A5002879400- Cancer Genomics and Diagnostics
- Colorectal Cancer Treatments and Studies
- Genetic factors in colorectal cancer
- Pancreatic and Hepatic Oncology Research
- Radiomics and Machine Learning in Medical Imaging
- Renal cell carcinoma treatment
- Gastric Cancer Management and Outcomes
- Single-cell and spatial transcriptomics
- Cancer Cells and Metastasis
- Plant Molecular Biology Research
- Molecular Biology Techniques and Applications
- Cancer Immunotherapy and Biomarkers
- Epigenetics and DNA Methylation
- Genetically Modified Organisms Research
- Cancer Research and Treatments
- Ferroptosis and cancer prognosis
- Cancer-related molecular mechanisms research
- Microtubule and mitosis dynamics
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Cancer, Lipids, and Metabolism
- Immune cells in cancer
- Prostate Cancer Diagnosis and Treatment
- Gene expression and cancer classification
- Plant Reproductive Biology
- Prostate Cancer Treatment and Research
La Ligue Contre le Cancer
2012-2023
IntegraGen (France)
2022-2023
Institut Gustave Roussy
2013
Département Santé des Plantes et Environnement
2009-2012
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2010
Université de Picardie Jules Verne
2004
Background Colon cancer (CC) pathological staging fails to accurately predict recurrence, and date, no gene expression signature has proven reliable for prognosis stratification in clinical practice, perhaps because CC is a heterogeneous disease. The aim of this study was establish comprehensive molecular classification based on mRNA profile analyses. Methods Findings Fresh-frozen primary tumor samples from large multicenter cohort 750 patients with stage I IV who underwent surgery between...
Intrahepatic cholangiocarcinoma (ICC) is a severe malignant tumor in which the standard therapies are mostly ineffective. The biological significance of desmoplastic microenvironment (TME) ICC has been stressed but was insufficiently taken into account search for classifications adapted to clinical trial design. We investigated heterogeneous stroma composition and built TME-based classification tumors that detects potentially targetable subtypes.We established bulk gene expression profiles...
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics PDAC. Here we perform multi-parametric integrative analyses chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation epigenomic landscapes for PDAC which can predict their relative aggressiveness...
Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC) either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively). Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These uncovered specific alterations DNA...
Malignant pleural mesothelioma (MPM) is recognized as heterogeneous based both on histology and molecular profiling. Histology addresses inter-tumor intra-tumor heterogeneity in MPM describes three major types: epithelioid, sarcomatoid biphasic, a combination of the former two types. Molecular profiling studies have not addressed to date. Here, we use deconvolution approach show that gradients shed new light MPM, leading reconsideration classifications. We each tumor can be decomposed...
Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify or in human tissue samples from transcriptomic data, few are available mouse studies. We introduce murine Microenvironment Cell Population counter (mMCP-counter), a method based on highly specific markers that accurately 16 cell populations. validated mMCP-counter with flow cytometry data showed outperforms existing methods. scores...
Chondrosarcomas are primary cancers of cartilaginous tissue with highly contrasting prognoses. These tumors defined by recurrent mutations in the IDH genes and other genetic alterations including inactivation CDKN2A COL2A1; however, these have no clinical value. Here we use multi-omics molecular profiles from a series cartilage find an mRNA classification that identifies two subtypes chondrosarcomas balance tumor differentiation cell cycle activation. The microRNA reveals importance loss...
Two tumor (Classical/Basal) and stroma (Inactive/active) subtypes of Pancreatic adenocarcinoma (PDAC) with prognostic theragnostic implications have been described. These molecular were defined by RNAseq, a costly technique sensitive to sample quality cellularity, not used in routine practice. To allow rapid PDAC subtyping study heterogeneity, we develop PACpAInt, multi-step deep learning model. PACpAInt is trained on multicentric cohort (n = 202) validated 4 independent cohorts including...
•ChallengES tumor mutation burden (TMB) and MSIsensor for predicting response to immunotherapy in MSI mCRC.•Demonstration that misdiagnoses lead a false ability of TMB predict ICI resistance mCRC.•Identification validation DNA RNA signatures predictive these patients with mCRC MSI.•Evidence fibrosis signature associated functional mCRC. BackgroundMismatch repair-deficient (dMMR) tumors displaying microsatellite instability (MSI) represent paradigm the success immune checkpoint inhibitor...
