named cytidine/uridine monophosphate kinase (CMPK), involved in the activation of cidofovir. The search of amino acid changes in this enzyme in cells from the donor (kidney) and in cells from the recipient will be performed. This genomic analysis will allow to identify natural variants, within the BKPyV or in the host-cell genomes, that confer resistance to cidofovir treatment and identify patterns of patient profiles suitable for cidofovir-based therapy.
What techniques and methods are used?

Sanger sequencing and next-generation sequencing are the main techniques used in this project. Variations in BKPyV genome will be investigate using Next-generation sequencing, allowing identification of subpopulation as low as 1% of the total viral population.
For CMPK1 genotyping, Sanger sequencing will be used to assess the presence of amino acid changes in the enzyme responsible for the activation of cidofovir.

What is the role of the student?
- The tasks of the student will be performed on his/her own
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
The student will have to perform polymerase chain reactions (PCR) prior next-generation sequencing analysis or Sanger sequencing analysis. Amplicons generated during PCR reactions will be purified using a commercial kit and quantified by means of picogreen-based assay (Qubit). In addition, the results of Sanger sequencing reaction will be analyzed by the student using a specific software (Seqscape software).
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
Articles will be provided to the student regarding the background of this project.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- No specific outcome is expected
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
The student will need to be rigorous, able to reproduce experiments and to be trustful. Workbench experience would be an asset.
Are there any legal limitations in the student’s involvement
No
Hours
7
Type of students accepted
This project accepts:
- Medical students
- Students in biomedical fields
Articles
- Biology of the BKPyV: An Update. Helle F; Brochot E; Handala L; Martin E; Castelain S; Francois C; Duverlie G. Viruses. 2017 Nov 3;9(11).
- The large tumor antigen: a "Swiss Army knife" protein possessing the functions required for the polyomavirus life cycle. Topalis D; Andrei G; Snoeck R.; Antiviral Res. 2013 Feb;97(2):122-36.
- Management of polyomavirus-associated nephropathy in renal transplant recipients. Kuypers DR. Nat Rev Nephrol. 2012 Apr 17;8(7):390-402
- Adjuvant low-dose cidofovir therapy for BK polyomavirus interstitial nephritis in renal transplant recipients. Kuypers DR; Vandooren AK; Lerut E; Evenepoel P; Claes K; Snoeck R; Naesens L; Vanrenterghem Y. Am J Transplant. 2005 Aug;5(8):1997-2004.