Mots-Clés

RNAseq multi-OMICS integration Cancer

Description

Context

IMMUcan stands for “Integrated iMMUnoprofiling of large adaptive CANcer patient cohorts”. The goal of IMMUcan is to understand how the immune system and tumours interact, and the impact of therapeutic interventions. It is an integrated European immuno-oncology profiling platform.

Some new cancer treatments harness the immune system to fight the disease. However, for most patients, they do not deliver a long-lasting response and they often cause serious side effects. To address these challenges, IMMUCAN aims to study the tumour microenvironment to gain a deeper understanding of how the immune system and cancer cells interact at the molecular level.

Using cutting-edge technologies, the consortium will analyse tumour tissue, blood, stool and saliva samples as well as clinical information from patients with colorectal, lung, head and neck, breast, gastric and renal cancers. By comparing patients who are not receiving immune therapy with patients who are, the project hopes to build up a detailed picture of the tumour and its microenvironment, and the impact of current treatments.

In the longer term, the project results could aid in the identification of biological markers that will show which patients are most likely to respond well to immune therapies, and which patients would benefit from a combination of immune therapies and conventional treatments.

Job description

Vassili Soumelis’ team has a crucial role in developing approaches to analyse and integrate complex multivariate datasets and biological knowledge generated in IMMUcan while maintaining a strong link between biological mechanisms and clinical impact. The team is looking for a bioinformatician fully dedicated to the IMMUcan project. The candidate’s work will be distributed in the following tasks:
     1) Bulk RNAseq transcriptomics data analysis: Quality control and analysis of transcriptomic data generated from FFPE samples.
     2) Multi-omic data integration: The multi-omics datasets include transcriptomic bulk and single-cell RNAseq data, secretome, whole-exome sequencing (WES), immunofluorescence, and imaging mass spectrometry. The complex biological variables will be connected to clinical data for diagnostic classification and prediction of patient outcomes.
     3) Public database curation: Updating an existing database of single-cell cancer studies.
     4) Reporting and communication: Collaboration with other IMMUcan project teams, listening and responding to the project needs in terms of data analysis. Following up on the project progress and building the data analysis approaches accordingly. Preparation of oral and written progress reports.

Profile

• PhD or Master in Bioinformatics, Biostatistics or Systems biology
• Strong experience in the transcriptomic data analysis approaches (bulk and single-cell RNA-seq)
• Good knowledge of complex data integration
• Mastering DESeq2, Seurat or Scanpy for the implementation of analysis workflows
• Demonstrated programming skills in at least one programming language, e.g. Python or R

Personal traits & work ethics

• Be organized and reactive in a fast-paced, high-achieving environment
• Ability to work independently, while nurturing a team spirit
• Strong verbal communication skills to interact with IMMUcan collaborators in an
interdisciplinary environment
• Excellent writing skills (reports, partner communication, manuscripts)
• English proficiency is mandatory, French would be a plus

You can learn more about the IMMUcan project: IMMUcan.eu