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108 results on '"Salvatore Spicuglia"'

1. Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network

Author

Marin Truchi, Caroline Lacoux, Cyprien Gille, Julien Fassy, Virginie Magnone, Rafael Lopes Goncalves, Cédric Girard-Riboulleau, Iris Manosalva-Pena, Marine Gautier-Isola, Kevin Lebrigand, Pascal Barbry, Salvatore Spicuglia, Georges Vassaux, Roger Rezzonico, Michel Barlaud, and Bernard Mari

Subjects
single-cell RNA-seq, lncRNAs, hypoxia, CRISPRi, sparse supervised autoencoder, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Single-cell CRISPR-based transcriptome screens are potent genetic tools for concomitantly assessing the expression profiles of cells targeted by a set of guides RNA (gRNA), and inferring target gene functions from the observed perturbations. However, due to various limitations, this approach lacks sensitivity in detecting weak perturbations and is essentially reliable when studying master regulators such as transcription factors. To overcome the challenge of detecting subtle gRNA induced transcriptomic perturbations and classifying the most responsive cells, we developed a new supervised autoencoder neural network method. Our Sparse supervised autoencoder (SSAE) neural network provides selection of both relevant features (genes) and actual perturbed cells. We applied this method on an in-house single-cell CRISPR-interference-based (CRISPRi) transcriptome screening (CROP-Seq) focusing on a subset of long non-coding RNAs (lncRNAs) regulated by hypoxia, a condition that promote tumor aggressiveness and drug resistance, in the context of lung adenocarcinoma (LUAD). The CROP-seq library of validated gRNA against a subset of lncRNAs and, as positive controls, HIF1A and HIF2A, the 2 main transcription factors of the hypoxic response, was transduced in A549 LUAD cells cultured in normoxia or exposed to hypoxic conditions during 3, 6 or 24 h. We first validated the SSAE approach on HIF1A and HIF2 by confirming the specific effect of their knock-down during the temporal switch of the hypoxic response. Next, the SSAE method was able to detect stable short hypoxia-dependent transcriptomic signatures induced by the knock-down of some lncRNAs candidates, outperforming previously published machine learning approaches. This proof of concept demonstrates the relevance of the SSAE approach for deciphering weak perturbations in single-cell transcriptomic data readout as part of CRISPR-based screening.

Published
2024
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2. P319: IL7-RECEPTOR EXPRESSION IS FREQUENT IN T-CELL ACUTE LYMPHOBLASTIC LEUKEMIA AND PREDICTS SENSITIVITY TO JAK-INHIBITION

Author

Lucien Courtois, Aurélie Cabannes-Hamy, Rathana Kim, Marine Delecourt, Antoine Pinton, Guillaume Charbonnier, Melanie Feroul, Charlotte Smith, Giulia Tueur, Cecile Pivert, Estelle Balducci, Mathieu Simonin, Salvatore Spicuglia, Nicolas Boissel, Guillaume Andrieu, Vahid Asnafi, Philippe Rousselot, and Ludovic Lhermitte

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Published
2023
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3. Severe COVID-19-associated variants linked to chemokine receptor gene control in monocytes and macrophages

Author

Bernard S. Stikker, Grégoire Stik, Antoinette F. van Ouwerkerk, Lianne Trap, Salvatore Spicuglia, Rudi W. Hendriks, and Ralph Stadhouders

Subjects
SARS-CoV-2, COVID-19, 3p21.31, GWAS, Monocyte, Macrophage, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Genome-wide association studies have identified 3p21.31 as the main risk locus for severe COVID-19, although underlying mechanisms remain elusive. We perform an epigenomic dissection of 3p21.31, identifying a CTCF-dependent tissue-specific 3D regulatory chromatin hub that controls the activity of several chemokine receptor genes. Risk SNPs colocalize with regulatory elements and are linked to increased expression of CCR1, CCR2 and CCR5 in monocytes and macrophages. As excessive organ infiltration of inflammatory monocytes and macrophages is a hallmark of severe COVID-19, our findings provide a rationale for the genetic association of 3p21.31 variants with elevated risk of hospitalization upon SARS-CoV-2 infection.

Published
2022
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4. TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3’ neo-enhancer

Author

Charlotte Smith, Ashish Goyal, Dieter Weichenhan, Eric Allemand, Anand Mayakonda, Umut Toprak, Anna Riedel, Estelle Balducci, Manisha Manojkumar, Anastasija Pejkovska, Oliver Mücke, Etienne Sollier, Ali Bakr, Kersten Breuer, Pavlo Lutsik, Olivier Hermine, Salvatore Spicuglia, Vahid Asnafi, Christoph Plass, and Aurore Touzart

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

T-cell acute lymphocytic leukemia protein 1 (TAL1) is one of the most frequently deregulated oncogenes in T-cell acute lymphoblastic leukemia (T-ALL). Its deregulation can occur through diverse cis-alterations, including SIL-TAL1 microdeletions, translocations with T-cell Receptor loci, and more recently described upstream intergenic non-coding mutations. These mutations consist of recurrent focal microinsertions that create an oncogenic neo-enhancer accompanied by activating epigenetic marks. This observation laid the groundwork for an innovative paradigm concerning the activation of proto-oncogenes via genomic alterations of non-coding intergenic regions. However, for the majority of T-ALL expressing TAL1 (TAL1+), the deregulation mechanism remains 'unresolved'. We took advantage of H3K27ac and H3K4me3 chromatin immunoprecipitation sequencing data of eight cases of T-ALL, including five TAL1+ cases. We identified a putative novel oncogenic neo-enhancer downstream of TAL1 in an unresolved monoallelic TAL1+ case. A rare but recurrent somatic heterozygous microinsertion within this region creates a de novo binding site for MYB transcription factor. Here we demonstrate that this mutation leads to increased enhancer activity, gain of active epigenetic marks, and TAL1 activation via recruitment of MYB. These results highlight the diversity of non-coding mutations that can drive oncogene activation.

Published
2023
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5. Epromoters function as a hub to recruit key transcription factors required for the inflammatory response

Author

David Santiago-Algarra, Charbel Souaid, Himanshu Singh, Lan T. M. Dao, Saadat Hussain, Alejandra Medina-Rivera, Lucia Ramirez-Navarro, Jaime A. Castro-Mondragon, Nori Sadouni, Guillaume Charbonnier, and Salvatore Spicuglia

Subjects
Science
Abstract

Some promoters, termed Epromoters, can display enhancer activity and regulate distal genes in their endogenous context. Here the authors report the broad involvement of Epromoters in the coordinated activation of interferon (IFN) response. They show activation of a number of IFN-inducible genes is a result of Epromoters regulating expression of an entire IFN response gene cluster.

Published
2021
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6. Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria

Author

Samia Nisar, Magali Torres, Alassane Thiam, Bruno Pouvelle, Florian Rosier, Frederic Gallardo, Oumar Ka, Babacar Mbengue, Rokhaya Ndiaye Diallo, Laura Brosseau, Salvatore Spicuglia, Alioune Dieye, Sandrine Marquet, and Pascal Rihet

Subjects
regulatory element, enhancer, promoter, SNP, functional genomics, gene reporter, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.

Published
2022
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7. Low level CpG island promoter methylation predicts a poor outcome in adult T-cell acute lymphoblastic leukemia

Author

Aurore Touzart, Nicolas Boissel, Mohamed Belhocine, Charlotte Smith, Carlos Graux, Mehdi Latiri, Ludovic Lhermitte, Eve-Lyne Mathieu, Françoise Huguet, Laurence Lamant, Pierre Ferrier, Norbert Ifrah, Elizabeth Macintyre, Hervé Dombret, Vahid Asnafi, and Salvatore Spicuglia

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

Cancer cells undergo massive alterations in their DNA methylation patterns which result in aberrant gene expression and malignant phenotypes. Abnormal DNA methylation is a prognostic marker in several malignancies, but its potential prognostic significance in adult T-cell acute lymphoblastic leukemia (T-ALL) is poorly defined. Here, we performed methylated DNA immunoprecipitation to obtain a comprehensive genome-wide analysis of promoter methylation in adult T-ALL (n=24) compared to normal thymi (n=3). We identified a CpG hypermethylator phenotype that distinguishes two T-ALL subgroups and further validated it in an independent series of 17 T-lymphoblastic lymphoma. Next, we identified a methylation classifier based on nine promoters which accurately predict the methylation phenotype. This classifier was applied to an independent series of 168 primary adult T-ALL treated accordingly to the GRAALL03/05 trial using methylation-specific multiplex ligation-dependent probe amplification. Importantly hypomethylation correlated with specific oncogenic subtypes of T-ALL and identified patients associated with a poor clinical outcome. This methylation-specific multiplex ligation-dependent probe amplification based methylation profiling could be useful for therapeutic stratification of adult T-ALL in routine practice. The GRAALL-2003 and -2005 studies were registered at http://www.clinicaltrials.gov as #NCT00222027 and #NCT00327678, respectively.

Published
2020
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8. IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells

Author

Darely Y. Gutiérrez-Reyna, Alejandra Cedillo-Baños, Linda A. Kempis-Calanis, Oscar Ramírez-Pliego, Lisa Bargier, Denis Puthier, Jose D. Abad-Flores, Morgane Thomas-Chollier, Denis Thieffry, Alejandra Medina-Rivera, Salvatore Spicuglia, and Maria A. Santana

Subjects
neonatal T cells, CD8+ T cells, RNA-sequencing, IL-12, T cell activation, neonatal immunity, Immunologic diseases. Allergy, RC581-607
Abstract

Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortality rates. CD8+ T lymphocytes are responsible for the elimination of infected cells. Understanding the response of these cells to normal and high stimulatory conditions is important to propose better treatments and vaccine formulations for neonates. We have previously shown that human neonatal CD8+ T cells overexpress innate inflammatory genes and have a low expression of cytotoxic and cell signaling genes. To investigate the activation potential of these cells, we evaluated the transcriptome of human neonatal and adult naïve CD8+ T cells after TCR/CD28 signals ± IL-12. We found that in neonatal cells, IL-12 signals contribute to the adult-like expression of genes associated with cell-signaling, T-cell cytokines, metabolism, and cell division. Additionally, IL-12 signals contributed to the downregulation of the neutrophil signature transcription factor CEBPE and other immaturity related genes. To validate the transcriptome results, we evaluated the expression of a series of genes by RT-qPCR and the promoter methylation status on independent samples. We found that in agreement with the transcriptome, IL-12 signals contributed to the chromatin closure of neutrophil-like genes and the opening of cytotoxicity genes, suggesting that IL-12 signals contribute to the epigenetic reprogramming of neonatal lymphocytes. Furthermore, high expression of some inflammatory genes was observed in naïve and stimulated neonatal cells, in agreement with the high inflammatory profile of neonates to infections. Altogether our results point to an important contribution of IL-12 signals to the reprogramming of the neonatal CD8+ T cells.

Published
2020
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9. Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene.

