ONCOBIOMICS
Principal investigator: MATHIAS CHAMAILLARD
Integrating the intra-tumoral microbiome to promote understanding on tumor plasticity
The partners of Oncobiomics proposed to study the tumoral microbiome have a source of cancer heterogeneity in colon cancer. Their aim is to integrate the intra-tumoral microbiome heterogeneity in order to promote understanding on tumor plasticity and offers new therapeutic options.
Works that led up to the project
Some past studies from the network led up to this project. First, they found a high load of bacteria in colon cancer tumors when compared to non tumoral mucosa and healthy patient mucosa. Moreover, this load is linked to tumor stage. With vivo mice xenograft models, they identified that pks + bacteria induce have a tumor-promoting activity, inducing bigger tumors than other bacterial stems.
Applying digital microbiology to tumor plasticity
First, the network performs a strong characterization of a cohort of 100 colorectal resections and their 100 no tumor adjacent tissue. Samples include tumors from Grade I to grade IV. Characterization is performed at different levels:
- Bacterial level by sequencing of 16s and by topographic analysis of bacterial infiltrate
- Genomical level by exome sequencing
- Transcriptomical
- Inflammation level by Immunoscore-like analysis
Mathematic modeling
With the data gathered, the network will mathematically model the functional dependencies of microbiome and tumoral cell in order to propose new drug development ideas. New therapeutics targets will be validated with in vivo, in vitro and ex vivo models.
Oncobiomics highlights a new alternative to the usual thinking about cancer heterogeneity. Such characterization of colon cancer microbiome heterogeneity and its integration with clinical and genomic aspect of the tumor will promote a new understanding we tumor plasticity and new ways of therapeutic solutions.
- Lab name: Center of Bioinformatics, Biostatistics and Integrative Biology
- Website: https://research.pasteur.fr/en/team/evolutionary-bioinformatics/
- Affiliations: Institut Pasteur
- Address: 25-28 Rue du Dr Roux, 75015 Paris
- Contact: olivier.gascuel@pasteur.fr
LAST PUBLICATIONS:
- Drug resistance mutations in HIV: new bioinformatics approaches and challenges
Luc Blassel - Correction to 'Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows'
Frédéric Lemoine - Measuring Phylogenetic Information of Incomplete Sequence Data
Tae-Kun Seo - Using machine learning and big data to explore the drug resistance landscape in HIV
Luc Blassel
- Lab name: Intestinal epithelial cell proliferation in physiology and cancer
- Website: https://www.institutcochin.fr/departments/drc/team-perret/group-b.-romagnolo
- Affiliations: Institut Cochin, Inserm U1016
- Address: 22 Rue Mechain, 75014 Paris
- Contact: beatrice.romagnolo@inserm.fr
LAST PUBLICATIONS:
- Cooperation Between the NRF2 Pathway and Oncogenic β-catenin During HCC Tumorigenesis
Mathilde Savall - NOTUM from Apc-mutant cells biases clonal competition to initiate cancer
Dustin J Flanagan - Author Correction: Lkb1 suppresses amino acid-driven gluconeogenesis in the liver
Pierre-Alexandre Just - Lkb1 suppresses amino acid-driven gluconeogenesis in the liver
Pierre-Alexandre Just
- Lab name: Biomics
- Website: https://research.pasteur.fr/en/member/sean-kennedy/
- Affiliations: Institut Pasteur
- Address: 25-28 Rue du Dr Roux, 75015 Paris
- Contact: sean.kennedy@pasteur.fr
LAST PUBLICATIONS:
- Complete Genome and Methylome Analysis of the Box-Shaped Halophilic Archaeon Haloarcula sinaiiensis ATCC 33800
Alexey Fomenkov - Protein supplementation during an energy-restricted diet induces visceral fat loss and gut microbiota amino acid metabolism activation: a randomized trial
Pierre Bel Lassen - Dynamics of extended-spectrum beta-lactamase-producing <em>Enterobacterales</em> colonization in long-term carriers following travel abroad
Laurence Armand-Lefèvre - Quantitative analysis of workplace morale in academic librarians and the impact of direct supervisors on workplace morale
Sean P Kennedy
- Lab name: Center of Bioinformatics, Biostatistics and Integrative Biology
- Website: https://research.pasteur.fr/en/team/evolutionary-bioinformatics/
- Affiliations: Institut Pasteur
- Address: 25-28 Rue du Dr Roux, 75015 Paris
- Contact: christophe.malabat@pasteur.fr
LAST PUBLICATIONS:
- Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast
Laurence Decourty - SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
Stevenn Volant - Antisense transcriptional interference mediates condition-specific gene repression in budding yeast
Alicia Nevers - Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen <em>Leptospira interrogans</em>
Anna Zhukova
