Mots-Clés
Single-cell transcriptomics
Spatial transcriptomics
Tumour-associated macrophages
Description
Project Description :
New therapies that promote anti-tumor immunity have been developed over the last decade. Most of these immunomodulatory approaches have focused on enhancing T-cell responses, either by targeting inhibitory pathways with immune checkpoint inhibitors, or by targeting activating pathways, as with chimeric antigen receptor T cells or bispecific antibodies. Although these therapies have led to unprecedented successes, only a minority of patients with cancer benefit from these treatments, highlighting the need to identify new targets that could be exploited in the next generation of immunotherapy. Harnessing tumor-associated myeloid cells is emerging as a promising therapeutic approach to improving the efficacy of cancer treatment and overcoming resistance to current immunotherapies targeting T cells. In particular, harnessing dendritic cell (DC) activation, or suppressing tumour-associated macrophages (TAMs) in cancer patients has been shown to synergize with current immunotherapy approaches.
We propose here to characterize DC and TAM states associated with the activation or inhibition of anti-tumour immunity and identify molecular targets to modulate their functions as innovative anti-cancer treatments.
Proposed approach :
Our projects are based on cutting-edge technologies. We aim at characterizing the transcriptomic profile of DC and TAM states in tissue from tumors in preclinical models and patients with cancer conditions, using high dimensional single cell and spatial multiomics analysis, including single cell and spatial transcriptomics, imaging mass cytometry and spectral flow cytometry.
Environnement :
The position is located at the CIML, an internationally renowned immunology center on the Luminy university campus, south of Marseille. You will work as part of a multidisciplinary team of experts in bioinformatics and immunologists. Your main activity will be the Lawrence team. The CB2M group (Computational Biology, Biostatistics & Modeling), which organizes and federates CIML bioinformaticians (~20 people), will co-supervise your activity. At CB2M, you will benefit from existing expertise in single cell & spatial transcriptomics analysis methods, and in the tools used to ensure reproducibility of results (Open Science / FAIR data). In a dedicated room, you will be surrounded daily by the majority of CIML’s bioinformaticians, and will play an active part in the dynamism of this community.
Main activities
• Designing bioinformatics analysis pipelines for processing transcriptomics data.
• Testing, implementing and deploying bioinformatics methods for single-cell RNA-seq and spatial transcriptomic data analysis (including cell segmentation, reference-based deconvolution and annotation, analysis of differentially expressed genes…)
• Reporting results in clear reports and presentations
Side activities
• Monitoring technological developments in the field of bioinformatics analysis of spatial transcriptomics data.
• Participating actively in team meetings.
• Participating in meetings and exchanges with the community of bioinformaticians at CIML and in the Marseilles region (BIOTIC network).
Skills
• Programming skills in R and PYTHON
• Proficiency in high-throughput sequencing data analysis tools (Illumina, Oxford Nanopore Technologies), preferably in transcriptomics (RNA-seq, single-cell RNA-seq).
• Practical understanding of different spatial transcriptomics methods.
• Practical understanding of mathematical methods for multidimensional data analysis.
• Fluency in written and spoken scientific English.
• Knowledge of Unix/Linux systems, Shell.
Aptitudes
• Willingness to evolve and learn
• Interest in methodological issues in computational biology.
• Rigor, organizational skills and ability to summarize technical and scientific results.
• Good communication skills with bioinformaticians and biologists.
• Good teamwork skills.
Working Conditions
• Work is performed in an office setting.
• This position will be based on our laboratory in the Center for Immunology of Marseille Luminy. We are seeking talented and passionate people to join our team. The desired start date for this position is July 2025.
The salary is of 2138.19 euros groos per month (ajusted with experience) This is a 2-year position with the possibility of extension based on performance.