Author

Jaafar Alomairi, Anne M Molitor, Nori Sadouni, Saadat Hussain, Magali Torres, Wiam Saadi, Lan T M Dao, Guillaume Charbonnier, David Santiago-Algarra, Jean Christophe Andrau, Denis Puthier, Tom Sexton, and Salvatore Spicuglia

Subjects
Medicine, Science
Abstract

The Ikzf1 locus encodes the lymphoid specific transcription factor Ikaros, which plays an essential role in both T and B cell differentiation, while deregulation or mutation of IKZF1/Ikzf1 is involved in leukemia. Tissue-specific and cell identity genes are usually associated with clusters of enhancers, also called super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. Several potential regulatory regions have been identified in close proximity of Ikzf1, however, the full extent of the regulatory landscape of the Ikzf1 locus is not yet established. In this study, we combined epigenomics and transcription factor binding along with high-throughput enhancer assay and 4C-seq to prioritize an enhancer element located 120 kb upstream of the Ikzf1 gene. We found that deletion of the E120 enhancer resulted in a significant reduction of Ikzf1 mRNA. However, the epigenetic landscape and 3D topology of the locus were only slightly affected, highlighting the complexity of the regulatory landscape regulating the Ikzf1 locus.

Published
2020
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10. Homeobox protein TLX3 activates miR-125b expression to promote T-cell acute lymphoblastic leukemia

Author

Laurent Renou, Pierre-Yves Boelle, Caroline Deswarte, Salvatore Spicuglia, Aissa Benyoucef, Julien Calvo, Benjamin Uzan, Mohamed Belhocine, Agata Cieslak, Judith Landman-Parker, Andre Baruchel, Vahid Asnafi, Françoise Pflumio, Paola Ballerini, and Irina Naguibneva

Subjects
Specialties of internal medicine, RC581-951
Abstract

Abstract: The oncogenic mechanisms driven by aberrantly expressed transcription factors in T-cell acute leukemia (T-ALL) are still elusive. MicroRNAs (miRNAs) play an important role in normal development and pathologies. Here, we examined the expression of 738 miRNA species in 41 newly diagnosed pediatric T-ALLs and in human thymus-derived cells. We found that expression of 2 clustered miRNAs, miR-125b/99a, peaks in primitive T cells and is upregulated in the T leukemia homeobox 3 (TLX3)–positive subtype of T-ALL. Using loss- and gain-of-function approaches, we established functional relationships between TLX3 and miR-125b. Both TLX3 and miR-125b support in vitro cell growth and in vivo invasiveness of T-ALL. Besides, ectopic expression of TLX3 or miR-125b in human hematopoietic progenitor cells enhances production of T-cell progenitors and favors their accumulation at immature stages of T-cell development resembling the differentiation arrest observed in TLX3 T-ALL. Ectopic miR-125b also remarkably accelerated leukemia in a xenograft model, suggesting that miR125b is an important mediator of the TLX3-mediated transformation program that takes place in immature T-cell progenitors. Mechanistically, TLX3-mediated activation of miR-125b may impact T-cell differentiation in part via repression of Ets1 and CBFβ genes, 2 regulators of T-lineage. Finally, we established that TLX3 directly regulates miR-125b production through binding and transactivation of LINC00478, a long noncoding RNA gene, which is the host of miR-99a/Let-7c/miR-125b. Altogether, our results reveal an original functional link between TLX3 and oncogenic miR-125b in T-ALL development.

Published
2017
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11. Recent advances in high-throughput approaches to dissect enhancer function [version 1; referees: 3 approved]

Author

David Santiago-Algarra, Lan T.M. Dao, Lydie Pradel, Alexandre España, and Salvatore Spicuglia

Subjects
Control of Gene Expression, Developmental Molecular Mechanisms, Genomics, Nuclear Structure & Function, Medicine, Science
Abstract

The regulation of gene transcription in higher eukaryotes is accomplished through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. It is now well acknowledged that enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Many strategies have been developed to identify and characterize enhancers. Here, we discuss recent advances in high-throughput approaches to assess enhancer activity, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We highlight how these approaches contribute toward a better understanding of enhancer function, eventually leading to the discovery of new types of regulatory sequences, and how the alteration of enhancers can affect transcriptional regulation.

Published
2017
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12. An early thymic precursor phenotype predicts outcome exclusively in HOXA-overexpressing adult T-cell acute lymphoblastic leukemia: a Group for Research in Adult Acute Lymphoblastic Leukemia study

Author

Jonathan Bond, Tony Marchand, Aurore Touzart, Agata Cieslak, Amélie Trinquand, Laurent Sutton, Isabelle Radford-Weiss, Ludovic Lhermitte, Salvatore Spicuglia, Hervé Dombret, Elizabeth Macintyre, Norbert Ifrah, Jean-François Hamel, and Vahid Asnafi

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

Gene expression studies have consistently identified a HOXA-overexpressing cluster of T-cell acute lymphoblastic leukemias, but it is unclear whether these constitute a homogeneous clinical entity, and the biological consequences of HOXA overexpression have not been systematically examined. We characterized the biology and outcome of 55 HOXA-positive cases among 209 patients with adult T-cell acute lymphoblastic leukemia uniformly treated during the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)-2003 and -2005 studies. HOXA-positive patients had markedly higher rates of an early thymic precursor-like immunophenotype (40.8% versus 14.5%, P=0.0004), chemoresistance (59.3% versus 40.8%, P=0.026) and positivity for minimal residual disease (48.5% versus 23.5%, P=0.01) than the HOXA-negative group. These differences were due to particularly high frequencies of chemoresistant early thymic precursor-like acute lymphoblastic leukemia in HOXA-positive cases harboring fusion oncoproteins that transactivate HOXA. Strikingly, the presence of an early thymic precursor-like immunophenotype was associated with marked outcome differences within the HOXA-positive group (5-year overall survival 31.2% in HOXA-positive early thymic precursor versus 66.7% in HOXA-positive non-early thymic precursor, P=0.03), but not in HOXA-negative cases (5-year overall survival 74.2% in HOXA-negative early thymic precursor versus 57.2% in HOXA-negative non-early thymic precursor, P=0.44). Multivariate analysis further revealed that HOXA positivity independently affected event-free survival (P=0.053) and relapse risk (P=0.039) of chemoresistant T-cell acute lymphoblastic leukemia. These results show that the underlying mechanism of HOXA deregulation dictates the clinico-biological phenotype, and that the negative prognosis of early thymic precursor acute lymphoblastic leukemia is exclusive to HOXA-positive patients, suggesting that early treatment intensification is currently suboptimal for therapeutic rescue of HOXA-positive chemoresistant adult early thymic precursor acute lymphoblastic leukemia. Trial Registration: The GRAALL-2003 and -2005 studies were registered at http://www.clinicaltrials.gov as #NCT00222027 and #NCT00327678, respectively.

Published
2016
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13. Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling.

Author

Stéphanie Cornen, Arnaud Guille, José Adélaïde, Lynda Addou-Klouche, Pascal Finetti, Marie-Rose Saade, Marwa Manai, Nadine Carbuccia, Ismahane Bekhouche, Anne Letessier, Stéphane Raynaud, Emmanuelle Charafe-Jauffret, Jocelyne Jacquemier, Salvatore Spicuglia, Hugues de The, Patrice Viens, François Bertucci, Daniel Birnbaum, and Max Chaffanet

Subjects
Medicine, Science
Abstract

Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.

Published
2014
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14. Characterisation of genome-wide PLZF/RARA target genes.

Author

Salvatore Spicuglia, Christelle Vincent-Fabert, Touati Benoukraf, Guillaume Tibéri, Andrew J Saurin, Joaquin Zacarias-Cabeza, David Grimwade, Ken Mills, Boris Calmels, François Bertucci, Michael Sieweke, Pierre Ferrier, and Estelle Duprez

Subjects
Medicine, Science
Abstract

The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming potential. However, molecular mechanisms associated with PLZF/RARA-dependent leukaemogenesis still remain unclear.We searched for specific PLZF/RARA target genes by ChIP-on-chip in the haematopoietic cell line U937 conditionally expressing PLZF/RARA. By comparing bound regions found in U937 cells expressing endogenous PLZF with PLZF/RARA-induced U937 cells, we isolated specific PLZF/RARA target gene promoters. We next analysed gene expression profiles of our identified target genes in PLZF/RARA APL patients and analysed DNA sequences and epigenetic modification at PLZF/RARA binding sites. We identify 413 specific PLZF/RARA target genes including a number encoding transcription factors involved in the regulation of haematopoiesis. Among these genes, 22 were significantly down regulated in primary PLZF/RARA APL cells. In addition, repressed PLZF/RARA target genes were associated with increased levels of H3K27me3 and decreased levels of H3K9K14ac. Finally, sequence analysis of PLZF/RARA bound sequences reveals the presence of both consensus and degenerated RAREs as well as enrichment for tissue-specific transcription factor motifs, highlighting the complexity of targeting fusion protein to chromatin. Our study suggests that PLZF/RARA directly targets genes important for haematopoietic development and supports the notion that PLZF/RARA acts mainly as an epigenetic regulator of its direct target genes.

Published
2011
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15. In vivo reinsertion of excised episomes by the V(D)J recombinase: a potential threat to genomic stability.

Author

Katrina Vanura, Bertrand Montpellier, Trang Le, Salvatore Spicuglia, Jean-Marc Navarro, Olivier Cabaud, Sandrine Roulland, Elodie Vachez, Immo Prinz, Pierre Ferrier, Rodrig Marculescu, Ulrich Jäger, and Bertrand Nadel

Subjects
Biology (General), QH301-705.5
Abstract

It has long been thought that signal joints, the byproducts of V(D)J recombination, are not involved in the dynamics of the rearrangement process. Evidence has now started to accumulate that this is not the case, and that signal joints play unsuspected roles in events that might compromise genomic integrity. Here we show both ex vivo and in vivo that the episomal circles excised during the normal process of receptor gene rearrangement may be reintegrated into the genome through trans-V(D)J recombination occurring between the episomal signal joint and an immunoglobulin/T-cell receptor target. We further demonstrate that cryptic recombination sites involved in T-cell acute lymphoblastic leukemia-associated chromosomal translocations constitute hotspots of insertion. Eventually, the identification of two in vivo cases associating episomal reintegration and chromosomal translocation suggests that reintegration events are linked to genomic instability. Altogether, our data suggest that V(D)J-mediated reintegration of episomal circles, an event likely eluding classical cytogenetic screenings, might represent an additional potent source of genomic instability and lymphoid cancer.

Published
2007
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16. Short tandem repeats are important contributors to silencer elements in T cells

Author

Saadat Hussain, Nori Sadouni, Dominic van Essen, Lan T M Dao, Quentin Ferré, Guillaume Charbonnier, Magali Torres, Frederic Gallardo, Charles-Henri Lecellier, Tom Sexton, Simona Saccani, Salvatore Spicuglia, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), and Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics
Abstract

The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.

