Mots-Clés

transcriptomique, génomique, pipeline, cancer resistance, gene duplications

Description

Investigating cancer resistance in non-model animals through the lens of multi-omics

Context

Studying cancer in non-model organisms offers the opportunity to identify natural mechanisms of cancer resistance, with the aim of transposing them for the development of innovative therapies. This approach has, for example, already shown that the low cancer prevalences observed in elephants or in the naked mole rat are respectively based on the duplication of the most important tumor suppressor gene known today (i.e. TP53) and on the overproduction of the high molecular weight hyaluronic acid (Tian et al. 2013, Abegglen et al. 2015).

The proposed training is part of a large project involving a dozen researchers and PhD students. The methods that will be developed, and the preliminary results obtained during this internship will then be used by this community.

Objectives

The general objective of the internship is to set up important methodologies to investigate transcriptomic response and genomic adaptation related to cancer in wildlife. Working with non-model animals requires specific adjustments in both regular transcriptomic and genomic analysis.

During this internship, the student will have to work on three mammalian and two bird species that will be selected based on a literature investigation and data availability. The first objective is to establish a pipeline to process transcriptomic data of non-model vertebrates from quality check to transcriptome assembly, transcript’s annotation, and mapping. The second objective concerns genomic data and is related to genome size and identification of gene duplications, in particular oncogenes and tumor-suppressor genes. For the same species used in transcriptomics, the student will have to determine the number of duplications of tumor-suppressor genes and oncogenes based on sequence similarity with transcripts and test for associations with variables such as genome size or cancer prevalence.

Skills

We are looking for an evolutionary biology, bioinformatics or an engineer student with strong interest in both development and data analyses. The following skills are assets:

• Knowledge of omics concepts and terminologies (transcriptomics, genomics)
• Knowledge of biological and statistical analysis of high-throughput data
• Use of at least one programming and/or analysis language (Python, R, ...)
• Mastery of the Unix/Linux environment and the Bash language

Environment

The internship is a joint collaboration between a team of the IBGC in Bordeaux and a team of the LIENSs in La Rochelle. The main supervisors will be Macha Nikolski (bioinformatics specialist), Domitille Chalopin-Fillot (immunity, genomics, bioinformatics) and Mathieu Giraudeau (cancer resistance in wildlife). The student will be located at the IBGC in Bordeaux but will interact on a regular basis with the team of La Rochelle.

Contacts: Mathieu Giraudeau (LIENSs team leader, giraudeau.mathieu@gmail.com), Domitille Chalopin-Fillot (domitille.chalopin-fillot@u-bordeaux.fr) and Macha Nikolski (IBGC team leader and CBiB director, macha.nikolski@u-bordeaux.fr).

Duration of the internship: 6 months

Amount of compensation: statutory internship compensation. The gratification will be provided by a grant attributed by the Grand Sud Ouest (GSO) Cancéropole.