Pierre-François Roux

Pierre-François Roux
French Institute of Health and Medical Research | Inserm · Montpellier Cancer Research Institute IRCM

PhD - In silico Biologist & Epigenomicist
Researcher

About

42
Publications
10,511
Reads
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Citations
Introduction
Cell fate decisions entail organized changes in gene expression. A fundamental question in biology is how genes and regulatory regions are organized and coordinated for transcription regulation in these processes. Recent findings, including those of the Bischof team, have demonstrated that alterations in chromatin architecture play a decisive role in gene-regulation, but their importance in cell-fate decisions is still unclear. To close this important gap in our knowledge, we seek to explore the role of chromatin structure changes in cellular senescence, a cell-fate crucial for tumor suppression and aging.
Additional affiliations
August 2019 - February 2021
Johnson & Johnson
Position
  • Researcher
Description
  • Healthy skin development & biology
March 2015 - July 2019
Institut Pasteur International Network
Position
  • PostDoc Position
Description
  • The dynamic of the epigenomic landscape during cellular senescence
September 2011 - December 2014
Agrocampus Ouest
Position
  • PhD Student
Description
  • Detecting single nucleotide polymorphisms at the genome scale for the genetic dissection of complex traits and the characterization of editomes
Education
September 2011 - December 2014
Agrocampus Ouest
Field of study
  • Genomics / Computational biology
September 2010 - September 2011
Université de Rennes 1
Field of study
  • Biochemistry and Molecular Biology
September 2009 - September 2011
Agrocampus Ouest
Field of study
  • Biology