Published
2023

18. IL7-receptor expression is frequent in T-cell acute lymphoblastic leukemia and predicts sensitivity to JAK-inhibition

Author

Lucien Courtois, Aurelie Cabannes-Hamy, Rathana Kim, Marine Delecourt, Antoine Pinton, Guillaume Charbonnier, Mélanie Féroul, Charlotte Smith, Giulia Tueur, Cecile Pivert, Estelle Balducci, Mathieu Simonin, Laure Hélène Angel, Salvatore Spicuglia, Nicolas Boissel, Guillaume P Andrieu, Vahid Asnafi, Philippe Rousselot, and Ludovic Lhermitte

Subjects
Immunology, Cell Biology, Hematology, Biochemistry
Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with a dismal prognosis related to refractory/relapsing diseases, raising the need for new targeted-therapies. Activating mutations of the IL7-receptor pathway genes (IL7Rp) play a proven leukemia-supportive role in T-ALL. JAK-inhibitors such as ruxolitinib have recently demonstrated preclinical efficacy. However, prediction markers for sensitivity to JAK-inhibitors are still lacking. Herein, we show that IL7R (CD127) expression is more frequent (~70%) than IL7Rp-mutations in T-ALL (~30%). We compared the so-called non-expressers (no IL7R-expression/IL7Rp-mutation), expressers (IL7R-expression without IL7Rp-mutation) and mutants (IL7Rp-mutations). Integrative multi-omics analysis outlined IL7R-deregulation in virtually all T-ALL subtypes, at the epigenetic-level in non-expressers, genetic-level in mutants, and post-transcriptional level in expressers. Ex-vivo data using primary-derived xenografts support that IL7Rp is functional whenever the IL7R is expressed, regardless of the IL7Rp mutational status. Consequently, ruxolitinib impaired T-ALL survival in both expressers and mutants. Interestingly, we show that expressers displayed ectopic IL7R-expression and IL7Rp-addiction conferring a deeper sensitivity to ruxolitinib. Conversely, mutants were more sensitive to venetoclax than expressers. Overall, combination of ruxolitinib and venetoclax resulted in synergistic effects in both groups. We illustrate the clinical relevance of this association by reporting achievement of complete remission in two patients with refractory/relapsed-T-ALL. This provides proof of concept for translation of this strategy into clinics as bridge to transplant. Altogether, IL7R-expression can be used as a biomarker for sensitivity to JAK-inhibition, thereby expanding the fraction of T-ALL patients eligible to ruxolitinib up to nearly ~70% of T-ALL.

Published
2023

19. Supplementary Methods, Figure Legends, Table Legend from Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia

Author

Vahid Asnafi, Jacques Ghysdael, Elizabeth Macintyre, Olivier Hermine, David-Alexandre Gross, Lucienne Chatenoud, Salvatore Spicuglia, Hervé Dombret, Norbert Ifrah, Françoise Pflumio, Els Verhoeyen, François-Loïc Cosset, Michael Dussiot, Melania Tesio, Ludovic Lhermitte, Cindy Da Costa de Jesus, Mohamed Belhocine, Benedetta Zaniboni, Francesca Rocchetti, Christine Tran Quang, Nuno R. dos Santos, and Amélie Trinquand

Abstract

Supplementary Methods, Figure Legends, Table Legend

Published
2023

20. Supplementary Figures 1 - 3, Table 1 from Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia

Author

Vahid Asnafi, Jacques Ghysdael, Elizabeth Macintyre, Olivier Hermine, David-Alexandre Gross, Lucienne Chatenoud, Salvatore Spicuglia, Hervé Dombret, Norbert Ifrah, Françoise Pflumio, Els Verhoeyen, François-Loïc Cosset, Michael Dussiot, Melania Tesio, Ludovic Lhermitte, Cindy Da Costa de Jesus, Mohamed Belhocine, Benedetta Zaniboni, Francesca Rocchetti, Christine Tran Quang, Nuno R. dos Santos, and Amélie Trinquand

Abstract

Supplementary Figure 1. Anti-CD3 stimulation of primary human T-ALLs. Supplementary Figure 2. TCR stimulation by in vivo administration of agonistic monoclonal antibody in a preventive setting inhibits human TCR+ T-ALL development. Supplementary Figure 3. TCR signaling is essential to the anti-leukemic effect of OKT3. Supplementary Table 1. Immunophenotypic and oncogenic characteristics of T-ALL samples.

Published
2023

22. Data from Epigenetic Silencing Affects l-Asparaginase Sensitivity and Predicts Outcome in T-ALL

Author

Vahid Asnafi, Nicolas Boissel, Mathilde Hunault, Elizabeth Macintyre, Hervé Dombret, Norbert Ifrah, Stéphane Leprêtre, Françoise Huguet, Yves Chalandon, Carlos Graux, Thibaut Leguay, Françoise Pflumio, Denis Puthier, Salvatore Spicuglia, Xavier Thomas, Charlotte Smith, Mohamed Belhocine, Mehdi Latiri, Etienne Lengliné, and Aurore Touzart

Abstract

Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depending on the underlying oncogenic events is a promising research area. TLX1- or TLX3-deregulated T-cell acute lymphoblastic leukemias (T-ALL; TLX1/3+) share an immature cortical phenotype and similar transcriptional signatures. However, their prognostic impacts differ, and inconsistent clinical outcome has been reported for TLX3. We therefore hypothesized that the overlapping transcriptional profiles of TLX1+ and TLX3+ T-ALLs would allow identification of candidate genes, which might determine their distinct clinical outcomes.Experimental Design:We compared TLX1+ and TLX3+ adult T-ALL outcome in the successive French national LALA-94 and GRAALL-2003/2005 multicentric trials and analyzed transcriptomic data to identify differentially expressed genes. Epigenetic regulation of asparagine synthetase (ASNS) and in vitro l-asparaginase sensitivity were evaluated for T-ALL cell lines and primary samples.Results:We show that TLX1+ patients expressed low levels of ASNS when compared with TLX3+ and TLX-negative patients, due to epigenetic silencing of ASNS by both DNA methylation and a decrease of active histone marks. Promoter methylation of the ASNS gene correlated with l-asparaginase sensitivity in both T-ALL cell lines and patient-derived xenografts. Finally, ASNS promoter methylation was an independent prognostic factor for both event-free survival [HR, 0.42; 95% confidence interval (CI), 0.24–0.71; P = 0.001] and overall survival (HR, 0.40; 95% CI, 0.23–0.70; P = 0.02) in 160 GRAALL-2003/2005 T-ALL patients and also in an independent series of 47 LL03-treated T lymphoblastic lymphomas (P = 0.012).Conclusions:We conclude that ASNS methylation status at diagnosis may allow individual adaptation of l-asparaginase dose.

Published
2023

23. Correspondence on H3K4 methylation at enhancers and broad promoters concerning the issues raised by Shah et al. in 'Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies'

Author

Aleksandra Pękowska, Charbonnier Guillaume, Andrau Jean-Christophe, and Salvatore Spicuglia

Abstract

Using a series of calibrated ChIP-seq experiments, Shah et al. previously determined the specificity of widely used antibodies recognizing different levels of histone 3 at lysine 4 methylation (H3K4me) (Shah et al., 2018). The authors concluded that a significant number of published studies reporting on H3K4me were “flawed” due to cross-reactivity of antibodies. Considering the potential impact of these conclusions, we investigated the source of the discrepancy between the previous studies and that of Shah et al.

Published
2023

24. Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers

Author

Cody Ashby, Brian A Walker, Marco Trevisan-Herraz, Sharmilan Thanendrarajan, Kent Fung, Agata Cieslak, Shmuel Yaccoby, Maurizio Zangari, Aneta Mikulasova, Daniel Rico, Vahid Asnafi, Lisa J. Russell, Nefeli Karataraki, Anne E. Corcoran, Daniel Kent, Sophie Hambleton, Carolina Schinke, Gareth J. Morgan, Salvatore Spicuglia, Frits van Rhee, and Chris A. Brackley

Subjects
Genetics, LMO2, Epigenomics, 0303 health sciences, Breakpoint, Chromosomal translocation, Oncogenes, Biology, Chromatin, Translocation, Genetic, Histones, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, biology.protein, Humans, Enhancer, Gene, Genetics (clinical), 030304 developmental biology, Immunoglobulin heavy locus
Abstract

Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with enhancers, often called enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (IGH) and proto-oncogene CCND1 that are common in B-cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterised the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with hijacking of super-enhancers of other common oncogenes in B-cell (MAF, MYC and FGFR3/NSD2) and T-cell malignancies (LMO2, TLX3 and TAL1). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of epigenomic translocation, where the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers.

Published
2021

25. Current challenges in understanding the role of enhancers in disease

Author

Judith Barbara Zaugg, Pelin Sahlén, Robin Andersson, Meritxell Alberich-Jorda, Wouter de Laat, Bart Deplancke, Jorge Ferrer, Susanne Mandrup, Gioacchino Natoli, Dariusz Plewczynski, Alvaro Rada-Iglesias, Salvatore Spicuglia, European Molecular Biology Laboratory (EMBL), Royal Institute of Technology, IT University of Copenhagen (ITU), Medicine Charles University and General Faculty Hospital in Prague, University Medical Center [Utrecht], School of Life Sciences [Lausanne], Ecole Polytechnique Fédérale de Lausanne (EPFL), Barcelona Institute of Science and Technology (BIST), University of Southern Denmark (SDU), IRCCS Istituto Nazionale dei Tumori [Milano], University of Warsaw (UW), University of Cantabria, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), European Project: 286079,EC:FP7:PEOPLE,FP7-PEOPLE-2011-IAPP,AIRFORS(2012), and European Commission

Subjects
Epigenomics, variants, super-enhancers, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Genomics, single-cell, burkitt-lymphoma, dissection, Structural Biology, beta-globin gene, expression, chromatin, identification, Molecular Biology, shadow enhancers
Abstract

Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing evidence that enhancer dysfunction due to genetic, structural or epigenetic mechanisms contributes to a broad range of human diseases referred to as enhanceropathies. Such mechanisms often underlie the susceptibility to common diseases, but can also play a direct causal role in cancer or Mendelian diseases. Despite the recent gain of insights into enhancer biology and function, we still have a limited ability to predict how enhancer dysfunction impacts gene expression. Here we discuss the major challenges that need to be overcome when studying the role of enhancers in disease etiology and highlight opportunities and directions for future studies, aiming to disentangle the molecular basis of enhanceropathies., All authors are members of the EU-funded Innovative Training Network ‘Molecular Basis of Human Enhanceropathies’ (Enhpathy, www.enhpathy.eu) and received funding from the Horizon 2020 research and innovation program under Marie Sklodowska-Curie grant agreement no. 860002.

Published
2022

26. Identification of

Author

Samia, Nisar, Magali, Torres, Alassane, Thiam, Bruno, Pouvelle, Florian, Rosier, Frederic, Gallardo, Oumar, Ka, Babacar, Mbengue, Rokhaya Ndiaye, Diallo, Laura, Brosseau, Salvatore, Spicuglia, Alioune, Dieye, Sandrine, Marquet, and Pascal, Rihet

Subjects
Plasma Membrane Calcium-Transporting ATPases, Humans, Genetic Predisposition to Disease, Regulatory Sequences, Nucleic Acid, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Malaria
Abstract

Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five

Published
2022

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

Author

Agata Cieslak, Mehdi Latiri, Salvatore Spicuglia, Anand Mayakonda, Nicolas Boissel, Jacques Ghysdael, Hervé Dombret, Guillaume Andrieu, Aurore Touzart, Pavlo Lutsik, Reka Toth, Norbert Ifrah, Charlotte Smith, Joschka Hey, Christine Tran Quang, Vahid Asnafi, Christoph Plass, Elizabeth Macintyre, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Heidelberg University, Intégrité du génome, ARN et cancer, Institut Curie [Paris]-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7), Hopital Saint-Louis [AP-HP] (AP-HP), Recherche clinique appliquée à l'hématologie ((EA_3518)), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), German Cancer Consortium [Heidelberg] (DKTK), and Spinelli, Lionel

Subjects
Adult, Epigenomics, 0301 basic medicine, T cell, [SDV]Life Sciences [q-bio], T-cell leukemia, Biology, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, IDH2, Epigenesis, Genetic, Mice, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Humans, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Gene Expression Profiling, General Medicine, DNA Methylation, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, medicine.anatomical_structure, Hypomethylating agent, Tumor progression, 030220 oncology & carcinogenesis, DNA methylation, Cancer research, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, TAL1
Abstract

International audience; 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 (C1-C5), which were either associated with co-occurring DNA methyltransferase 3 alpha (DNMT3A)/isocitrate dehydrogenase [NADP(+)] 2 (IDH2) mutations (C1), TAL bHLH transcription factor 1, erythroid differentiation factor (TAL1) deregulation (C2), T cell leukemia homeobox 3 (TLX3) (C3), TLX1/in cis-homeobox A9 (HOXA9) (C4), or in trans-HOXA9 overexpression (C5). Integrative analysis of DNA methylation and gene expression identified potential cluster-specific oncogenes and tumor suppressor genes. In addition to an aggressive hypomethylated subgroup (C1), our data identified an unexpected subset of hypermethylated T-ALL (C5) 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; P = 0.001 for C3, 0.01 for C4, and 0.0253 for C5) delayed tumor progression. These findings suggest that epigenetic-based therapies may provide an alternative treatment option in hypermethylated T-ALL.