Plant growth and development are sensitive to light. Light-responsive DNA-binding transcription factors have been functionally identified. However, how initiation complex integrates light signals from enhancer-bound remains unknown. In this work, we characterized mutations within the Arabidopsis HAF2 gene encoding TATA-binding protein-associated factor TAF1 (or TAF(II)250). The mutation of induced decreases on chlorophyll accumulation, light-induced mRNA levels, promoter activity. Genetic...
A significant gap in pancreatic ductal adenocarcinoma (PDAC) patient's care is the lack of molecular parameters characterizing tumours and allowing a personalized treatment. Patient-derived xenografts (PDX) were obtained from 76 consecutive PDAC classified according to their histology into five groups. gradient (PAMG) was constructed PDX transcriptomes recapitulating histological groups along continuous gradient. The prognostic predictive value for PMAG evaluated in: i/ two independent...
•An RNA signature of gemcitabine-sensitivity is developed from in vitro and vivo models pancreatic cancer.•The resulting GemPred identifies a subgroup patients who are sensitive to adjuvant gemcitabine.•The predictive value validated two cohorts on both OS disease-free survival. BackgroundChemotherapy the only systemic treatment approved for ductal adenocarcinoma (PDAC), with selection regimens based patients' performance status expected efficacy. The establishment potent stratification...
Abstract Purpose: The consensus molecular subtypes (CMS) represent a significant advance in the understanding of intertumor heterogeneity colon cancer. Intratumor (ITH) is new frontier for refining prognostication and treatment resistance. This study aims at deciphering transcriptomic ITH cancer its potential prognostic implications. Experimental Design: We deconvoluted profiles 1,779 tumors from PETACC8 trial 155 cell lines as weighted sums four CMSs, using Weighted In Silico Pathology...
Trihelix DNA‐binding factors (or GT factors) bind to elements found in the promoters of many plant genes. Although binding specificity and transcriptional activity some members (e.g. GT‐1 GT‐2) have been studied, regulatory function this family transcription remains largely unknown. In work, we characterised a new factor, namely GT‐3a, closely related member, GT‐3b. We show that (1) they can form either homo‐ or heterodimers but do not interact with GT‐1; (2) are predominantly expressed...
Abstract Aims The only two procedures for surgical treatment of ultra‐low rectal cancer without a permanent abdominal stoma are the intersphincteric resection (ISR) and abdominoperineal (APR) plus perineal pseudocontinent colostomy (PCC). This study compared functional results quality life following these techniques. Methods Between January 1995 December 2011, 36 patients had undergone an ISR (n = 14) or PPC 22) very low cancer. Cleveland Clinica Florida (Wexner) fecal incontinence...
Metastatic colorectal cancers (mCRC) harboring microsatellite instability (MSI) are sensitive to immune checkpoint inhibitors (ICIs), but the mechanisms of resistance ICIs remain unclear. Dissociated responses in patients with ICI-treated cancer suggest that certain organs may serve as sanctuary sites due tumor microenvironment. This case series describes five MSI mCRC disease progression limited adrenal glands. At ICI initiation, three were free metastasis Four experienced objective...
3509 Background: The molecular subtyping of colon cancers (CC) has been the subject several recent publications, leading to an international consensus. clinical relevance these classifications remains be evaluated on large prospective patient cohorts using a tool that can widely used formalin-fixed paraffin-embedded (FFPE) samples. Methods: We aimed evaluate two systems, CMS (Guinney et al. 2015) and CCMST (Marisa 2013), PETACC-8 cohort, randomized phase III trial comparing adjuvant FOLFOX...
Background & AimsRecent studies have shown that cancers arise as a result of the positive selection driver somatic events in tumor DNA, with negative playing only minor role, if any. However, these investigations were concerned alterations at nonrepetitive sequences and did not take into account mutations repetitive very high pathophysiological relevance tumors showing microsatellite instability (MSI) resulting from mismatch repair deficiency investigated present study.MethodsWe performed...
BioTechniquesVol. 52, No. 3 Application Forum - Sponsored PaperOpen AccessHomogenization of cartilage tumors to extract total RNA microarray and sequencing analysis using Precellys bead-beating technologyGuillaume Banneau, Mira Ayadi, Lucile Armenoult & Esmeralda CarvalhoGuillaume BanneauQuality Control Platform Nucleic Acids, Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, 1 avenue C, Vellefaux, 75475 Paris Cedex 1, France, AyadiQuality ArmenoultQuality...