U1278-Biologie de l’ARN, Signalisation et Cancer

Publications de l’équipe

Année de publication : 2021

Isabelle Girault, Julien Adam, Shensi Shen, Séverine Roy, Caroline Brard, Sara Faouzi, Emilie Routier, Jeremy Lupu, Sarah Warren, Kristina Sorg, SuFey Ong, Pascale Morel, Jean-Yves Scoazec, Stephan Vagner, Caroline Robert (2021 Nov 16)

A PD-1 /PD-L1 proximity assay as a theranostic marker for PD-1 blockade in patients with metastatic melanoma.

Clinical cancer research : an official journal of the American Association for Cancer Research : DOI : clincanres.1229.2021 En savoir plus
Résumé

Less than 50% of patients with melanoma respond to anti-PD1, and this treatment can induce severe toxicity. Predictive markers are thus needed to improve the benefit/risk ratio of immune checkpoint inhibitors (ICI). Baseline tumor parameters such as PD-L1 expression, CD8 T cell infiltration, mutational burden and various transcriptomic signatures are associated with response to ICI but their predictive values are not sufficient. Interaction between PD1 and its main ligand, PDL1 appears a valuable target of anti-PD1 therapy. Thus, instead of looking at PD-L1 expression only, we evaluated the predictive value of the proximity between PD1 and its neighboring PD-L1 molecules in terms of response to anti-PD1 therapy.

Replier
Lucilla Fabbri, Alina Chakraborty, Caroline Robert, Stéphan Vagner (2021 Sep 4)

The plasticity of mRNA translation during cancer progression and therapy resistance.

Nature reviews. Cancer : 558-577 : DOI : 10.1038/s41568-021-00380-y En savoir plus
Résumé

Translational control of mRNAs during gene expression allows cells to promptly and dynamically adapt to a variety of stimuli, including in neoplasia in response to aberrant oncogenic signalling (for example, PI3K-AKT-mTOR, RAS-MAPK and MYC) and microenvironmental stress such as low oxygen and nutrient supply. Such translational rewiring allows rapid, specific changes in the cell proteome that shape specific cancer phenotypes to promote cancer onset, progression and resistance to anticancer therapies. In this Review, we illustrate the plasticity of mRNA translation. We first highlight the diverse mechanisms by which it is regulated, including by translation factors (for example, eukaryotic initiation factor 4F (eIF4F) and eIF2), RNA-binding proteins, tRNAs and ribosomal RNAs that are modulated in response to aberrant intracellular pathways or microenvironmental stress. We then describe how translational control can influence tumour behaviour by impacting on the phenotypic plasticity of cancer cells as well as on components of the tumour microenvironment. Finally, we highlight the role of mRNA translation in the cellular response to anticancer therapies and its promise as a key therapeutic target.

Replier
Claire Catherinet, Diana Passaro, Stéphanie Gachet, Hind Medyouf, Anne Reynaud, Charlène Lasgi, Jacques Ghysdael, Christine Tran Quang (2021 Jul 7)

NFAT transcription factors are essential and redundant actors for leukemia initiating potential in T-cell acute lymphoblastic leukemia.

PloS one : e0254184 : DOI : 10.1371/journal.pone.0254184 En savoir plus
Résumé

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy with few available targeted therapies. We previously reported that the phosphatase calcineurin (Cn) is required for LIC (leukemia Initiating Capacity) potential of T-ALL pointing to Cn as an interesting therapeutic target. Calcineurin inhibitors have however unwanted side effect. NFAT transcription factors play crucial roles downstream of calcineurin during thymocyte development, T cell differentiation, activation and anergy. Here we elucidate NFAT functional relevance in T-ALL. Using murine T-ALL models in which Nfat genes can be inactivated either singly or in combination, we show that NFATs are required for T-ALL LIC potential and essential to survival, proliferation and migration of T-ALL cells. We also demonstrate that Nfat genes are functionally redundant in T-ALL and identified a node of genes commonly deregulated upon Cn or NFAT inactivation, which may serve as future candidate targets for T-ALL.

Replier
Charlotte Audoynaud, Stéphan Vagner, Sarah Lambert (2021 Jul 5)

Non-homologous end-joining at challenged replication forks: an RNA connection?

Trends in genetics : TIG : DOI : S0168-9525(21)00166-9 En savoir plus
Résumé

Defective DNA replication, known as ‘replication stress’, is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.

Replier
Shensi Shen, Isabelle Girault, Hélène Malka-Mahieu, Caroline Robert, Stéphan Vagner (2021 Jun 23)

detection of the eIF4F translation initiation complex in mammalian cells and tissues.