Published
2021

28. PRC2 loss of function confers a targetable vulnerability to BET proteins in T-ALL

Author

Vahid Asnafi, Mathieu Simonin, Guillaume Charbonnier, Carlos Graux, Guillaume P. Andrieu, Philippe Rousselot, Françoise Huguet, Charlotte L. Smith, Milena Kohn, Agata Cieslak, Véronique Lhéritier, Salvatore Spicuglia, Marie-Emilie Dourthe, Nicolas Boissel, Hervé Dombret, UCL - (MGD) Service d'hématologie, UCL - SSS/IREC/MONT - Pôle Mont Godinne, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Spinelli, Lionel, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Catholique de Louvain = Catholic University of Louvain (UCL), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM), Coordination du Groupe GRAALL [CH Lyon-Sud], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Université Paris Diderot, Sorbonne Paris Cité, Paris, France, Université Paris Diderot - Paris 7 (UPD7), Centre Hospitalier de Versailles André Mignot (CHV), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Male, BLOOD COMMENTARY, [SDV]Life Sciences [q-bio], Mice, SCID, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, Biochemistry, Epigenesis, Genetic, Histones, 0302 clinical medicine, Loss of Function Mutation, Tumor Cells, Cultured, Medicine, 0303 health sciences, Lymphoid Neoplasia, biology, Gene Expression Regulation, Leukemic, Polycomb Repressive Complex 2, JAK-STAT signaling pathway, Hematology, Middle Aged, 3. Good health, [SDV] Life Sciences [q-bio], 030220 oncology & carcinogenesis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, Stem cell, PRC2, Adult, Adolescent, Antineoplastic Agents, Hormonal, Immunology, [SDV.CAN]Life Sciences [q-bio]/Cancer, macromolecular substances, 03 medical and health sciences, Young Adult, [SDV.CAN] Life Sciences [q-bio]/Cancer, Cell Line, Tumor, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, Epigenetics, Interleukin-7 receptor, Loss function, 030304 developmental biology, business.industry, Cell Biology, Minimal residual disease, Bromodomain, biology.protein, Cancer research, Prednisone, business, Transcription Factors
Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is a group of aggressive hematological cancers with dismal outcomes that are in need of new therapeutic options. Polycomb repressor complex 2 (PRC2) loss-of-function alterations were reported in pediatric T-ALL, yet their clinical relevance and functional consequences remain elusive. Here, we extensively analyzed PRC2 alterations in a large series of 218 adult T-ALL patients. We found that PRC2 genetic lesions are frequent events in T-ALL and are not restricted to early thymic precursor ALL. PRC2 loss of function associates with activating mutations of the IL7R/JAK/STAT pathway. PRC2-altered T-ALL patients respond poorly to prednisone and have low bone marrow blast clearance and persistent minimal residual disease. Furthermore, we identified that PRC2 loss of function profoundly reshapes the genetic and epigenetic landscapes, leading to the reactivation of stem cell programs that cooperate with bromodomain and extraterminal (BET) proteins to sustain T-ALL. This study identifies BET proteins as key mediators of the PRC2 loss of function-induced remodeling. Our data have uncovered a targetable vulnerability to BET inhibition that can be exploited to treat PRC2-altered T-ALL patients.

Published
2021

29. Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation

Author

Frederic Koch, Olivier Joffre, Amal Zine El Aabidine, Tom Sexton, Romain Fenouil, Jean-Christophe Andrau, Anne Molitor, Lan T.M. Dao, Muhammad Ahmad Maqbool, Nezih Karasu, Léo Pioger, Georges Lacaud, Salvatore Spicuglia, Francois van Laethem, Ivo Gut, Guillaume Charbonnier, Marta Gut, Sebastian Amigorena, University of Manchester [Manchester], Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universitat Pompeu Fabra [Barcelona] (UPF), Barcelona Institute of Science and Technology (BIST), Institut Curie [Paris], Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, 0301 basic medicine, Gene isoform, CapSTARR-seq, T-Lymphocytes, [SDV]Life Sciences [q-bio], Polycomb-Group Proteins, macromolecular substances, Computational biology, General Biochemistry, Genetics and Molecular Biology, Mice, enhancer and promoter usage, long-distance enhancer-promoter interactions, 03 medical and health sciences, 0302 clinical medicine, enhancer redundancy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Enhancer, Gene, Epigenomics, biology, Manchester Cancer Research Centre, ResearchInstitutes_Networks_Beacons/mcrc, Cell Differentiation, Promoter, Phenotype, 3. Good health, 030104 developmental biology, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, PRC2, 030217 neurology & neurosurgery, Function (biology), T cell enhancerome
Abstract

During thymic development and upon peripheral activation, T cells undergo extensive phenotypic and functional changes coordinated by lineage-specific developmental programs. To characterize the regulatory landscape controlling T cell identity, we perform a wide epigenomic and transcriptional analysis of mouse thymocytes and naive CD4 differentiated T helper cells. Our investigations reveal a dynamic putative enhancer landscape, and we could validate many of the enhancers using the high-throughput CapStarr sequencing (CapStarr-seq) approach. We find that genes using multiple promoters display increased enhancer usage, suggesting that apparent "enhancer redundancy" might relate to isoform selection. Furthermore, we can show that two Runx3 promoters display long-range interactions with specific enhancers. Finally, our analyses suggest a novel function for the PRC2 complex in the control of alternative promoter usage. Altogether, our study has allowed for the mapping of an exhaustive set of active enhancers and provides new insights into their function and that of PRC2 in controlling promoter choice during T cell differentiation. This work was supported in J.-C.A.’s lab by grants from Fondation pour la Recherche Médicale (FRM) “Amorçage Jeunes Equipes” AJE20130728183, Agence Nationale de la Recherche (ANR) isplice (ANR-11-BSV8-0013), ANR ChromaTin (ANR-10-BLAN-1326), ITMO INCA “Dys3Dpoly,” ESGI 2011 (FP7 funding for high-throughput sequencing), and Ligue Régionale contre le Cancer (Hérault). L.P. was supported by a grant from FRM (4eme année thèse FDT201904007910). The T.S. lab was supported by funds from the European Research Council (ERC) (H2020, Starting Grant 678624 - CHROMTOPOLOGY), the ATIP-Avenir program, and the grant ANR-10-LABX-0030-INRT, under program ANR-10-IDEX-0002-02. A.M.M. is supported by funds from IDEX (University of Strasbourg) and the Institut National Du Cancer.

Published
2020

30. Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes

Author

Mathieu Simonin, Denis Puthier, Guillaume Charbonnier, Iris Manosalva, Aneta Mikulasova, Eve-Lyne Mathieu, Pierre Ferrier, Charlotte Smith, José David Abad Flores, Mohamed Belhocine, Lydie Pradel, Vahid Asnafi, Salvatore Spicuglia, Daniel Rico, Lisa J. Russell, Hendrik G. Stunnenberg, Joost H.A. Martens, Muhammad Ahmad Maqbool, Agata Cieslak, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Radboud University [Nijmegen], University of Manchester [Manchester], Newcastle University [Newcastle], Centre d'Immunologie de Marseille - Luminy (CIML), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
biology, T cell, [SDV]Life Sciences [q-bio], Oncogenes, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, Cell biology, Epigenesis, Genetic, Histones, medicine.anatomical_structure, T cell differentiation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, biology.protein, medicine, Demethylase, H3K4me3, Humans, Ectopic expression, Epigenetics, Gene, Transcription factor, Molecular Biology, Genetics (clinical)
Abstract

International audience; Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain–associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain–associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain–associated genes in preleukemic cells. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extent and number of broad domains. Our results show that the regulation of broad H3K4me3 domains is associated with leukemogenesis, and suggest that the presence of these structures might be used for epigenetic prioritization of cancer-relevant genes, including long noncoding RNAs.

Published
2020

31. OLOGRAM : Determining significance of total overlap length between genomic regions sets

Author

Cécile Capponi, Frédéric Lopez, Nori Sadouni, Badih Ghattas, Denis Puthier, Salvatore Spicuglia, Yasmina Kermezli, Guillaume Charbonnier, Quentin Ferré, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Informatique et Systèmes (LIS), Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), éQuipe d'AppRentissage de MArseille (QARMA), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Spinelli, Lionel, and Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Statistics and Probability, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer science, [SDV]Life Sciences [q-bio], computer.software_genre, Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Functional relation, [STAT]Statistics [stat], [SDV] Life Sciences [q-bio], 03 medical and health sciences, Computational Mathematics, 0302 clinical medicine, Computational Theory and Mathematics, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Molecular Biology, computer, 030217 neurology & neurosurgery, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

Motivation Various bioinformatics analyses provide sets of genomic coordinates of interest. Whether two such sets possess a functional relation is a frequent question. This is often determined by interpreting the statistical significance of their overlaps. However, only few existing methods consider the lengths of the overlap, and they do not provide a resolutive P-value. Results Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF. It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length. Exclusion of user-defined genomic areas during the shuffling is supported. Availability and implementation This tool is available through the command line interface of the pygtftk toolkit. It has been tested on Linux and OSX and is available on Bioconda and from https://github.com/dputhier/pygtftk under the GNU GPL license. Contact denis.puthier@univ-amu.fr Supplementary information Supplementary data are available at Bioinformatics online.

