Easy as ATCG

Pierre-François Roux

PhD in biology

Inserm - IRCM - Montpellier

The advent of high-throughput approaches and integrative -omics strategies has profoundly transformed the way biological questions are addressed. Throughout my various professional experiences, I have developed ambitious integrative biology projects aimed at understanding the genetic and molecular mechanisms involved in metabolism regulation, its influence on the skin microbiome, and its dynamics during cellular senescence. These projects have allowed me to gain expertise in molecular and cellular biology, as well as in computational biology, including bioinformatics, data integration, and systems biology. This rare combination of experimental and computational expertise has enabled me to develop a comprehensive understanding of metabolism, epigenetics, and systems biology applied to oncology and aging. Moving forward, I aim to further expand these complementary skills and apply them to address pathophysiological questions at the intersection of metabolism, epigenetics, and aging.

I am currently working at the Montpellier Cancer Research Institute as a postdoctoral fellow, in the unit Molecular Oncogenesis headed by Laurent Le Cam.

Interests

Functional genomics
Genetics
Epigenomics
Metabolism
Systems biology
Cellular senescence
Cancer biology

Education

PhD in Genetics and Genomics, 2014

Agrocampus Ouest, Rennes, France
MEng in Agronomical Science, 2011

Agrocampus Ouest, Rennes, France
MSc in Cell and Molecular Biology, 2011

Université Rennes 1, Rennes, France
MSc in Environment and Oceanology, 2009

Université des Sciences et Technologies, Lille, France

Hobbies

Photography
Drawing
Scuba diving
Botany
Traveling

CNU

CNU 64: biochemistry and molecular biology
CNU 65: cell biology

Publications

M. Di Michele, A. Attina, P.F. Roux*, I. Tabet, S. Laguesse, J.Florido, M. Houdeville, A. Choquet, B. Encislai, G. Arena, C. De Blasio, O. Wendling, F.X. Frenois, L. Papon, L. Stuani, M. Fuentes, C. Jahannault Talignani, M. Rousseau, J. Guégan, Y. Buscail, P. Dupré, H.A. Michaud, G. Rodier, F. Bellvert, H. Kulyk, C. Ferraro Peyret, H. Mathieu, P. Close, F. Rapino, C. Chaveroux, N. Pirot, L. Rubio, A. Torro, T. Sorg, F. Ango, C. Hirtz, V. Compan, E. Lebigot, A. Legati, D. Ghezzi, L. Nguyen, A. David, C. Sardet, M. Lacroix, L. Le Cam. E4F1 coordinates pyruvate metabolism and the activity of the elongator complex to ensure translation fidelity during brain development. In Nature Communications, 2025.

T. Sata, J. Nikolovski, R. Gould, I. Lboukili, P.F. Roux, G. Al-Ghalith, J. Orie, R. Insel, G. N. Stamatas. Skin surface biomarkers are associated with future development of atopic dermatitis in children with family history of allergic disease. In Skin Research & Technology, 2023.

G. N. Stamatas, P.F. Roux*, E. Boireau-Adamezyk, I. Lboukili, T. Oddos. Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome. In Experimental Dermatology, 2023.

R. Y. Martinez-Zamudio, A. Stefa, J. de Freitas, T. Vasilopoulos, M. Simpson, G. Doré, P.F. Roux, M. A. Galan, R. J. Chokshi, O. Bischof, U. Herbig. Escape from oncogene-induced senescence is controlled by POU2F2 and memorized by chromatin scars. In Cell Genomics, 2023.

A. Guerrero, A. Innes, P.F. Roux, S. Buisman, J. Jung, L. Ortet, V. Moiseeva, V. Wagner, L. Robinson, A. Ausema, A. Potapova, E. Perdiguero, E. Weersing, M. Aarts, N. Martin, T. Wuestefeld, P. Muñoz-Cánoves, G. de Haan, O. Bischof, J. Gil. 3-Deazaadenosine alleviates senescence to promote cellular fitness and cell therapy efficiency in mice. In Nature Aging, 2022.

C. Mangez, P.F. Roux, G. Stamatas, T. Oddos, C. Brun. An integrative multi-omic analysis reveals a major metabolic rewiring between baby foreskin keratinocytes and adult female abdominal keratinocytes. In Experimental Dermatology, 2021.

P.F. Roux, T. Oddos, G. Stamatas. Deciphering the role of skin surface microbiome on skin health: an integrative multi-omics approach reveals three distinct microbial / metabolic clusters. In Journal of Investigative Biology, 2021.

T. Ondet, P.F. Roux, M. Monshouwer, G. Stamatas. Unlocking the mechanisms of Cutaneous Adverse Drug Reactions: Activation of the PI3K/AKT pathway by EGFR inhibitors triggers keratinocyte differentiation and polarization of epidermal immune responses. In JID Innovations, 2021.

R. Martinez, P.F. Roux*, J. de Freitas, L. Robinson, G. Doré, B. Sun, D. Belenki, M. Milanovic, U. Herbig, C. Schmitt, J. Gil, O. Bischof. AP-1 imprints a reversible transcriptional programme of senescent cells. In Nature Cell Biology, 2020.

I. López, E. Chalatsi, S. Ellenbroek, A. Andrieux, P.F. Roux, J. Cerapio, G. Jouvion, J. van Rheenen, J. Seeler, A. Dejean. An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. In Oncogene, 2020.