Publications

Publications (42)
Preprint
Full-text available
Although oncogene-induced senescence (OIS) is a potent tumor-suppressor mechanism, recent studies revealed that cells can escape from OIS with features of transformed cells. However, the mechanisms that promote OIS escape remain unclear, and evidence of post-senescent cells in human cancers is missing. Here, we unravel the regulatory mechanisms und...
Article
Full-text available
Even though its development starts early in utero, neonatal skin is still immature at birth relative to adult and undergoes a maturation process extending to the first years of life. It is now established that the stratum corneum is thinner and dryer, and that skin contains less natural moisturizing factors and lipids in newborns compared to childr...
Article
Full-text available
The advent of 16S RNA profiling and shotgun metagenomics has enabled a holistic approach to the study of the skin microbiome composition. Despite the interesting findings in this rapidly developing scientific area, the big question remains: What role does the microbiome play in skin physiology? To begin answering this question, we employed an integ...
Article
Full-text available
Epidermal Growth Factor inhibitors (EGFRi) used in oncology therapy modify the keratinocyte differentiation processes, impairing proper skin barrier formation and leading to Cutaneous Adverse Drug Reactions (CADR). To uncover the molecular signatures associated with CADRs, we applied phospho-proteomic and transcriptomic assays on Reconstructed Huma...
Article
Full-text available
Sumoylation is an essential posttranslational modification in eukaryotes that has emerged as an important pathway in oncogenic processes. Most human cancers display hyperactivated sumoylation and many cancer cells are remarkably sensitive to its inhibition, thus supporting application of chemical sumoylation inhibitors in cancer treatment. Here we...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Senescent cells affect many physiological and pathophysiological processes. While select genetic and epigenetic elements for senescence induction have been identified, the dynamics, epigenetic mechanisms and regulatory networks defining senes- cence competence, induction and maintenance remain poorly understood, precluding the deliberate therapeuti...
Research
Full-text available
In the version of this Article originally published, there were several errors in Fig. 8, Extended Data Fig. 1, and source data. Mean values for CCNA2 were inadvertently copied as s.e.m. values for CCNA2 in statistical source data for Extended Data Fig. 1m. In addition, the s.e.m. values for CCNE2 were inadvertently copied as mean values for CDKN2A...
Article
Full-text available
In this Article, the pCaMIN construct consisted of ‘mouse MYC and mouse NrasG12V’ instead of ‘mouse Myc and human NRASG12V; and the pCAMIA construct consisted of ‘mouse Myc and human AKT1’ instead of ‘mouse Myc and Akt1’ this has been corrected online.
Article
Full-text available
Primary liver cancer represents a major health problem. It comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), which differ markedly with regards to their morphology, metastatic potential and responses to therapy. However, the regulatory molecules and tissue context that commit transformed hepatic cells towards HCC o...
Article
Full-text available
Background: Because the cost of cereals is unstable and represents a large part of production charges for meat-type chicken, there is an urge to formulate alternative diets from more cost-effective feedstuff. We have recently shown that meat-type chicken source is prone to adapt to dietary starch substitution with fat and fiber. The aim of this st...
Article
Full-text available
Culture medium of mesenchymal stromal cells (MSCs) is usually supplemented with either human platelet lysate (HPL) or fetal calf serum (FCS). Many studies have demonstrated that proliferation and cellular morphology are affected by these supplements - it is therefore important to determine if they favor outgrowth of different subpopulations and the...
Article
Cellular senescence is a fundamental cell fate, important both in physiological and pathophysiological processes. This SnapShot focuses on the role of cellular senescence in health, disease, and aging.
Article
Cellular senescence is a fundamental cell fate, playing important physiological and pathophysiological roles. This SnapShot focuses on major signaling pathways and transcriptional control mechanisms that consolidate the senescence phenotype.
Article
Full-text available
The senescence of mammalian cells is characterized by a proliferative arrest in response to stress and the expression of an inflammatory phenotype. Here we show that histone H2A.J, a poorly studied H2A variant found only in mammals, accumulates in human fibroblasts in senescence with persistent DNA damage. H2A.J also accumulates in mice with aging...
Conference Paper
Cellular senescence is currently viewed as a cell fate decision arising from a variety of (epi)genomic stresses and developmental cues, and is known to play crucial roles as an anti-tumour and in age-related pathologies. However, our present view of senescence is a rather static one that does not describe the dynamic genomic regulation that orchest...
Article
Global transcriptome analysis of chicken whole blood to discover biomarkers of different phenotypes or physiological disorders has never been investigated so far. Whole blood provides significant advantages, allowing large scale and non-invasive sampling. However, generation of gene expression data from the blood of non-mammalian species remains a...
Article
Full-text available
RNA editing is a post-transcriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, raising contradictory conclusion...
Conference Paper
Cellular senescence is currently viewed as a cell fate decision arising from a variety of (epi)genomic stresses and developmental cues, and is known to play crucial roles as an anti-­tumour and in age-­related pathologies. However, our present view of senescence is a rather static one that does not describe the dynamic genomic regulation that orche...
Conference Paper
Full-text available
Cellular senescence is currently viewed as a cell fate decision arising from a variety of (epi)genomic stresses and developmental cues, and is known to play crucial roles as an anti-tumour and in age-related pathologies. However, our present view of senescence is a rather static one that does not describe the transcription factor (TF) networks unde...
Article
Full-text available
Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annot...
Article
Full-text available
RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I)...
Conference Paper
Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size ofQTLs, and most of them were identified thanks to functional links already known with the targeted phenotype.Here we propose to combine selection signature detection, SNP annotation, and expression analyses to identifycausal genes underly...
Conference Paper
The increasing use of unconventional feedstuffs in broiler's diets results in the substitution of starch by lipids as the mainenergy source. To evaluate the responses of genetically fat or lean broilers to such diets, male chickens were fed during 6weeks isoenergetic and isoproteic diets with high lipid (8 %), high fiber content (HL) or low lipid (...
Article
Full-text available
Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size of QTLs, and most of them were identified thanks to functional links already known with the targeted phenotype. Here we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify po...
Thesis
Full-text available
Démocratisées à la fin des années 2000, les technologies de séquençage haut-débit (NGS) ont progressivement révolutionné les domaines de la génétique et de la transcriptomique. Alors qu’historiquement, les premières études basées sur ces technologies s’attachaient à la création de séquences de référence pour des espèces variées, la diminution des c...
Article
The number of polymorphisms identified with next-generation sequencing approaches depends directly on the sequencing depth and therefore on the experimental cost. Although higher levels of depth ensure more sensitive and more specific SNP calls, economic constraints limit the increase of depth for whole-genome resequencing (WGS). For this reason, c...
Article
Full-text available
In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal...
Preprint
Full-text available
RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-...
Article
Full-text available
Early in life, cystic fibrosis (CF) patients are infected with microorganisms. The role of macrophages has largely been underestimated in literature, whereas the focus being mostly on neutrophils and epithelial cells. Macrophages may however play a significant role in the initiating stages of this disease, via an inability to act as a suppressor ce...
Article
Full-text available
We report an analysis of allele specific expression (ASE) and parent-of-origin expression in adult mouse liver using next generation sequencing (RNA-Seq) of reciprocal crosses of heterozygous F1 mice from the parental strains C57BL/6J and DBA/2J. We found a 60% overlap between genes exhibiting ASE and putative cis-acting expression quantitative tra...
Conference Paper
Les nouvelles technologies de séquençage appelées « NGS » offrent aujourd’hui la possibilité d’analyser les génomes dans leur intégralité. Dans ce contexte nouveau, cette étude vise à caractériser à l’échelle du génome les polymorphismes de lignées expérimentales INRA de poulets de chair et poules de ponte, divergentes respectivement pour le poids...

Questions

Question (1)
Question
We are currently having a hard time defining precisely molarities of our MNase-ChIP-seq libraries before sequencing using the rather classical combination between 2100 Bioanalyzer (for average fragment size estimation) and Qubit or qPCR (for quantification), and some of our runs failed due to lane saturation.
The problem we have is related to the fact that, in this type of libraries, the distribution of fragment size is rather broad. Due to cell number limitations and other biological considerations, we can't go through gel size selection step.
Has anyone any suggestion ?
Thans a lot. 

Projects

Projects (2)
Project
Decipher gene regulatory networks during senescence