Published
2020

32. Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation

Author

Joost H.A. Martens, Guillaume Hypolite, Guillaume Andrieu, Charlotte Smith, Melania Tesio, Denis Puthier, Eva M. Janssen-Megens, Guillaume Charbonnier, Hendrik G. Stunnenberg, Ivo Gut, Salvatore Spicuglia, Marta Gut, Mohamed Belhocine, Nicolas Boissel, Eve-Lyne Mathieu, Vahid Asnafi, Elizabeth Macintyre, Arnaud Petit, Aurore Touzart, Agata Cieslak, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Radboud university [Nijmegen], Universitat Pompeu Fabra [Barcelona] (UPF), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Plan Cancer2015 (C15076AS), PlBio-INCA, and Equipe Labelis ́ee Ligue contrele Cancer, ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), European Project: 282510,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,BLUEPRINT(2011), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Radboud University [Nijmegen]

Subjects
Lymphoma, Cellular differentiation, [SDV]Life Sciences [q-bio], T-Lymphocytes, Lymphocyte Activation, Histones, Epigenome, Mice, 0302 clinical medicine, Immunology and Allergy, Epigenomics, 0303 health sciences, Thymocytes, Leukemia, Stem Cells, Cell Differentiation, Chromatin, 3. Good health, Cell biology, DNA Demethylation, medicine.anatomical_structure, Enhancer Elements, Genetic, 030220 oncology & carcinogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, Protein Binding, T cell, Immunology, Receptors, Antigen, T-Cell, Thymus Gland, Biology, Gene Rearrangement, T-Lymphocyte, Article, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Humans, Enhancer, Transcription factor, Molecular Biology, 030304 developmental biology, Cell Nucleus, Homeodomain Proteins, T-cell receptor, DNA Methylation, Hematopoiesis, Leukemia & Lymphoma, Gene Expression Regulation, T cell differentiation, Apoptosis Regulatory Proteins, Protein Processing, Post-Translational
Abstract

This manuscript presents a comprehensive epigenomic analysis of human thymocyte development and provides new molecular insights into the mechanism by which the TCRA enhancer is activated during thymic maturation by developmentally programmed repression of HOXA factors., Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes in T cell acute lymphoblastic leukemia. These results highlight an analogous enhancer repression mechanism at play in normal and cancer conditions, but imposing distinct developmental constraints., Graphical Abstract

Published
2020

33. Approches haut débit pour l’étude des séquences cis-régulatrices

Author

Salvatore Spicuglia, Alexandre P. España, David Santiago-Algarra, and Lydie Pradel

Subjects
0301 basic medicine, 03 medical and health sciences, 030104 developmental biology, Biology, Molecular biology, General Biochemistry, Genetics and Molecular Biology
Abstract

La regulation de la transcription des genes chez les eucaryotes superieurs implique l’action d’elements regulateurs proximaux (promoteurs) ou distaux (amplificateurs ou enhancers ) du site d’initiation de la transcription (Transcription Start Site , TSS). Il est aujourd’hui bien connu que les elements enhancers jouent un role essentiel dans le developpement et la differenciation cellulaire. Les alterations genetiques de ces elements sont une cause majeure de pathologies humaines. De nombreuses strategies ont ete developpees pour identifier et caracteriser les enhancers . Ici, nous discutons des progres recents pour evaluer de facon systematique l’activite des enhancers allant des approches haut debit de type « gene rapporteur » aux recentes technologies basees sur le systeme CRISPR/Cas9. Nous soulignons comment ces approches contribuent a une meilleure comprehension de la fonction des enhancers en conduisant a la decouverte de nouveaux types de sequences de regulation et comment l’alteration des enhancers peut affecter la regulation transcriptionnelle.

Published
2017

34. Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4

Author

Otoniel, Rodríguez-Jorge, Linda A, Kempis-Calanis, Wassim, Abou-Jaoudé, Darely Y, Gutiérrez-Reyna, Céline, Hernandez, Oscar, Ramirez-Pliego, Morgane, Thomas-Chollier, Salvatore, Spicuglia, Maria A, Santana, and Denis, Thieffry

Subjects
CD4-Positive T-Lymphocytes, Toll-Like Receptor 5, Models, Immunological, Receptors, Antigen, T-Cell, Humans, Lymphocyte Activation, Signal Transduction
Abstract

CD4

Published
2019

35. Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4 + T cell activation

Author

María Angélica Santana, Morgane Thomas-Chollier, Céline Hernandez, Linda A Kempis-Calanis, Denis Thieffry, Salvatore Spicuglia, Oscar Ramírez-Pliego, Wassim Abou-Jaoudé, Otoniel Rodríguez-Jorge, Darely Y. Gutiérrez-Reyna, Universidad Autonoma del Estado de Morelos (UAEM), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-16-CE15-0024,TMod,Biologie intégrative et modélisation de la différenciation des cellules T auxiliaires chez l'homme(2016), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris

Subjects
0303 health sciences, Toll-like receptor, biology, Chemistry, T cell, [SDV]Life Sciences [q-bio], T-cell receptor, CD28, Cell Biology, CREB, Biochemistry, Cell biology, 03 medical and health sciences, TLR2, 0302 clinical medicine, medicine.anatomical_structure, medicine, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, Signal transduction, Receptor, Molecular Biology, 030304 developmental biology, 030215 immunology
Abstract

International audience; CD4 + T cells recognize antigens through their T cell receptors (TCRs); however, additional signals involving co-stimulatory receptors, for example CD28, are required for proper T cell activation. Alternative co-stimulatory receptors have been proposed, including members of the Toll-like receptor (TLR) family, such as TLR5 and TLR2. To understand the molecular mechanism underlying this co-stimulatory function, we generated detailed molecular maps and logical models for the TCR and TLR5 signaling pathways, together with a merged model accounting for cross-interactions. Furthermore, we validated the resulting model by analyzing the responses of T cells to the activation of these pathways alone or in combination, in terms of the activation of the transcriptional regulators CREB, AP-1 (c-Jun), and NF-B (p65). Our merged model accurately reproduces the experimental results, showing that the activation of TLR5 can play a similar role to that of CD28 activation with respect to AP-1, CREB, and NF-кB activation, thereby providing insights regarding the cross-regulation of these pathways in CD4 + T cells.

Published
2019

36. A comprehensive catalog of LncRNAs expressed in T-cell acute lymphoblastic leukemia

Author

Wiam Saadi, Marc-Antoine Garibal, Yasmina Kermezli, Vahid Asnafi, Mourad Aribi, Eve-Lyne Mathieu, Salvatore Spicuglia, Denis Puthier, Mohamed Belhocine, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Tlemcen, FundingWork in the TAGC laboratory was supported by recurrent funding from INSERM and Aix-Marseille University and by the Foundation for Cancer Research ARC (ARC PJA 20151203149) and A*MIDEX (ANR-11-IDEX-0001-02), the Cancéropôle PACA, Plan Cancer 2015 (C15076AS) and Ligue Nationale contre le Cancer, of which the TAGC lab is an ‘Equipe Labellisée’. Y.K. and W.S. were supported, by the Franco-Algerian partnership Hubert Curien (PHC) Tassili (15MDU935)., ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), and ANR-11-IDEX-0001-02/11-IDEX-0001,AMIDEX,AMIDEX(2011)

Subjects
Cancer Research, oncogenes, T cell, Lymphoblastic Leukemia, [SDV]Life Sciences [q-bio], Thymus Gland, Computational biology, T cell acute leukemia, Biology, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Cell Line, Tumor, medicine, Humans, Epigenetics, Gene Expression Profiling, Reproducibility of Results, Hematology, Lncrna expression, medicine.disease, LncRNA, Gene Expression Regulation, Neoplastic, Leukemia, Cell Transformation, Neoplastic, medicine.anatomical_structure, Oncology, 030220 oncology & carcinogenesis, Large non-coding RNA, [SDV.IMM]Life Sciences [q-bio]/Immunology, RNA, Long Noncoding, Cancer development, T-ALL, 030215 immunology, T-cell acute leukemia
Abstract

International audience; Several studies have demonstrated that LncRNAs can play major roles in cancer development. The creation of a catalog of LncRNAs expressed in T cell acute lymphoblastic leukemia (T-ALL) is thus of particular importance. However, this task is challenging as LncRNA expression is highly restricted in time and space manner and thus may greatly differ between samples. We performed a systematic transcript discovery in RNA-Seq data obtained from T-ALL primary cells and cell lines. This led to the identification of 2560 novel LncRNAs. After the integration of these transcripts into a large compendium of LncRNAs (n = 30478) containing both known LncRNAs and those previously described in T-ALLs, we then performed a systematic genomic and epigenetic characterization of these transcript models demonstrating that these novel LncRNAs share properties with known LncRNAs. Finally, we provide evidence that these novel transcripts could be enriched in LncRNAs with potential oncogenic effects and identified a subset of LncRNAs coregulated with T-ALL oncogenes. Overall, our study represents a comprehensive resource of LncRNAs expressed in T-ALL and might provide new cues on the role of lncRNAs in this type of leukemia.

Published
2019

37. Explore, edit and leverage genomic annotations using Python GTF toolkit

Author

N. Zweig, Aitor González, Frédéric Lopez, Salvatore Spicuglia, Mourad Aribi, Mohamed Belhocine, Quentin Ferré, Denis Puthier, Yasmina Kermezli, Guillaume Charbonnier, Spinelli, Lionel, INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates, Aix Marseille Université (AMU), The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria, and ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)

Subjects
Statistics and Probability, Computer science, [SDV]Life Sciences [q-bio], computer.software_genre, Biochemistry, 03 medical and health sciences, Exon, Ensembl, Leverage (statistics), Bigwig, Molecular Biology, Gene, 030304 developmental biology, computer.programming_language, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, Programming language, Command-line interface, 030302 biochemistry & molecular biology, Intron, Computational Biology, Genomics, Python (programming language), Computer Science Applications, [SDV] Life Sciences [q-bio], Computational Mathematics, Computational Theory and Mathematics, Scripting language, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract

Motivation While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format. Results We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses. Availability and implementation pygtftk and gtftk have been tested on Linux and MacOSX and are available from https://github.com/dputhier/pygtftk under the MIT license. The libgtftk dynamic library written in C is available from https://github.com/dputhier/libgtftk.

Published
2019

38. Protein complexes associated with β‐catenin differentially influence the differentiation profile of neonatal and adult CD8 + T cells

Author

Rosario Guadalupe Labastida-Conde, Darely Y. Gutiérrez-Reyna, María Angélica Santana, Erick Cuevas-Fernández, Oscar H. López-Portales, Bárbara Lino-Alfaro, Oscar Ramírez-Pliego, Luis Eugenio González-de la Vara, Gerson N Hernández-Acevedo, Alicia Chagolla-López, Salvatore Spicuglia, Linda A Kempis-Calanis, Oscar B Aguilar-Luviano, Spinelli, Lionel, Universidad Autonoma del Estado de Morelos (UAEM), Theories and Approaches of Genomic Complexity (TAGC), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Adult, 0301 basic medicine, Cell signaling, CBP/p300, [SDV.IMM] Life Sciences [q-bio]/Immunology, Physiology, T cell, [SDV]Life Sciences [q-bio], Clinical Biochemistry, CD8-Positive T-Lymphocytes, Biology, CD8+ T cells, 03 medical and health sciences, 0302 clinical medicine, proteomics, Protein Interaction Mapping, medicine, Humans, Cytotoxic T cell, Promoter Regions, Genetic, Wnt Signaling Pathway, beta Catenin, Infant, Newborn, Wnt signaling pathway, Cell Differentiation, beta-catenin, Cell Biology, 3. Good health, Cell biology, [SDV] Life Sciences [q-bio], 030104 developmental biology, medicine.anatomical_structure, neonate immunity, Gene Expression Regulation, Multiprotein Complexes, 030220 oncology & carcinogenesis, Catenin, [SDV.IMM]Life Sciences [q-bio]/Immunology, Stem cell, Chromatin immunoprecipitation, CD8, Protein Binding
Abstract

International audience; The canonical Wnt signaling pathway is a master cell regulator involved in CD8+ T cell proliferation and differentiation. In human CD8+ T cells, this pathway induces differentiation into memory cells or a “stem cell memory like” population, which is preferentially present in cord blood. To better understand the role of canonical Wnt signals in neonatal or adult blood, we compared the proteins associated with β‐catenin, in nonstimulated and Wnt3a‐stimulated human neonatal and adult naive CD8+ T cells. Differentially recruited proteins established different complexes in adult and neonatal cells. In the former, β‐catenin‐associated proteins were linked to cell signaling and immunological functions, whereas those of neonates were linked to proliferation and metabolism. Wnt3a stimulation led to the recruitment and overexpression of Wnt11 in adult cells and Wnt5a in neonatal cells, suggesting a differential connexion with planar polarity and Wnt/Ca2+ noncanonical pathways, respectively. The chromatin immunoprecipitation polymerase chain reaction β‐catenin was recruited to a higher level on the promoters of cell renewal genes in neonatal cells and of differentiation genes in those of adults. We found a preferential association of β‐catenin with CBP in neonatal cells and with p300 in the adult samples, which could be involved in a higher self‐renewal capacity of the neonatal cells and memory commitment in those of adults. Altogether, our results show that different proteins associated with β‐catenin during Wnt3a activation mediate a differential response of neonatal and adult human CD8+ T cells.

