Ugo Szachnowski

PROCA11 early activation fuels prostate cancer neuroendocrine traits by regulating cell survival and migration

Rocco Cipolla, Marc Gabriel, Ugo Szachnowski, Zhimin Wang et autres

-differentiation remains unknown. Using a prostate cancer model mimicking the onset of castration-resistant and neuroendocrine phenotypes, we uncovered rapid lncRNA changes, with PROCA11 emerging as the most prominent. PROCA11 is highly expressed in advanced adenocarcinoma and neuroendocrine prostate cancer tumors. This predominantly …

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The role of nonsense-mediated mRNA decay in restricting long noncoding RNA expression has been conserved in RNAi-capable budding yeast

Maxime Wéry, Ugo Szachnowski, Constance Creux, Quentin Fouilleul et autres

In most eukaryotes, sense/antisense RNA duplexes can be processed into small interfering RNAs by the ribonuclease III Dicer, a key component of the RNA interference (RNAi) machinery, which has been lost by the budding yeast Saccharomyces cerevisiae . Previous studies in this …

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Analyse de données scRNA-seq sans référence pour identifier de nouvelles identités cellulaires tumorales

Ugo Szachnowski

Le séquençage ARN en cellule unique (scRNA-seq) est une des technologies les plus utilisées pour étudier l'hétérogénéité cellulaire dans de nombreux contextes biologiques. L'analyse des données en est complexe, mais la plupart des méthodes reposent sur l'alignement des reads (séquences d'ADN complémentaire) …

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Reference-free analysis of scRNA-seq data to unveil new identities in tumor

Ugo Szachnowski

Analyse de données scRNA-seq sans référence pour identifier de nouvelles identités cellulaires tumorales Le séquençage ARN en cellule unique (scRNA-seq) est une des technologies les plus utilisées pour étudier l'hétérogénéité cellulaire dans de nombreux contextes biologiques. L'analyse des données en est complexe, …

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Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence

M. Perez, Gertjan Laenen, Isabelle Loı̈odice, Mickaël Garnier et autres

Quiescent (Q) cells are seemingly inactive, developmentally arrested cells, whose universal characteristic is the ability to promptly re-enter the cell cycle upon sensing of external cues. Q cells are responsive to the environment and flexible enough to adapt to available resources. In …

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Transcriptional heterogeneity shapes stress-adaptive responses in yeast

Mariona Nadal‐Ribelles, Guillaume Lieb, Carme Solé, Yaima Matas et autres

In response to stress, cells activate signaling pathways that coordinate broad changes in gene expression to enhance cell survival. Remarkably, complex variations in gene expression occur even in isogenic populations and in response to similar signaling inputs. However, the molecular mechanisms underlying …

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Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis

Ugo Szachnowski, E. Becker, Igor Stuparević, Maxime Wéry et autres

Previous RNA profiling studies revealed coexpression of overlapping sense/antisense (s/a) transcripts in pro- and eukaryotic organisms. Functional analyses in yeast have shown that certain s/a mRNA/mRNA and mRNA/lncRNA pairs form stable double-stranded RNAs (dsRNAs) that affect transcript stability. Little is known, however, …

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Transcriptome-Wide Analysis of the 5′ Cap Status of RNA Using 5′ Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing

Maxime Wéry, Ugo Szachnowski, Sara Andjus, Antonin Morillon

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The 5‐Fluorouracil RNA Expression Viewer (5‐FUR) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast

Ugo Szachnowski, Oliver Sallou, Matéo Boudet, Anthony Bretaudeau et autres

ABSTRACT Saccharomyces cerevisiae is an excellent model to study the effect of external cues on cell division and stress response. 5‐Fluorocuracil (5‐FU) has been used to treat solid tumors since several decades. The drug was initially designed to interfere with DNA replication …

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Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast

Sara Andjus, Ugo Szachnowski, Nicolas Vogt, Stamatia Gioftsidi et autres

Despite being predicted to lack coding potential, cytoplasmic long noncoding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNA translation remain poorly studied. In yeast, cytoplasmic Xrn1-sensitive unstable transcripts (XUTs) are targeted by nonsense-mediated mRNA decay (NMD), suggesting …

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Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2

Anvita Bhargava, Ugo Szachnowski, Maxime Chazal, Dominika Foretek et autres

Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling …

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A novel lncRNA PROCA11 regulates cell plasticity in response to androgen deprivation of prostate cancer cells

Rocco Cipolla, Marc Gabriel, Giorgia Ianese Regin, Micaela Piemontese et autres

Abstract Long non-coding RNAs (lncRNAs) represent vast and yet poorly characterized family of genes that can fine tune cellular plasticity, thereby allowing the emergence of aggressive therapy-resistant and metastatic cancers. Androgen deprivation therapies (ADT) are commonly used to treat prostate cancer by …

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