Mots-Clés

Cancer biology spatial transcriptomic spatial proteomic tumor heterogeneity

Description

Ingénieur.e d’étude – biologie spatiale multiplexée pour l’étude de l’hétérogénéité des tumeurs solides

Description

One position in bioinformatics & biostatistics (Ingénieur.e d’étude, 24 months, F/M) applied to spatial multiplexed cancer biology is available at IRCM (Institut de Recherche en Cancérologie de Montpellier) in the scope of the SIRIC Montpellier Cancer.

The context

SIRIC Montpellier Cancer brings together clinicians and researchers from the Montpellier Cancer Institute, Montpellier University Hospital and eight research institutes affiliated with Inserm, CNRS and Montpellier's two universities. Drawing on multidisciplinary research teams (clinical, biological, physical, mathematical, human and social sciences) and cutting-edge technological platforms, the SIRIC Montpellier Cancer implements integrated and innovative research around three central themes - radiotherapy, prevention and supportive care, onco-metabolism - with the ultimate aim of transforming clinical practices in cancerology.

In this context, the new recruit will join a collaborative effort between the Institut de Recherche en Cancérologie de Montpellier (IRCM), the Institut de Génomique Fonctionnelle (IGF) and the Institut de Génétique Moléculaire de Montpellier (IGMM) aiming at characterizing at the molecular and histological levels tumor collections of human or murine origins (with a focus on melanoma, lymphoma, gliomas and pancreatic cancers) using a combination of state-of-the-art multiplexed and spatially resolved technics interrogating the transcriptome (10X Genomics – Xenium, MERFISH technology) and/or the proteome (Fluidigm – Hyperion, Imaging Mass Cytometry technology). She / he will evolve in a stimulating network, working in close collaboration with other engineers specialized in bioinformatics & biostatistics also on-board in the SIRIC Montpellier Cancer program and located at IGMM and IGF, and will benefit from their respective expertise in state-of-the-art single-cell transcriptomics and epigenomics (scRNA-seq, ATAC-seq, ChIP-seq, Cut&Run). At IRCM, she/he will work at the interface between two laboratories headed by Dr Nathalie Bonnefoy (expert in the cancer immune microenvironment) and by Dr Laurent Le Cam (expert in cancer metabolism).

Location

Institut de Recherche en Cancérologie de Montpellier (www.ircm.fr)

Tasks and responsibilities 

The main mission is to establish bioinformatics and biostatistics workflows and standards to analyze spatial multiplexed data generated from these tumor collections under the supervision of a steering committee including experts in cancer biology and in computational biology. This includes :

• Setting up, maintaining and improving pipeline to process spatial transcriptomic data generated on murine and human melanoma, lymphoma, gliomas and pancreatic cancer samples. The equipment will be housed at IRCM in the context of the spatial biology platform.
• Data mining of single cell transcriptomic datasets to design custom probe panels to be used with 10X Genomics – Xenium technology.
• Analyzing matched spatial transcriptomics and proteomics datasets (generated using the Fluidigm – Hyperion technology, already present at IRCM) in collaboration with the Le Cam and the Bonnefoy laboratories and provide comprehensive biological portraying of the samples.
• Integrating the data into 3D reconstructions of the tumors generated from digitalized hematoxylin and eosin-stained tissue sections.
• Maintaining an active bibliographic survey and evaluating published tools and methods for spatial multiplexed data analysis and integration.
• Developing, if necessary, new analytical methods and tools, especially for cell segmentation, discovery of rare populations and studying cellular neighborhoods.

Duration

Fixed term for 24 months with option to extend further.

Starting date

To be discussed, preferably before the end of 2023.

Salary

Depends on the Inserm salary scale (from 2 409 € to 3139€ brut monthly depending on previous professional experiences)

Candidate profile

The candidate is expected to have a master's degree or an engineering degree in computational biology, biostatistics or applied mathematics. Experience with (single cell) next-generation sequencing technics is required. Experience with spatially resolved technics and / or image analysis would be highly appreciated. The candidate should be familiar with R and Python, should be autonomous and able to deal with several projects at once. Excellent oral and written English skills are necessary.

To apply

Applications (letter of motivation, CV, and names of two referees) should be sent to laurent.lecam@inserm.fr and pierre-francois.roux@inserm.fr