STAR protocols : 100621 : DOI : 10.1016/j.xpro.2021.100621 En savoir plus
Résumé

The eukaryotic translation initiation complex eIF4F plays an important role in gene expression. The methods that are used to monitor the formation of the eIF4F complex are usually indirect and provide no information on its subcellular localization. This protocol describes a proximity ligation assay-based procedure allowing the direct visualization of the eIF4F complex, as well as its absolute quantification per cell using adapted image analysis software. For complete details on the use and execution of this protocol, please refer to Boussemart et al. (2014).

Replier
Aurore Touzart, Anand Mayakonda, Charlotte Smith, Joschka Hey, Reka Toth, Agata Cieslak, Guillaume P Andrieu, Christine Tran Quang, Mehdi Latiri, Jacques Ghysdael, Salvatore Spicuglia, Hervé Dombret, Norbert Ifrah, Elizabeth Macintyre, Pavlo Lutsik, Nicolas Boissel, Christoph Plass, Vahid Asnafi (2021 May 26)

Epigenetic analysis of patients with T-ALL identifies poor outcomes and a hypomethylating agent-responsive subgroup.

Science translational medicine : DOI : eabc4834 En savoir plus
Résumé

Adult « T cell » acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that is associated with poor outcomes, requiring additional therapeutic options. The DNA methylation landscapes of adult T-ALL remain undercharacterized. Here, we systematically analyzed the DNA methylation profiles of normal thymic-sorted T cell subpopulations and 143 primary adult T-ALLs as part of the French GRAALL 2003-2005 trial. Our results indicated that T-ALL is epigenetically heterogeneous consisting of five subtypes (C-C), which were either associated with co-occurring ()/ [()] () mutations (C), , () deregulation (C), () (C), /in – () (C), or in – overexpression (C). Integrative analysis of DNA methylation and gene expression identified potential cluster-specific oncogenes and tumor suppressor genes. In addition to an aggressive hypomethylated subgroup (C), our data identified an unexpected subset of hypermethylated T-ALL (C) associated with poor outcome and primary therapeutic response. Using mouse xenografts, we demonstrated that hypermethylated T-ALL samples exhibited therapeutic responses to the DNA hypomethylating agent 5-azacytidine, which significantly (survival probability; = 0.001 for C, 0.01 for C, and 0.0253 for C) delayed tumor progression. These findings suggest that epigenetic-based therapies may provide an alternative treatment option in hypermethylated T-ALL.

Replier
Olivier Saulnier, Katia Guedri-Idjouadiene, Marie-Ming Aynaud, Alina Chakraborty, Jonathan Bruyr, Joséphine Pineau, Tina O'Grady, Olivier Mirabeau, Sandrine Grossetête, Bartimée Galvan, Margaux Claes, Zahra Al Oula Hassoun, Benjamin Sadacca, Karine Laud, Sakina Zaïdi, Didier Surdez, Sylvain Baulande, Xavier Rambout, Franck Tirode, Martin Dutertre, Olivier Delattre, Franck Dequiedt (2021 May 19)

ERG transcription factors have a splicing regulatory function involving RBFOX2 that is altered in the EWS-FLI1 oncogenic fusion.

Nucleic acids research : DOI : 10.1093/nar/gkab305 En savoir plus
Résumé

ERG family proteins (ERG, FLI1 and FEV) are a subfamily of ETS transcription factors with key roles in physiology and development. In Ewing sarcoma, the oncogenic fusion protein EWS-FLI1 regulates both transcription and alternative splicing of pre-messenger RNAs. However, whether wild-type ERG family proteins might regulate splicing is unknown. Here, we show that wild-type ERG proteins associate with spliceosomal components, are found on nascent RNAs, and induce alternative splicing when recruited onto a reporter minigene. Transcriptomic analysis revealed that ERG and FLI1 regulate large numbers of alternative spliced exons (ASEs) enriched with RBFOX2 motifs and co-regulated by this splicing factor. ERG and FLI1 are associated with RBFOX2 via their conserved carboxy-terminal domain, which is present in EWS-FLI1. Accordingly, EWS-FLI1 is also associated with RBFOX2 and regulates ASEs enriched in RBFOX2 motifs. However, in contrast to wild-type ERG and FLI1, EWS-FLI1 often antagonizes RBFOX2 effects on exon inclusion. In particular, EWS-FLI1 reduces RBFOX2 binding to the ADD3 pre-mRNA, thus increasing its long isoform, which represses the mesenchymal phenotype of Ewing sarcoma cells. Our findings reveal a RBFOX2-mediated splicing regulatory function of wild-type ERG family proteins, that is altered in EWS-FLI1 and contributes to the Ewing sarcoma cell phenotype.

