Mots-Clés

single-cell RNA-seq, CITE-seq, oncology, immunology

Description

Protein tyrosine kinases are involved in many physiological cellular processes and are also key players in tumor growth and dissemination and in immunity. This is the case for surface receptor tyrosine kinase 7 (PTK7) which is currently the target of drugs to treat solid tumors. Recently, PTK7 has also been found on the surface of immune cells such as dendritic cells (DCs) that infiltrate the tumor microenvironment and are essential in the anti-tumor response. However, no study to date has systematically explored PTK7 expression in the immune cell compartment and its potential impact in cancer.

In order to address this issue, we are conducting a study based on single cell sequencing: scRNA-seq and CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) which has the advantage of integrating single cell transcriptomic and protein data. We have preliminary results on Ptk7 expression in cells from subcutaneous lymph nodes (cLN). We are currently performing the same sequencing in hepatocarcinoma and melanoma models. The objective of this internship will be to build a mapping of Ptk7 expression in cLNs and different tumors from scRNA-seq data. Specifically the student will have to:

1. Control the quality of the sequencing data

2. Normalize the transcriptomic and protein datasets

3. Integrate these datasets to:

     - Identify cellular clusters within cLNs that express genes and or PTK7 protein

    - Perform function enrichment analysis of PTK7+ clusters