Published
2019

39. CD8 + T Cells from Human Neonates Are Biased toward an Innate Immune Response

Author

Oscar Ramírez-Pliego, Hélène Holota, Aurélie Bergon, Ariel O. Galindo-Albarrán, José Antonio Sánchez-Villanueva, Oscar H. López-Portales, Alfonso Valencia, Otoniel Rodríguez-Jorge, Enrique Carrillo-de Santa Pau, M. Angélica Santana, Pierre Ferrier, Salvatore Spicuglia, Jean Imbert, Darely Y. Gutiérrez-Reyna, Armando Hernández-Mendoza, Béatrice Loriod, Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Transcriptomic Genomic Marseille-Luminy (TGML), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Spanish National Cancer Research Center (CNIO), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Consejo Nacional de Ciencia y Tecnologia (CONACYT), European Research Council, Programa de Mejoramiento del Profesorado, Aix-Marseille University, and Association pour la Recherche contre le Cancer (ARC)

Subjects
Adult, Cytotoxicity, Immunologic, 0301 basic medicine, [SDV]Life Sciences [q-bio], Antimicrobial peptides, epigenome, CD8-Positive T-Lymphocytes, Biology, immune response, General Biochemistry, Genetics and Molecular Biology, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Immune system, human immunity, Gene expression, T lymphocyte, Humans, Cytotoxic T cell, Epigenomics, Innate immune system, Gene Expression Profiling, T-cell receptor, Infant, Newborn, Gene Expression Regulation, Developmental, Immunity, Innate, 3. Good health, 030104 developmental biology, Immunology, CD8, Transcription Factors, 030215 immunology
Abstract

To better understand why human neonates show a poor response to intracellular pathogens, we compared gene expression and histone modification profiles of neonatal naive CD8+ T cells with that of their adult counterparts. We found that neonatal lymphocytes have a distinct epigenomic landscape associated with a lower expression of genes involved in T cell receptor (TCR) signaling and cytotoxicity and a higher expression of genes involved in the cell cycle and innate immunity. Functional studies corroborated that neonatal CD8+ T cells are less cytotoxic, transcribe antimicrobial peptides, and produce reactive oxygen species. Altogether, our results show that neonatal CD8+ T cells have a specific genetic program biased toward the innate immune response. These findings will contribute to better diagnosis and management of the neonatal immune response. This project was specifically supported by a joint EcosNord-Anuies-SEP-Con-acyt project (M11S01). Work in the M.A.S. laboratory is supported by grantsfrom Consejo Nacional de Ciencia y Tecnologı ́a(CONACYT; CB-2011-01168182) and Programa de Mejoramiento del Profesorado (PROMEPSI-UAEM/13/342). Work in the S.S. laboratory is supported by recurrent fundingfrom the Inserm and Aix-Marseille University and by specific grants from theEuropean Union’s FP7 Program (agreement 282510-BLUEPRINT), the Associ-ation pour la Recherche contre le Cancer (ARC) (project SFI20111203756), andthe Aix-Marseille initiative d’excelence (A*MIDEX) project ANR-11-IDEX-0001-02. We thank Centro Estatal de la Transfusio ́n Sanguı ́nea in Cuernavaca for thedonation of leukocyte concentrates and the mothers and babies of HospitalGeneral Parres in Cuernavaca for the donation of cord blood. This study makesuse of data generated by the Blueprint and Roadmap consortia. A full list of theinvestigators who contributed to the generation of the data is availablefromwww.blueprint-epigenome.euandhttp://www.roadmapepigenomics.org/. Funding for the Blueprint project was provided by the European Union’sSeventh Framework Program (FP7/2007-2013) under grant agreement282510 – BLUEPRINT. The Roadmap consortium is financed by the NIH. Weare grateful to Professor C.I. Pogson for critical reading of the manuscript. Sí

Published
2016

40. Transcriptional regulation by promoters with enhancer function

Author

Salvatore Spicuglia, Lan T.M. Dao, Theories and Approaches of Genomic Complexity (TAGC), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, Indoles, Transcription, Genetic, Epromoter, Thiophenes, Computational biology, Biology, Biochemistry, Mice, 03 medical and health sciences, 0302 clinical medicine, Genetics, Transcriptional regulation, Animals, Humans, CRISPR, Point-of-View, Epigenetics, Promoter Regions, Genetic, Enhancer, CRISPR/Cas9, Gene Editing, Mice, Knockout, Regulation of gene expression, Reporter gene, Promoter, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Reporter-assay, Gene regulation, Thiazoles, Enhancer Elements, Genetic, Pyrimidines, 030104 developmental biology, Gene Expression Regulation, Drosophila, Interferons, CRISPR-Cas Systems, K562 Cells, Chromatin immunoprecipitation, 030217 neurology & neurosurgery, HeLa Cells, Biotechnology
Abstract

Promoters with enhancer activity have been described recently. In this point of view, we will discuss current findings highlighting the commonality of this type of regulatory elements, their genetic and epigenetic characteristics, their potential biological roles in the regulation of gene expression and the underlining molecular mechanisms.Abbreviations: TSS: transcription start site; IFN: interferon; STARR-seq: Self-Transcribing Active Regulatory Region sequencing; MPRA: Massively Parallel Reporter Assay; ChIP: chromatin immunoprecipitation; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; lncRNA: long non-coding RNA.

Published
2018

41. Widespread Enhancer Activity from Core Promoters

Author

David Santiago-Algarra, Alejandra Medina-Rivera, Salvatore Spicuglia, Denis Puthier, Laboratorio Internacional de Investigación sobre el Genoma Humano Juriquilla, Universidad Nacional Autónoma de México ( UNAM ), Theories and Approaches of Genomic Complexity ( TAGC ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Universidad Nacional Autónoma de México (UNAM), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM)

Subjects
0301 basic medicine, Reporter-assays, [SDV]Life Sciences [q-bio], Computational biology, Biology, Biochemistry, Genome, 03 medical and health sciences, Gene expression, Animals, Humans, CRISPR, Promoter Regions, Genetic, Enhancer, Molecular Biology, CRISPR/Cas9, ComputingMilieux_MISCELLANEOUS, Epigenomics, Regulation of gene expression, ePromoters, [ SDV ] Life Sciences [q-bio], Promoter, High-Throughput Screening Assays, Gene regulation, Enhancer Elements, Genetic, 030104 developmental biology, Gene Expression Regulation, Regulatory sequence, Promoters
Abstract

Gene expression in higher eukaryotes is precisely regulated in time and space through the interplay between promoters and gene-distal regulatory regions, known as enhancers. The original definition of enhancers implies the ability to activate gene expression remotely, while promoters entail the capability to locally induce gene expression. Despite the conventional distinction between them, promoters and enhancers share many genomic and epigenomic features. One intriguing finding in the gene regulation field comes from the observation that many core promoter regions display enhancer activity. Recent high-throughput reporter assays along with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-related approaches have indicated that this phenomenon is common and might have a strong impact on our global understanding of genome organisation and gene expression regulation.

Published
2018

42. [High-throughput approaches to study cis-regulating elements]

Author

Alexandre P, España, David, Santiago-Algarra, Lydie, Pradel, and Salvatore, Spicuglia

Subjects
Gene Editing, Enhancer Elements, Genetic, Gene Expression Regulation, Animals, High-Throughput Nucleotide Sequencing, Humans, Clustered Regularly Interspaced Short Palindromic Repeats, Sequence Analysis, DNA
Abstract

Gene expression in higher eukaryotes is regulated through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. Enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Here, we discuss recent advances in high-throughput approaches to identify and characterize enhancer elements, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We discuss how these approaches contribute toward a better understanding of enhancer function in normal and pathological conditions.

Published
2018

43. Novel Intergenically Spliced Chimera, NFATC3-PLA2G15 , Is Associated with Aggressive T-ALL Biology and Outcome

Author

Jacques Ghysdael, Nicolas Boissel, Elizabeth Macintyre, Vahid Asnafi, Guillaume Hypolite, Jonathan Bond, Salvatore Spicuglia, Gaëlle Cordonnier, Christine Tran Quang, Aurélie Bergon, Mohamed Belhocine, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Systèmes et Applications des Technologies de l'Information et de l'Energie (SATIE), École normale supérieure - Cachan (ENS Cachan)-Université Paris-Sud - Paris 11 (UP11)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-École normale supérieure - Rennes (ENS Rennes)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Centre National de la Recherche Scientifique (CNRS), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), École normale supérieure - Rennes (ENS Rennes)-Université Paris-Sud - Paris 11 (UP11)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Université Gustave Eiffel (UNIV GUSTAVE EIFFEL), Service d'hématologie-immunologie-oncologie pédiatrique [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP]-Sorbonne Université (SU), Université Paris-Seine-Université Paris-Seine-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
0301 basic medicine, Cancer Research, [SDV]Life Sciences [q-bio], RNA-sequencing, T-acute lymphoblastic leukemia, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, T Acute Lymphoblastic Leukemia, 03 medical and health sciences, Chimera (genetics), 0302 clinical medicine, Nuclear Factor of Activated T-cells, NFAT Pathway, Transcription (biology), In vivo, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, Oncogene, fungi, In vitro, Intergenically-spliced chimera, 3. Good health, 030104 developmental biology, Oncology, 030220 oncology & carcinogenesis, Cancer research
Abstract

International audience; Leukemias are frequently characterized by the expression of oncogenic fusion chimeras that normally a rise due to chromosomal rearrangements. Cis-splicing of adjacent genes (cis-SAGe) results in transcription of intergenically-spliced chimeric RNAs (ISCs) in the absence of structural genomic changes, and aberrant ISC expression is now recognized as a potential cancer driver. We performed high-throughput RNA-sequencing of human T-acute lymphoblastic leukemia (T-ALL)samples, and used targeted analysis pipelines to detect fusion chimeras. We identified 55 candidate T-ALL-related ISCs, with a median of 4 per patient. We performed additional in-depth characterization of the NFATC3-PLA2G15 chimera, which was expressed at variable levels in primary T-ALL cases. Experimental analysis revealed that the fusion had lower activity than wild-type NFATC3 in vitro, and that T-ALL blasts with elevated NFATC3-PLA2G15 levels had reducedtranscription of canonical NFAT pathway genes in vivo. Strikingly, we found that high expression of the NFATC3-PLA2G15 chimera in leukemic blasts correlated with aggressive disease biology in murine patient-derived T-ALL xenografts,andpoor prognosis in human T-ALLpatients treated as part of the Francophone multinational GRAALL-2003 and -2005 studies. Our results suggest that ISCs are common in T-ALL, and that expression of specific ISCs may correlate with patient outcome.