Replier
Roland Chanet, Dorothée Baïlle, Marie-Pierre Golinelli-Cohen, Sylvie Riquier, Olivier Guittet, Michel Lepoivre, Meng-Er Huang, Laurence Vernis (2021 May 1)

Fe-S coordination defects in the replicative DNA polymerase delta cause deleterious DNA replication in vivo and subsequent DNA damage in the yeast Saccharomyces cerevisiae.

G3 (Bethesda, Md.) : DOI : jkab124 En savoir plus
Résumé

B-type eukaryotic polymerases contain a [4Fe-4S] cluster in their C-terminus domain, whose role is not fully understood yet. Among them, DNA polymerase delta (Polδ) plays an essential role in chromosomal DNA replication, mostly during lagging strand synthesis. Previous in vitro work suggested that the Fe-S cluster in Polδ is required for efficient binding of the Pol31 subunit, ensuring stability of the Polδ complex. Here we analyzed the in vivo consequences resulting from an impaired coordination of the Fe-S cluster in Polδ. We show that a single substitution of the very last cysteine coordinating the cluster by a serine is responsible for the generation of massive DNA damage during S phase, leading to checkpoint activation, requirement of homologous recombination for repair, and ultimately to cell death when the repair capacities of the cells are overwhelmed. These data indicate that impaired Fe-S cluster coordination in Polδ is responsible for aberrant replication. More generally, Fe-S in Polδ may be compromised by various stress including anti-cancer drugs. Possible in vivo Polδ Fe-S cluster oxidation and collapse may thus occur, and we speculate this could contribute to induced genomic instability and cell death, comparable to that observed in pol3-13 cells.

Replier
Martin Dutertre, Rym Sfaxi, Stéphan Vagner (2021 Feb 27)

Reciprocal Links between Pre-messenger RNA 3′-End Processing and Genome Stability.

Trends in biochemical sciences : DOI : S0968-0004(21)00023-2 En savoir plus
Résumé

The 3′-end processing of most pre-messenger RNAs (pre-mRNAs) involves RNA cleavage and polyadenylation and is coupled to transcription termination. In both yeast and human cells, pre-mRNA 3′-end cleavage is globally inhibited by DNA damage. Recently, further links between pre-mRNA 3′-end processing and the control of genome stability have been uncovered, as reviewed here. Upon DNA damage, various genes related to the DNA damage response (DDR) escape 3′-end processing inhibition or are regulated through alternative polyadenylation (APA). Conversely, various pre-mRNA 3′-end processing factors prevent genome instability and are found at sites of DNA damage. Finally, the reciprocal link between pre-mRNA 3′-end processing and genome stability control seems important because it is conserved in evolution and involved in disease development.

Replier
Andrey Kleshnin, Léa Monet, Marina Plays, Hugo Vaysset, Claire Rougeulle, Stéphan Vagner (2021 Jan 6)

Amid darkness, light will prevail – a report on the 2020 annual SFC meeting on “Dark genome and Cancer”

Bulletin du cancer : DOI : S0007-4551(20)30510-5 En savoir plus
Résumé

.

Replier

Année de publication : 2020

Shensi Shen, Stéphan Vagner, Caroline Robert (2020 Nov 12)

Persistent Cancer Cells: The Deadly Survivors.

Cell : 860-874 : DOI : S0092-8674(20)31391-X En savoir plus
Résumé

Persistent cancer cells are the discrete and usually undetected cells that survive cancer drug treatment and constitute a major cause of treatment failure. These cells are characterized by their slow proliferation, highly flexible energy consumption, adaptation to their microenvironment, and phenotypic plasticity. Mechanisms that underlie their persistence offer highly coveted and sought-after therapeutic targets, and include diverse epigenetic, transcriptional, and translational regulatory processes, as well as complex cell-cell interactions. Although the successful clinical targeting of persistent cancer cells remains to be realized, immense progress has been made in understanding their persistence, yielding promising preclinical results.

Replier
(2020 Oct 1)

Flavaglines as natural products targeting eIF4A and prohibitins: From traditional Chinese medicine to antiviral activity against coronaviruses

Eur J Med Chem. : DOI : 10.1016/j.ejmech.2020.112653 En savoir plus
Résumé

Flavaglines are cyclopenta[b]benzofurans found in plants of the genus Aglaia, several species of which are used in traditional Chinese medicine. These compounds target the initiation factor of translation eIF4A and the scaffold proteins prohibitins-1 and 2 (PHB1/2) to exert various pharmacological activities, including antiviral effects against several types of viruses, including coronaviruses. This review is focused on the antiviral effects of flavaglines and their therapeutic potential against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Replier
(2020 Jun 1)

