Identification of RNA prognosis and mechanistic biomarkers associated with healthy and premature cardiovascular and renal ageing


Background

Large scale analysis of human cell’s transcriptome revealed the expression of a huge number of non-coding RNAs (ncRNAs) (1): small ncRNAs (sncRNAs), like tRNAs, miRNAs, siRNAs or snoRNAs, as well as a huge number of long non-coding RNAs (lncRNAs), which are generally spliced and polyadenylated. NcRNAs were found to be involved in most of the cellular processes, chromatin architecture and activity (lncRNAs), replication, transcription, post-transcriptional modifications of other RNAs (snoRNAs), translation (mi- and siRNAs), RNA transport, RNA splicing (snRNAs), RNA stability… However, only a tiny amount of the activity of human ncRNAs has been characterized. Deregulation of their expression, as well as, the presence of SNPs or mutations in their genes can participate to disease development (2). In addition, to ncRNAs, other genomic non-coding sequences play a crucial role in protein production, the intron sequences which are eliminated from pre-mRNA transcripts at the splicing step. This process is as much complex as depending on the cell type or the physiological state of the cells, different intron sequences can be removed from a given pre-mRNA transcript (alternative splicing). Mutation in non-coding sequences can alter this process, so that they also participate to disease development. Importantly, several sncRNAs are stable in biologic fluids, since they are included in vesicles (exosomes) or associated with protein complexes. Therefore, both blood and urine are useful sources for the detection of potential predictive RNA markers of pathologies and for stratification of patients with a given pathology. In addition, to be a source of plasma circulating ncRNAs, blood is also an interesting material for the study of RNA splicing, since complete transcriptome can be analyzed from peripheral mononuclear cells (PBMCs). As a large number of the human protein and ncRNA genes are expressed in PBMCs, this opens the possibility to study their splicing pattern. To which extent this process is associated with a cardiovascular and renal healthy and disease ageing is unknown, and may pave the ground to new theragnostic strategies, whilst using a precision medicine approach, within the Framework of the FHU CARTAGE.

 

Aims and methods

We already developed all the methods for purification of RNAs from various blood fractions (PBMC, plasma), followed by next generation sequencing (NGS) of the collected RNAs and computer analysis of the data.  The CARTAGE FHU and CIC team are in charge of several French and international cohorts of patients with cardiovascular or kidney diseases including the Stanislas cohort (http://www.fhu-cartage.com/index.php/existing-cohorts), a longitudinal cohort established 20 years ago with initially 4000 heathy individuals from Lorraine with a follow up every 5 years. Blood and urine were collected at each visit, PBMCs were prepared for about 600 individuals at the 4th visit, along with a standardized  cardiovascular and renal phenotyping (including intima media thickness, pulse wave velocity and echocardiography at the 4th visit (20 year apart)). A number of the participants of this cohort have developed infraclinic cardiovascular or kidney disease which opens the possibility to study the mechanisms involved in the onset of premature ageing.

Through deep sequencing of various blood fractions (I Motorine, NGS platform of Nancy) special focus will be made on snc- and lncRNA expression, as well as on alternative splicing events in mRNAs and lncRNAs. Data from NGS will be validated by QRT-PCR analysis. A special attention will be paid to the ANRIL lncRNA already shown to be involved in arteriosclerosis (level of expression, splicing isoforms) (3,4). In parallel, mechanisms of regulation and deregulation of the ANRIL alternative splicing can be studied in cellulo (I Behm-Ansmant is a specialist in this field). The possible role of ANRIL in epigenetics of patient PBMCs can be investigated, since DNA fractions from PBMCs have been collected in parallel with RNA fractions. S Maenner (MCU) who studied the role of lncRNA in epigenetics will mentor the candidate for this part of the work. In parallel, the candidate will perform investigation on possible RNA biomarkers of chronic kidney disease using both blood and urine (exosomes) RNA fractions. A special focus will be made on miR-1207-5p and its host lncRNA gene Pvt1 which were proposed as mediators of extracellular matrix accumulation in kidney (5) and on the urinary exosomal miR-29c proposed to be a predictor of early renal fibrosis in lupus nephritis (6).

Through this program and with the large number of advisors including, in addition to the two PhD directors, Pr F Zannad, Dr N Girerd, Pr I Motorine, Dr S Maenner and Dr C Branlant, and within the  FHU Carthage environment, the candidate will acquire a large expertise in both cardiovascular and kidney diseases, the RNA field and epigenetics. We expect that she will get original data important for understanding pathology mechanisms and for clinical applications.

Reference list: 1 Jacquier, 2009, PMID: 19920851; 2 Broadbent et al., 2008, PMID: 18048406; 3 Hodt et al., 2010, PMID: 20056914; 4 Folkersen et al., 2009, PMID: 19888323; 5 Alvarez et al., 2013, PMID: 24204837; 6 Sole et al., 2015, PMID: 26040904

Supervision

Co-PhD directors: Pr Patrick Rossignol (CIC-P INSERM and U1116) and Dr I Behm-Ansmant (CR1 CNRS, UMR 7365) PhD applicant: Miss BASU MEENAKSHI (from India)

Partners:
UMR_S1116 INSERM-UL “Défaillance Cardiaque Aiguë et Chronique”,
UMR 7365 CNRS-UL “Ingénierie Moléculaire et Physiopathologie Articulaire”

Doctoral school for PhD recruitment/follow-up: BioSE (Biology, Health, Environment – ED 266)

 

Contacts: Pr Patrick Rossignol (p.rossignol@chu-nancy.fr) and Dr Isabelle Behm-Ansmant (isabelle.behm@univ-lorraine.fr)

 

How to apply

In order to prepare a PhD thesis within the Lorraine Université d’Excellence Program, the interested candidate should consult the PhD topics offered in each social and economic challenges.
These PhD thesis topics are proposed by faculty members or researchers accredited to supervise research.

Candidate application period: according to graduate school schedule (visit each topic)
Each candidate may submit an application on up to three separate research topics.

Application analysis period by each graduate school
The graduate school reviews the applicants for a doctoral contract in the relevant disciplines. They check the level of supervision for each supervisor and the situation of trained doctors. Each candidate will meet the laboratory director, supervisor and a representative from the graduate school. This interview is to identify the candidate’s motivations and suitability as a candidate for the PhD project proposed by the supervisor. A recommendation will be made to the graduate school. This will summarize the strengths and/or weaknesses of the application.

PhD grants will include monthly income for the PhD student (roughly 1700 € for research only, complement can be provided for teaching missions) and environment for research in the research unit.

Please be aware that in order to offer a variety of subjects, more positions are posted here than available funding. The LUE executive committee will make the final choice on the granted funding (up to 12 positions), based on the recommendations by the doctoral schools.