Published
2018

44. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Author

Sergio Abrignani, David Adams, Melanie de Almeida, ALTUCCI, Lucia, Viren Amin, Ido Amit, Stylianos E, Antonarakis, Samuel Aparicio, Takahiro Arima, Laura Arrigoni, Rob Arts, Vahid Asnafi, Manel Esteller, Jae Bum Bae, Kevin Bassler, Stephan Beck, Benjamin Berkman, Bradley E, Bernstein, Mikhail Bilenky, Adrian Bird, Christoph Bock, Bernhard Boehm, Guillaume Bourque, Charles E, Breeze, Benedikt Brors, David Bujold, Oliver Burren, Marion J, Bussemakers, Adam Butterworth, Elias Campo, Enrique Carrillo de Santa Pau, Lisa Chadwick, Kui Ming Chan, Wei Chen, Tom H, Cheung, Luca Chiapperino, Nak Hyen Choi, Ho Ryun Chung, Laura Clarke, Joseph M, Connors, Philippe Cronet, John Danesh, Manolis Dermitzakis, Gerard Drewes, Pawel Durek, Stephanie Dyke, Tomasz Dylag, Connie J, Eaves, Peter Ebert, Roland Eils, Jürgen Eils, Catherine A, Ennis, Tariq Enver, Elise A, Feingold, Bärbel Felder, Anne Ferguson Smith, Jude Fitzgibbon, Paul Flicek, Roger S, Y, Foo, Peter Fraser, Mattia Frontini, Eileen Furlong, Sitanshu Gakkhar, Nina Gasparoni, Gilles Gasparoni, Daniel H, Geschwind, Petar Glažar, Thomas Graf, Frank Grosveld, Xin Yuan Guan, Roderic Guigo, Ivo G, Gut, Alf Hamann, Bok Ghee Han, R, Alan Harris, Simon Heath, Kristian Helin, Jan G, Hengstler, Alireza Heravi Moussavi, Karl Herrup, Steven Hill, Jason A, Hilton, Benjamin C, Hitz, Bernhard Horsthemke, Ming Hu, Joo Yeon Hwang, Nancy Y, Takashi Ito, Biola Maria Javierre, Sasa Jenko, Thomas Jenuwein, Yann Joly, Steven J, M, Jones, Yae Kanai, Hee Gyung Kang, Aly Karsan, Alexandra K, Kiemer, Song Cheol Kim, Bong Jo Kim, Hyeon Hoe Kim, Hiroshi Kimura, Sarah Kinkley, Filippos Klironomos, In Uk Koh, Myrto Kostadima, Christopher Kressler, Roman Kreuzhuber, Anshul Kundaje, Ralf Küppers, Carolyn Larabell, Paul Lasko, Mark Lathrop, S, Lee, Suman Lee, Hans Lehrach, Elsa Leitão, Thomas Lengauer, Åke Lernmark, David Leslie, Gilberto K, K, Leung, Danny Leung, Markus Loeffler, Yussanne Ma, Antonello Mai, Thomas Manke, Eric R, Marcotte, Marco A, Marra, Joost H, A, Martens, Jose Ignacio Martin Subero, Karen Maschke, Christoph Merten, Aleksandar Milosavljevic, Saverio Minucci, Totai Mitsuyama, Richard A, Moore, Fabian Müller, Andrew J, Mungall, Mihai G, Netea, Karl Nordström, Irene Norstedt, Hiroaki Okae, Vitor Onuchic, Francis Ouellette, Willem Ouwehand, Massimiliano Pagani, Vera Pancaldi, Thomas Pap, Tomi Pastinen, Ronak Patel, Dirk S, Paul, Michael J, Pazin, Pier Giuseppe Pelicci, Anthony G, Phillips, Julia Polansky, Bo Porse, J, Andrew Pospisilik, Shyam Prabhakar, Dena C, Procaccini, Andreas Radbruch, Nikolaus Rajewsky, Vardham Rakyan, Wolf Reik, Bing Ren, David Richardson, Andreas Richter, Daniel Rico, David J, Roberts, Philip Rosenstiel, Mark Rothstein, Abdulrahman Salhab, Hiroyuki Sasaki, John S, Satterlee, Sascha Sauer, Claudia Schacht, Florian Schmidt, Gerd Schmitz, Stefan Schreiber, Christopher Schröder, Dirk Schübeler, Joachim L, Schultze, Ronald P, Schulyer, Marcel Schulz, Martin Seifert, Katsuhiko Shirahige, Reiner Siebert, Thomas Sierocinski, Laura Siminoff, Anupam Sinha, Nicole Soranzo, Salvatore Spicuglia, Mikhail Spivakov, Christian Steidl, Seth Strattan, Michael Stratton, Peter Südbeck, Hao Sun, Narumi Suzuki, Yutaka Suzuki, Amos Tanay, David Torrents, Frederick L, Tyson, Thomas Ulas, Sebastian Ullrich, Toshikazu Ushijima, Alfonso Valencia, Edo Vellenga, Martin Vingron, Chris Wallace, Stefan Wallner, Jörn Walter, Huating Wang, Stephanie Weber, Nina Weiler, Andreas Weller, Andrew Weng, Steven Wilder, Sam M, Wiseman, Angela R, Zhenguo Wu, Jieyi Xiong, Yasuhiro Yamashita, Xinyi Yang, Desmond Y, Yap, Kevin Y, Yip, Stephen Yip, Jae Il Yoo, Daniel Zerbino, Gideon Zipprich, Antonarakis, Stylianos, International Human Epigenome Consortium, [0000-0002-8682-6748], Apollo - University of Cambridge Repository, Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Radboud University Medical Center [Nijmegen], Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Hematology, University of Groningen and University Medical Center Groningen, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Universitat de Barcelona, Sergio, Abrignani, David, Adam, Melanie de, Almeida, Altucci, Lucia, Viren, Amin, Ido, Amit, Stylianos, E, Antonarakis, Samuel, Aparicio, Takahiro, Arima, Laura, Arrigoni, Rob, Art, Vahid, Asnafi, Manel, Esteller, Jae Bum, Bae, Kevin, Bassler, Stephan, Beck, Benjamin, Berkman, Bradley, E, Bernstein, Mikhail, Bilenky, Adrian, Bird, Christoph, Bock, Bernhard, Boehm, Guillaume, Bourque, Charles, E, Breeze, Benedikt, Bror, David, Bujold, Oliver, Burren, Marion, J, Bussemakers, Adam, Butterworth, Elias, Campo, Enrique Carrillo de Santa, Pau, Lisa, Chadwick, Kui Ming, Chan, Wei, Chen, Tom, H, Cheung, Luca, Chiapperino, Nak Hyen, Choi, Ho Ryun, Chung, Laura, Clarke, Joseph, M, Connors, Philippe, Cronet, John, Danesh, Manolis, Dermitzaki, Gerard, Drewe, Pawel, Durek, Stephanie, Dyke, Tomasz, Dylag, Connie, J, Eaves, Peter, Ebert, Roland, Eil, Jürgen, Eil, Catherine, A, Ennis, Tariq, Enver, Elise, A, Feingold, Bärbel, Felder, Anne Ferguson, Smith, Jude, Fitzgibbon, Paul, Flicek, Roger, S, Y, Foo, Peter, Fraser, Mattia, Frontini, Eileen, Furlong, Sitanshu, Gakkhar, Nina, Gasparoni, Gilles, Gasparoni, Daniel, H, Geschwind, Petar, Glažar, Thomas, Graf, Frank, Grosveld, Xin Yuan, Guan, Roderic, Guigo, Ivo, G, Gut, Alf, Hamann, Bok Ghee, Han, R, Alan, Harri, Simon, Heath, Kristian, Helin, Jan, G, Hengstler, Alireza Heravi, Moussavi, Karl, Herrup, Steven, Hill, Jason, A, Hilton, Benjamin, C, Hitz, Bernhard, Horsthemke, Ming, Hu, Joo Yeon, Hwang, Nancy, Y, Ip, Takashi, Ito, Biola Maria, Javierre, Sasa, Jenko, Thomas, Jenuwein, Yann, Joly, Steven, J, M, Jone, Yae, Kanai, Hee Gyung, Kang, Aly, Karsan, Alexandra, K, Kiemer, Song Cheol, Kim, Bong Jo, Kim, Hyeon Hoe, Kim, Hiroshi, Kimura, Sarah, Kinkley, Filippos, Klironomo, In Uk, Koh, Myrto, Kostadima, Christopher, Kressler, Roman, Kreuzhuber, Anshul, Kundaje, Ralf, Küpper, Carolyn, Larabell, Paul, Lasko, Mark, Lathrop, S, Lee, Suman, Lee, Hans, Lehrach, Elsa, Leitão, Thomas, Lengauer, Åke, Lernmark, David, Leslie, Gilberto, K, K, Leung, Danny, Leung, Markus, Loeffler, Yussanne, Ma, Antonello, Mai, Thomas, Manke, Eric, R, Marcotte, Marco, A, Marra, Joost, H, A, Marten, Jose Ignacio Martin, Subero, Karen, Maschke, Christoph, Merten, Aleksandar, Milosavljevic, Saverio, Minucci, Totai, Mitsuyama, Richard, A, Moore, Fabian, Müller, Andrew, J, Mungall, Mihai, G, Netea, Karl, Nordström, Irene, Norstedt, Hiroaki, Okae, Vitor, Onuchic, Francis, Ouellette, Willem, Ouwehand, Massimiliano, Pagani, Vera, Pancaldi, Thomas, Pap, Tomi, Pastinen, Ronak, Patel, Dirk, S, Paul, Michael, J, Pazin, Pier Giuseppe, Pelicci, Anthony, G, Phillips, Julia, Polansky, Bo, Porse, J, Andrew, Pospisilik, Shyam, Prabhakar, Dena, C, Procaccini, Andreas, Radbruch, Nikolaus, Rajewsky, Vardham, Rakyan, Wolf, Reik, Bing, Ren, David, Richardson, Andreas, Richter, Daniel, Rico, David, J, Roberts, Philip, Rosenstiel, Mark, Rothstein, Abdulrahman, Salhab, Hiroyuki, Sasaki, John, S, Satterlee, Sascha, Sauer, Claudia, Schacht, Florian, Schmidt, Gerd, Schmitz, Stefan, Schreiber, Christopher, Schröder, Dirk, Schübeler, Joachim, L, Schultze, Ronald, P, Schulyer, Marcel, Schulz, Martin, Seifert, Katsuhiko, Shirahige, Reiner, Siebert, Thomas, Sierocinski, Laura, Siminoff, Anupam, Sinha, Nicole, Soranzo, Salvatore, Spicuglia, Mikhail, Spivakov, Christian, Steidl, Seth, Strattan, Michael, Stratton, Peter, Südbeck, Hao, Sun, Narumi, Suzuki, Yutaka, Suzuki, Amos, Tanay, David, Torrent, Frederick, L, Tyson, Thomas, Ula, Sebastian, Ullrich, Toshikazu, Ushijima, Alfonso, Valencia, Edo, Vellenga, Martin, Vingron, Chris, Wallace, Stefan, Wallner, Jörn, Walter, Huating, Wang, Stephanie, Weber, Nina, Weiler, Andreas, Weller, Andrew, Weng, Steven, Wilder, Sam, M, Wiseman, Angela, R, Wu, Zhenguo, Wu, Jieyi, Xiong, Yasuhiro, Yamashita, Xinyi, Yang, Desmond, Y, Yap, Kevin, Y, Yip, Stephen, Yip, Jae Il, Yoo, Daniel, Zerbino, and Gideon, Zipprich

Subjects
Epigenomics, 0301 basic medicine, [SDV]Life Sciences [q-bio], ADN, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Medizin, Biology, Genoma humà, General Biochemistry, Genetics and Molecular Biology, Epigenesis, Genetic, World Wide Web, 03 medical and health sciences, Human health, 0302 clinical medicine, Blueprint, Databases, Genetic, Humans, Disease, ddc:576.5, DNA methylation, databases, genetic, disease, histone code, humans, epigenesis, genetic, epigenomics, genome, human, biochemistry, genetics and molecular biology (all), Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Human genome, Genome, Human, DNA, Epigenome, DNA Methylation, Human cell, Epigenètica, Histone Code, 030104 developmental biology, 030220 oncology & carcinogenesis, Epigenetics
Abstract

Item does not contain fulltext The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC) highlight the coordinated achievements of IHEC teams to gather and interpret comprehensive epigenomic datasets to gain insights in the epigenetic control of cell states relevant for human health and disease. PAPERCLIP.