- Lab name: Nods-like receptors in infection and immunity
- Website: http://www.ciil.fr/research-teams/nods-like-receptors-in-infection-and-immunity/
- Affiliations: Institut Pasteur, Inserm U1019, CNRS UMR8204, Université́ de Lille
- Address: 1 Rue du Professeur Calmette, 59000 Lille
- Contact: mathias.chamaillard@inserm.fr
LAST PUBLICATIONS:
- Virulent Bacteria as Inflammatory and Immune Co-Factor in Colon Carcinogenesis: Evidence From Two Monozygotic Patients and Validation in CRC Patient and Healthy Cohorts
Iradj Sobhani - Role of NLRs in the Regulation of Type I Interferon Signaling, Host Defense and Tolerance to Inflammation
Ioannis Kienes - NOD1 sensing of house dust mite-derived microbiota promotes allergic experimental asthma
Saliha Ait Yahia - The role of the gut microbiome on radiation therapy efficacy and gastrointestinal complications: A systematic review
Marion Tonneau
- Lab name: Microbes Intestin Inflammation et susceptibilité́ de l’hôte
- Website: http://www.u-clermont1.fr/m2ish-old.html
- Affiliations: Inserm UMR 1071, Université d’Auvergne
- Address: 28, place Henri-Dunant 63001 Clermont-Ferrand
- Contact: rbonnet@chu-clermontferrand.fr
LAST PUBLICATIONS:
- Increased risk of near term global warming due to a recent AMOC weakening
Rémy Bonnet - Host Colonization as a Major Evolutionary Force Favoring the Diversity and the Emergence of the Worldwide Multidrug-Resistant <em>Escherichia coli</em> ST131
Richard Bonnet - Successful Dissemination of Plasmid-Mediated Extended-Spectrum β-Lactamases in Enterobacterales over Humans to Wild Fauna
Racha Beyrouthy - Yersiniabactin Siderophore of Crohn's Disease-Associated Adherent-Invasive <em>Escherichia coli</em> Is Involved in Autophagy Activation in Host Cells
Guillaume Dalmasso
- Lab name: Stroma, Inflammation and Tissue Repair
- Website: https://research.pasteur.fr/en/team/group-lucie-peduto/
- Affiliations: Institut Pasteur, Inserm U1124
- Address: 25-28 Rue du Dr Roux, 75015 Paris
- Contact: pedutol@pasteur.fr
LAST PUBLICATIONS:
- T cells regulate lymph node-resident ILC populations in a tissue and subset-specific way
Priscillia Bresler - Mesenchymal perivascular cells in immunity and disease
Adam Benabid - Genetic screens reveal mechanisms for the transcriptional regulation of tissue-specific genes in normal cells and tumors
Ikrame Naciri - Peyer's patch myeloid cells infection by <em>Listeria</em> signals through gp38<sup>+</sup> stromal cells and locks intestinal villus invasion
Olivier Disson
- Lab name: Pathogénie Microbienne Moléculaire
- Website: https://research.pasteur.fr/en/team/molecular-microbial-pathogenesis/
- Affiliations: Institut Pasteur, Inserm U1202
- Address: 25-28 Rue du Dr Roux, 75015 Paris
- Contact: philippe.sansonetti@pasteur.fr
LAST PUBLICATIONS:
- Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition
K E Huus - Analyzing Oxidative Stress in Murine Intestinal Organoids using Reactive Oxygen Species-Sensitive Fluorogenic Probe
Aline Stedman - Cytokine receptor cluster size impacts its endocytosis and signaling
Laura Salavessa - Factors Associated with Stunted Growth in Children Under Five Years in Antananarivo, Madagascar and Bangui, Central African Republic
Pascale Vonaesch
- Lab name: Mucins, epithelial differentiation and carcinogenesis
- Website: http://crjpa.frneurosciences/mucines-differenciation-et-cancerogenese-epitheliales?lang=en
- Affiliations: Inserm UMR-S1172, JPARC
- Address: Bâtiment Biserte 1, place de Verdun 59045 Lille Cédex
- Contact: isabelle.vanseuningen@inserm.fr
LAST PUBLICATIONS:
- The EGF Domains of MUC4 Oncomucin Mediate HER2 Binding Affinity and Promote Pancreatic Cancer Cell Tumorigenesis
Nicolas Stoup - Loss of Polycomb Repressive Complex 2 Function Alters Digestive Organ Homeostasis and Neuronal Differentiation in Zebrafish
Ludivine Raby - A new pancreatic adenocarcinoma-derived organoid model of acquired chemoresistance to FOLFIRINOX: First insight of the underlying mechanisms
Elsa Hadj Bachir - Analysis of the proximal promoter of the human colon-specific B4GALNT2 (Sd<sup>a</sup> synthase) gene: B4GALNT2 is transcriptionally regulated by ETS1
Cindy Wavelet-Vermuse
This French program is organized by ITMO Cancer, in collaboration with ITMO BCDE (Cell Biology, Development and Evolution) and ITMO Technologies for Health of the National Alliance for Life Sciences and Health (AVIESAN) with the National Cancer Institute (INCA) and Inserm within the framework of the Cancer Plan. Operational management is entrusted to Inserm.
It was launch in order to develop a critical mass of resources and skills in order to conduct interdisciplinary research projects in the field of functional heterogeneity of cellular tumor relations in their ecosystem: the "HTE Program".
Initiation of HTE Program