Preclinical Efficacy of Humanized, non-FcgammaR Binding Anti-CD3 Antibodies in T-cell Acute Lymphoblastic Leukemia

Blood. : DOI : 10.1182/blood.2019003801 En savoir plus
Résumé

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy that accounts for about 20% ALL cases. Intensive chemotherapy regimens result in >85% cure rates in children and <50% in adults, calling for the search of novel therapeutic strategies. While immune-based therapies have tremendously improved the treatment of B-ALL and other B-cell malignancies, they are not available yet in T-ALL. We report here that humanized, non-FcgR binding monoclonal antibodies to CD3 have anti-leukemic properties in xenograft (PDX) models of CD3+ T-ALL, resulting in prolonged host survival. We also report that these antibodies cooperate with chemotherapy to enhance anti-leukemic effects and host survival. As these antibodies show only minor, manageable side effects in humans, they offer a new therapeutic option for the treatment of T-ALL. Our results also show that the anti-leukemic properties of anti-CD3 mAbs are largely independent Fcg-receptor mediated pathways in T-ALL PDX.

Replier
Iris Tanaka, Alina Chakraborty, Olivier Saulnier, Clara Benoit-Pilven, Sophie Vacher, Dalila Labiod, Eric W F Lam, Ivan Bièche, Olivier Delattre, Frédéric Pouzoulet, Didier Auboeuf, Stéphan Vagner, Martin Dutertre (2020 Jan 17)

ZRANB2 and SYF2-mediated splicing programs converging on ECT2 are involved in breast cancer cell resistance to doxorubicin.

Nucleic acids research : DOI : gkz1213 En savoir plus
Résumé

Besides analyses of specific alternative splicing (AS) variants, little is known about AS regulatory pathways and programs involved in anticancer drug resistance. Doxorubicin is widely used in breast cancer chemotherapy. Here, we identified 1723 AS events and 41 splicing factors regulated in a breast cancer cell model of acquired resistance to doxorubicin. An RNAi screen on splicing factors identified the little studied ZRANB2 and SYF2, whose depletion partially reversed doxorubicin resistance. By RNAi and RNA-seq in resistant cells, we found that the AS programs controlled by ZRANB2 and SYF2 were enriched in resistance-associated AS events, and converged on the ECT2 splice variant including exon 5 (ECT2-Ex5+). Both ZRANB2 and SYF2 were found associated with ECT2 pre-messenger RNA, and ECT2-Ex5+ isoform depletion reduced doxorubicin resistance. Following doxorubicin treatment, resistant cells accumulated in S phase, which partially depended on ZRANB2, SYF2 and the ECT2-Ex5+ isoform. Finally, doxorubicin combination with an oligonucleotide inhibiting ECT2-Ex5 inclusion reduced doxorubicin-resistant tumor growth in mouse xenografts, and high ECT2-Ex5 inclusion levels were associated with bad prognosis in breast cancer treated with chemotherapy. Altogether, our data identify AS programs controlled by ZRANB2 and SYF2 and converging on ECT2, that participate to breast cancer cell resistance to doxorubicin.

Replier

Année de publication : 2019

Shensi Shen, Sara Faouzi, Amandine Bastide, Sylvain Martineau, Hélène Malka-Mahieu, Yu Fu, Xiaoxiao Sun, Christine Mateus, Emilie Routier, Severine Roy, Laurent Desaubry, Fabrice André, Alexander Eggermont, Alexandre David, Jean-Yves Scoazec, Stéphan Vagner, Caroline Robert (2019 Dec 18)

An epitranscriptomic mechanism underlies selective mRNA translation remodelling in melanoma persister cells.

Nature communications : 5713 : DOI : 10.1038/s41467-019-13360-6 En savoir plus
Résumé

Cancer persister cells tolerate anticancer drugs and serve as the founders of acquired resistance and cancer relapse. Here we show that a subpopulation of BRAF mutant melanoma cells that tolerates exposure to BRAF and MEK inhibitors undergoes a reversible remodelling of mRNA translation that evolves in parallel with drug sensitivity. Although this process is associated with a global reduction in protein synthesis, a subset of mRNAs undergoes an increased efficiency in translation. Inhibiting the eIF4A RNA helicase, a component of the eIF4F translation initiation complex, abrogates this selectively increased translation and is lethal to persister cells. Translation remodelling in persister cells coincides with an increased N6-methyladenosine modification in the 5′-untranslated region of some highly translated mRNAs. Combination of eIF4A inhibitor with BRAF and MEK inhibitors effectively inhibits the emergence of persister cells and may represent a new therapeutic strategy to prevent acquired drug resistance.

Replier