Published
2016

45. Novel Intergenically Spliced Chimera

Author

Jonathan, Bond, Christine, Tran Quang, Guillaume, Hypolite, Mohamed, Belhocine, Aurélie, Bergon, Gaëlle, Cordonnier, Jacques, Ghysdael, Elizabeth, Macintyre, Nicolas, Boissel, Salvatore, Spicuglia, and Vahid, Asnafi

Subjects
Male, Mice, Phospholipases A2, HEK293 Cells, NFATC Transcription Factors, Oncogene Proteins, Fusion, RNA Splicing, Animals, Humans, Heterografts, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, Survival Analysis, Acyltransferases
Abstract

Leukemias are frequently characterized by the expression of oncogenic fusion chimeras that normally arise due to chromosomal rearrangements. Intergenically spliced chimeric RNAs (ISC) are transcribed in the absence of structural genomic changes, and aberrant ISC expression is now recognized as a potential driver of cancer. To better understand these potential oncogenic drivers, high-throughput RNA sequencing was performed on T-acute lymphoblastic leukemia (T-ALL) patient specimens (

Published
2017

46. Genome-wide characterization of mammalian promoters with distal enhancer functions

Author

Nicolas Fernandez, Charbel Souaid, Jacques van Helden, Alejandra Medina-Rivera, Charlotte Andrieu-Soler, Aurélien Griffon, Eric Soler, Ariel O. Galindo-Albarrán, Lan T.M. Dao, Denis Puthier, Jaafar Alomairi, Salvatore Spicuglia, David Martin, Guillaume Charbonnier, Magali Torres, Tharshana Stephen, Laurent Vanhille, Jaime A. Castro-Mondragon, Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physique des interactions ioniques et moléculaires (PIIM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche des Cordeliers ( CRC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -École pratique des hautes études ( EPHE ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Technologies avancées pour le génôme et la clinique ( TAGC ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Physique des interactions ioniques et moléculaires ( PIIM ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, Epigenomics, Biology, 03 medical and health sciences, Mice, STARR-seq, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics, Animals, Humans, Enhancer, Promoter Regions, Genetic, Gene, Regulation of gene expression, Mammals, Reporter gene, Interferon-alpha, Promoter, 3T3 Cells, 030104 developmental biology, Enhancer Elements, Genetic, Gene Ontology, Gene Expression Regulation, Regulatory sequence, CRISPR-Cas Systems, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], K562 Cells, HeLa Cells
Abstract

International audience; Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene promoters. Extensive CRISPR-Cas9 genomic manipulation demonstrated the involvement of these promoters in the cis regulation of expression of distal genes in their natural loci. Our results have important implications for the understanding of complex gene regulation in normal development and disease.

Published
2017

47. TCRα rearrangements identify a subgroup of NKL-deregulated adult T-ALLs associated with favorable outcome

Author

Mohamed Belhocine, Audrey Petit, Patrick Villarese, S Le Noir, C Lours, Anthonie Willem Langerak, M. Tesio, M. Lelorc’h, A Cieslak, Vahid Asnafi, Norbert Ifrah, Elizabeth Macintyre, Nicolas Boissel, Salvatore Spicuglia, Ludovic Lhermitte, Amélie Trinquand, Hervé Dombret, Institut Necker Enfants-Malades (INEM) ( INEM - UM 111 (UMR 8253 / U1151) ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Technologies avancées pour le génôme et la clinique ( TAGC ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Immunology

Subjects
Adult, Male, 0301 basic medicine, Cancer Research, Lineage (genetic), Receptors, Antigen, T-Cell, alpha-beta, T cell, Cellular differentiation, [SDV]Life Sciences [q-bio], Biology, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, 03 medical and health sciences, Antigen, Cell Line, Tumor, medicine, Humans, Leukemia-Lymphoma, Adult T-Cell, Receptor, Gene, ComputingMilieux_MISCELLANEOUS, Homeodomain Proteins, [ SDV ] Life Sciences [q-bio], T-cell receptor, Cell Differentiation, Receptors, Antigen, T-Cell, gamma-delta, Hematology, Molecular biology, 030104 developmental biology, medicine.anatomical_structure, Oncology, Female, Ectopic expression, HeLa Cells
Abstract

T-cell acute lymphoblastic leukemia (T-ALL) results from leukemic transformation of T-cell precursors arrested at specific differentiation stages, including an 'early-cortical' thymic maturation arrest characterized by expression of cytoplasmic TCRβ but no surface T-cell receptor (TCR) and frequent ectopic expression of the TLX1/3 NK-like homeotic proteins (NKL). We designed a TCRα VJC PCR to identify clonal TCRα rearrangements in 32% of 127 T-ALLs, including 0/52 immature/TCRγδ lineage cases and 41/75 (55%) TCRαβ lineage cases. Amongst the latter, TCRα rearrangements were not identified in 30/54 (56%) of IMβ/pre-αβ early-cortical T-ALLs, of which the majority (21/30) expressed TLX1/3. We reasoned that the remaining T-ALLs might express other NKL proteins, so compared transcript levels of 46 NKL in T-ALL and normal thymic subpopulations. Ectopic overexpression of 10 NKL genes, of which six are unreported in T-ALL (NKX2-3, BARHL1, BARX2, EMX2, LBX2 and MSX2), was detectable in 17/104 (16%) T-ALLs. Virtually all NKL overexpressing T-ALLs were TCRα unrearranged and ectopic NKL transcript expression strongly repressed Eα activity, suggesting that ectopic NKL expression is the major determinant in early-cortical thymic T-ALL maturation arrest. This immunogenetic T-ALL subtype, defined by TCRβ VDJ but no TCRα VJ rearrangement, is associated with a favorable outcome in GRAALL-treated adult T-ALLs.

Published
2017

48. Recent advances in high-throughput approaches to dissect enhancer function

Author

Alexandre P. España, Salvatore Spicuglia, David Santiago-Algarra, Lan T.M. Dao, Lydie Pradel, Technologies avancées pour le génôme et la clinique (TAGC), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Nuclear Structure & Function, Cellular differentiation, [SDV]Life Sciences [q-bio], Review, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, enhancer function, STARR-seq, Transcriptional regulation, CRISPR, General Pharmacology, Toxicology and Pharmaceutics, Enhancer, ComputingMilieux_MISCELLANEOUS, General Immunology and Microbiology, Cas9, Promoter, Articles, Genomics, General Medicine, Developmental Molecular Mechanisms, MPRA, gene transcription, 030104 developmental biology, Regulatory sequence, Control of Gene Expression
Abstract

The regulation of gene transcription in higher eukaryotes is accomplished through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. It is now well acknowledged that enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Many strategies have been developed to identify and characterize enhancers. Here, we discuss recent advances in high-throughput approaches to assess enhancer activity, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We highlight how these approaches contribute toward a better understanding of enhancer function, eventually leading to the discovery of new types of regulatory sequences, and how the alteration of enhancers can affect transcriptional regulation.

Published
2017

49. Ascorbic acid drives the differentiation of mesoderm-derived embryonic stem cells. Involvement of p38 MAPK/CREB and SVCT2 transporter

Author

Benoit Bordignon, Fryad Rahman, Michel Fontes, Jean-François Landrier, Malek Djabali, Raphaël Culerrier, Franck Peiretti, Salvatore Spicuglia, Nutrition, obésité et risque thrombotique (NORT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Landrier, Jean-Francois, Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Nutrition, obésité et risque thrombotique ( NORT ), Institut National de la Recherche Agronomique ( INRA ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération ( LBCMCP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Technologies avancées pour le génôme et la clinique ( TAGC ), and Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
0301 basic medicine, Cellular differentiation, Rex1, Retinoic acid, Tretinoin, Muscle Development, Osteocytes, p38 Mitogen-Activated Protein Kinases, Mesoderm, Mice, 03 medical and health sciences, chemistry.chemical_compound, Osteogenesis, Adipocytes, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, Mesoderm derivatives, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Obesity, Sodium-Coupled Vitamin C Transporters, Cells, Cultured, Embryonic Stem Cells, ComputingMilieux_MISCELLANEOUS, Muscle Cells, Adipogenesis, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, Myogenesis, Cell Differentiation, Overweight, Ascorbic acid, CREB-Binding Protein, Embryonic stem cell, Molecular biology, Cell biology, 030104 developmental biology, chemistry, Differentiation, Stem cell, Food Science, Biotechnology
Abstract

International audience; Scope: Here we tested the hypothesis that ascorbic acid (AA) is a signaling molecule acting on stem cells via the differentiation of mesoderm derivatives, including myocytes, osteocytes, and adipocytes.Material and methods: Investigations used a murine embryonic stem cell line CGR8 able to differentiate into different cell types and treated or not with ascorbic acid. Differentiation was tracked mainly through cellular anatomy (including presence of beating cardiomyocytes) and expression of specific markers.Conclusion: The study demonstrated that AA drives mesoderm-derived stem cell differentiation toward myogenesis and osteogenesis and also inhibits adipogenesis. Further experiments found that AA competes with retinoic acid (RA) to drive cell differentiation in a dose-dependent manner: AA inhibited neurogenic differentiation and stimulated myogenesis whereas RA did the reverse. The AA-dependent differentiation of embryonic stem cells was shown to involve a p38 MAPK/CREB pathway, probably stimulated by cAMP via adenylate cyclases. In addition, SVCT2, the intracellular transporter of AA, acted as a receptor. Finally, we showed that activa-tion/repression of specific differentiation markers is associated with epigenetic changes in their associated promoters. We discuss the impact of these findings in terms of obesity and aging.

Published
2017

50. Rôle des longs ARN non codants dans le développement normal et pathologique

Author

Salvatore Spicuglia, Lan T.M. Dao, Denis Puthier, Eve-Lyne Mathieu, and Mohamed Belhocine

Subjects
Genetics, Regulation of gene expression, 0303 health sciences, RNA, General Medicine, Computational biology, Cell cycle, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Transcription (biology), Eukaryotic genome, 030220 oncology & carcinogenesis, Functional studies, Induced pluripotent stem cell, Reprogramming, 030304 developmental biology
Abstract

The transcription of essentially the entire eukaryotic genome generates a myriad of non-coding RNA species that show complex overlapping patterns of expression and regulation. In the last decade, several large scale genomic analyses have shed light on the widespread existence of long non-coding RNAs (lncRNAs) in mammals. Although the function of most lncRNAs remains unknown, many of them have been suggested to play important roles in the regulation of gene expression during normal development and diseases, including cancers. Indeed, functional studies have demonstrated that lncRNAs participate in various biological processes, including reprogramming of pluripotent stem cells, oncogenic progression and cell cycle regulation. In this review, we summarize recent findings about the biology of lncRNAs and their functions in normal and pathological development in mammals.

Published
2014

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