Société Française de Bioinformatique

Mots-Clés

single nuclei transcriptomics cancer R

Description

Context:

High-grade serous carcinoma (HGSC) of the ovary is the leading cause of death among gynecological cancers. Despite therapeutic advances, most patients relapse and current immunotherapies have shown limited efficacy. One key reason is the establishment of an immunosuppressive tumor microenvironment early in disease progression.
While extensive efforts have focused on advanced tumors, little is known about pre-cancerous stages, particularly serous tubal intraepithelial carcinoma (STIC), the earliest morphologically recognizable precursor lesions within the fallopian tube. Understanding the molecular and immune events bridging these precursor and malignant stages is critical to uncover new therapeutic vulnerabilities.

Goals:

The ImmunoSTIC project integrates cutting-edge transcriptomic and imaging technologies to chart the immune and epithelial heterogeneity throughout ovarian carcinogenesis. Using a collection of rare patient samples harboring precursor lesions, this project aims to:
- Characterize the immune contexture and its dysregulation during preneoplastic transformation.
- Build the first comprehensive single-nuclei RNA sequencing (snRNA-seq) and spatial transcriptomics atlas of these lesions.
- Identify signaling pathways and immune escape mechanisms that could serve as future therapeutic targets.
Current analyses include a pilot Xenium in situ spatial transcriptomics experiment and a snRNA-seq dataset to define major cell populations and their characteristics across stages of tumor development.

Internship mission:

The intern will join the ImmunoSTIC team to:
- Process and integrate snRNA-seq datasets using state-of-the-art bioinformatics pipelines.
- Design and implement an interactive application (R Shiny / Python-based) to visualize and explore snRNAseq results.
- Contribute to biological interpretation together with the rest of the team.

Candidate profile:

• Educational background: M2 or final-year engineering student in bioinformatics
• Required skills:
  • Strong experience with R or Python-based single-cell analysis (Seurat, Differential expression, Gene set enrichment).
  • Solid understanding of transcriptomic data handling and quality control.
  • Interest in immuno-oncology.

Internship details:

• Start date: early 2026 (flexible)
• Duration: 5–6 months
• Location: Cancer Research Center of Lyon (CRCL), 19 bld Jean XXIII, 69008 Lyon
• Supervision:
  Olivia LE SAUX, MD, PhD (Medical oncologist, head of the ImmunoSTIC team) Olivia.LESAUX@lyon.unicancer.fr
  Léa IKHLEF, PhD (Postdoctoral researcher) – lea.ikhlef@lyon.unicancer.fr