M. Seehawer, F. Heinzmann, L. D’Artista, P.F. Roux, L. Hoenicke, H. Dang, S. Klotz, L. Robinson, G. Doré, N. Rozenblum, T.W. Kang, R. Chawla, T. Buch, M. Vucur, M. Roth, J. Zuber, T.Luedde, B. Sipos, T. Longerich, M. Heikenwälder, X.W. Wang, O. Bischof, L. Zender. Necroptosis microenvironment directs lineage commitment in liver cancer. In Nature, 2018.

C. Désert, E. Baeza, M. Aite, M. Boutin, A. Le Cam, J. Montfort, M. Houée-Bigot, Y. Blum, P.F. Roux, C. Hennequet-Antier, C. Berri, S. Metayer-Coustard, A. Collin, S. Allais, E. Le Bihan, D. Causeur, F. Gondret, M. Duclos, S. Lagarrigue. Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis. In BMC Genomics, 2018.

R. Martínez-Zamudio, L. Robinson, P.F. Roux, O. Bischof. Snapshot: cellular senescence in pathophysiology. In Cell, 2017.

R. Martínez-Zamudio, L. Robinson, P.F. Roux, O. Bischof. Snapshot: cellular senescence pathways. In Cell, 2017.

E. Fernandez-Rebollo, B. Mentrup, R. Ebert, J. Franzen, G. Abagnale, T. Sieben, A. Ostrowska, P. Hoffmann, P.F. Roux, B. Rath, M. Goodhardt, J.M. Lemaitre, O. Bischof, F. Jakob, W. Wagner. Human platelet lysate versus fetal calf serum: these supplements do not select for different mesenchymal stromal sells. In Scientific Reports, 2017.

L. Frésard, S. Leroux, P.F. Roux, C. Klopp, D. Esquerré, P. Dehais, A. Djari, D. Gourichon, S. Lagarrigue, F. Pitel. Genome-wide characterization of RNA editing in chicken embryos reveals common features among vertebrates. In PLoS One, 2017.

K. Contrepois, C. Coudereau, B.A. Benayoun, N. Schuler, P.F. Roux, O. Bischof, R. Courbeyrette, C. Carvalho, J.Y. Thuret, Z. Ma, C. Derbois, M.C. Nevers, H. Volland, C.E. Redon, W.M. Bonner, J.F. Deleuze, C. Wiel, D. Bernard, M.P. Snyder, C.E. Rübe, R. Olaso, F. Fenaille, C. Mann. Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression. In Nature Communications, 2017.

C. Désert, E. Merlot, T. Zerjal, B. Bed’hom, S. Härtle, A. Le Cam, P.F. Roux, E. Baeza, F. Gondret, M.J. Duclos, S. Lagarrigue. Transcriptomes of whole blood and PBMC in chicken. In Comparative Biochemistry and Physiology, 2016.

P.F. Roux, S. Marthey, A. Djari, M. Moroldo, D. Esquerré, J. Estellé, C. Klopp, S. Lagarrigue, O. Demeure. Comparison of whole-genome (13X) and capture (87X) resequencing methods for SNP and genotype callings. In Animal Genetics, 2015.

P.F. Roux, L. Frésard, M. Boutin, S. Leroux, C. Klopp, A. Djari, D. Esquerré, P. Martin, T. Zerjal, D. Gourichon, F. Pitel, S. Lagarrigue. The extent of mRNA editing is limited in chicken liver and adipose, but impacted by tissular context, genotype, age and feeding as exemplified with a conserved edited site in COG3. In Genes Genomes Genetics, 2015.

J. Smith, D.W. Burt, the Avian RNAseq Consortium. Third report on chicken genes and chromosomes. In Cytogenetic and Genome Research, 2015.

P.F. Roux, S. Boitard, Y. Blum, B. Parks, A. Montagner, E. Mouisel, A. Djari, D. Esquerré, C. Désert, M. Boutin, S. Leroux, F. Lecerf, E. Le Bihan - Duval, C. Klopp, B. Servin, F. Pitel, M. Duclos, H. Guillou, A.J. Lusis, O. Demeure, S. Lagarrigue. Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation. In Genes Genomes Genetics, 2015.

P.F. Roux, M. Boutin, C. Désert, A. Djari, D. Esquerré, C. Klopp, S. Lagarrigue, O. Demeure. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken. In PLoS One, 2014.

K. Simonin - Le Jeune, A. Le Jeune, S. Jouneau, C. Belleguic, P.F. Roux, M. Jaguin, M.T. Dimanche - Boitrel, V. Lecureur, C. Leclerq, B. Desrues, G. Desruers, G. Brinchault, J.P. Gangneux, C. Martin - Chouly. Impaired function of macrophage from cystic fibrosis patients: CD11b, TLR-5 decrease and sCD24, inflammatory cytokines increase. In PLOS One, 2013.

S. Lagarrigue, L. Martin, F. Hormozdiari, P.F. Roux, A. van Nas, O. Demeure, A. Ghazalpour, E. Eskin, A.J. Lusis. Analysis of allele-specific expression in mouse liver by RNA-seq: a comparison with cis-eQTL identified using genetic linkage. In Genetics, 2013.

Photos

Madagascar

Projects

Toward a systems view of cellular senescence

Combined DNA and RNA sequencing for RNA editing event discovery

Integrating linkage analysis with whole genome sequencing to dissect complex phenotypes

Teaching

In silico and statistical analyses of epigenomic data with UNIX and R

In silico in-depth analyses of transcriptomic data with UNIX

Visualisation of genomic data with ggplot

Tags

Contact

pierre-francois.roux@inserm.fr
Campus Val d'Aurelle, 208 avenue des Apothicaires, 34298 Montpellier cedex 5 FRANCE