Publications by Alexandre Coudray

Evolutionarily recent transcription factors partake in human cell cycle regulation

Didier Trono, Sandra Eloise Kjeldsen, Charlène Mireille Raymonde Raclot, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Evaristo Jose Planet Letschert, Filipe Amândio Brandão Sanches Vong Martins, Alex Russell Lederer, Olga Marie Louise Rosspopoff, Romain Forey

The cell cycle is a fundamental process in eukaryotic biology and is accordingly controlled by a highly conserved core signaling cascade. However, whether recently evolved proteins also influence this process is unclear. Here, we systematically map the inf ...

2025

Deconvolution of ex-vivo drug screening data and bulk tissue expression predicts the abundance and viability of cancer cell subpopulations

Alexandre Coudray

Ex-vivo drug sensitivity screening (DSS) allows the prediction of cancer treatment effectiveness in a personalized fashion. However, it only provides a readout on mixtures of cells, potentially occulting important information on clinically relevant cell su ...

EPFL2023

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Julien Léonard Duc, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Shaoline Sheppard, Evaristo Jose Planet Letschert, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville, Julien Paul André Pontis, Delphine Yvette L Grun

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Genetic features and genomic targets of human KRAB-zinc finger proteins

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Sandra Eloise Kjeldsen, Jonas Caspar De Tribolet-Hardy, Bara Khubieh, Jacques Fellay, Michaël Imbeault, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Evaristo Jose Planet Letschert, Christian Axel Wandall Thorball, Romain Forey

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

2023

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

Didier Trono, Laurence Gouzi Abrami, Julien Léonard Duc, Sandra Eloise Kjeldsen, Alexandre Coudray, Sagane Dind, Evaristo Jose Planet Letschert, Laia Simo Riudalbas

The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...

Nature Research2022

KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Jonas Caspar De Tribolet-Hardy, Alexandra Iouranova, Michaël Imbeault, Alexandre Coudray, Tamara Rossy, Alexandre Louis André Persat, Delphine Yvette L Grun

Background Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to g ...

2022

Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain

Didier Trono, Julien Léonard Duc, Alexandre Coudray, Sagane Dind, Shaoline Sheppard, Evaristo Jose Planet Letschert, Christopher James Playfoot

Transposable elements (TEs) account for more than 50% of the human genome and many have been co-opted throughout evolution to provide regulatory functions for gene expression networks. Several lines of evidence suggest that these networks are fine-tuned by ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2021

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

Didier Trono, Laurence Gouzi Abrami, Julien Léonard Duc, Sandra Eloise Kjeldsen, Alexandre Coudray, Sagane Dind, Evaristo Jose Planet Letschert, Laia Simo Riudalbas

AMER ASSOC CANCER RESEARCH2021

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Bart Deplancke, Charlène Mireille Raymonde Raclot, Alexandre Coudray, Christian Axel Wandall Thorball, Julien Paul André Pontis, Evgeniia Pankevich, Delphine Yvette L Grun, Christopher James Playfoot

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influen ...

2020

Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression

Didier Trono, Priscilla Turelli, Alexandre Coudray

Gene expression aberration is a hallmark of cancers, but the mechanisms underlying such aberrations remain unclear. Human endogenous retroviruses (HERVs) are genomic repetitive elements that potentially function as enhancers. Since numerous HERVs are epige ...

AMER ASSOC ADVANCEMENT SCIENCE2020

DPPA2 and DPPA4 are necessary to establish a 2C‐like state in mouse embryonic stem cells

Didier Trono, Julien Léonard Duc, Alexandre Coudray, Alberto De Iaco

After fertilization of the transcriptionally silent oocyte, expression from both parental chromosomes is launched through zygotic genome activation (ZGA), occurring in the mouse at the 2-cell (2C) stage. Among the first elements to be transcribed are the D ...

2019

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Sandra Eloise Kjeldsen, Julien Duc, Alexandre Coudray, Evaristo Jose Planet Letschert, Julien Paul André Pontis

Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expre ...

2019

PAX5 as a model to study the evolution of transcription factors' regulatory networks

Didier Trono, Alexandre Coudray, Filipe Amândio Brandão Sanches Vong Martins

E M H SWISS MEDICAL PUBLISHERS LTD2019

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

Philipp Bucher, Alexandre Coudray

To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of soma ...

2018

KRAB-ZFPs and transposable elements rewire early human embryonic development transcriptional networks

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Julien Duc, Alexandra Iouranova, Michaël Imbeault, Alexandre Coudray

MARY ANN LIEBERT, INC2018

DPPA2 and DPPA4 regulate expression of Dux in mouse embryonic stem cells

Didier Trono, Alexandre Coudray, Alberto De Iaco

MARY ANN LIEBERT, INC2018