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1.
Genome Res ; 32(7): 1328-1342, 2022 07.
Article in English | MEDLINE | ID: mdl-34162697

ABSTRACT

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.


Subject(s)
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma , Epigenesis, Genetic , Histones/metabolism , Humans , Oncogenes , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics
2.
J Exp Med ; 217(9)2020 09 07.
Article in English | MEDLINE | ID: mdl-32667968

ABSTRACT

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 αß 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.


Subject(s)
Enhancer Elements, Genetic , Hematopoiesis/genetics , Receptors, Antigen, T-Cell/genetics , Thymus Gland/cytology , Animals , Apoptosis Regulatory Proteins/genetics , Cell Differentiation/genetics , Cell Nucleus/metabolism , Chromatin/metabolism , DNA Demethylation , DNA Methylation/genetics , Epigenome , Gene Expression Regulation , Gene Rearrangement, T-Lymphocyte , Histones/metabolism , Homeodomain Proteins/genetics , Humans , Lymphocyte Activation/immunology , Mice , Protein Binding , Protein Processing, Post-Translational , Stem Cells/cytology , T-Lymphocytes/cytology , Thymocytes/metabolism
3.
Haematologica ; 105(6): 1575-1581, 2020 06.
Article in English | MEDLINE | ID: mdl-31537687

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.


Subject(s)
Precursor Cell Lymphoblastic Leukemia-Lymphoma , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma , Adult , CpG Islands , DNA Methylation , Humans , Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Promoter Regions, Genetic , T-Lymphocytes
4.
Leuk Lymphoma ; 60(8): 2002-2014, 2019 08.
Article in English | MEDLINE | ID: mdl-30648438

ABSTRACT

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.


Subject(s)
Gene Expression Regulation, Neoplastic , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , RNA, Long Noncoding/genetics , Cell Line, Tumor , Cell Transformation, Neoplastic/genetics , Epigenesis, Genetic , Gene Expression Profiling , Humans , Oncogenes , Reproducibility of Results , Thymus Gland/immunology , Thymus Gland/metabolism
5.
Med Sci (Paris) ; 30(8-9): 790-6, 2014.
Article in French | MEDLINE | ID: mdl-25174757

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.


Subject(s)
Disease/genetics , Growth and Development/genetics , RNA, Long Noncoding/physiology , Animals , Biomarkers , Genetic Therapy/methods , High-Throughput Nucleotide Sequencing , Humans
6.
PLoS Genet ; 8(5): e1002676, 2012.
Article in English | MEDLINE | ID: mdl-22570633

ABSTRACT

Mutations in the l(3)mbt tumour suppressor result in overproliferation of Drosophila larval brains. Recently, the derepression of different gene classes in l(3)mbt mutants was shown to be causal for transformation. However, the molecular mechanisms of dL(3)mbt-mediated gene repression are not understood. Here, we identify LINT, the major dL(3)mbt complex of Drosophila. LINT has three core subunits-dL(3)mbt, dCoREST, and dLint-1-and is expressed in cell lines, embryos, and larval brain. Using genome-wide ChIP-Seq analysis, we show that dLint-1 binds close to the TSS of tumour-relevant target genes. Depletion of the LINT core subunits results in derepression of these genes. By contrast, histone deacetylase, histone methylase, and histone demethylase activities are not required to maintain repression. Our results support a direct role of LINT in the repression of brain tumour-relevant target genes by restricting promoter access.


Subject(s)
Brain Neoplasms/genetics , Drosophila Proteins , Drosophila melanogaster/genetics , Multiprotein Complexes , Repressor Proteins , Animals , Animals, Genetically Modified , Binding Sites , Cell Line , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Gene Expression Regulation , Genome, Insect , Germ Cells/metabolism , Histones/genetics , Histones/metabolism , Larva/genetics , Larva/metabolism , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Mutation , Polytene Chromosomes/genetics , RNA Interference , Repressor Proteins/genetics , Repressor Proteins/metabolism
7.
Nucleic Acids Res ; 40(11): 4879-91, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22362736

ABSTRACT

The ATP-dependent chromatin remodeler dMi-2 can play both positive and negative roles in gene transcription. Recently, we have shown that dMi-2 is recruited to the hsp70 gene in a heat shock-dependent manner, and is required to achieve high transcript levels. Here, we use chromatin immunoprecipitation sequencing (ChIP-Seq) to identify other chromatin regions displaying increased dMi-2 binding upon heat shock and to characterize the distribution of dMi-2 over heat shock genes. We show that dMi-2 is recruited to the body of at least seven heat shock genes. Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs. We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A. Rather, dMi-2 binding is restricted to transcribed regions. Our results suggest that dMi-2 distribution over active heat shock genes are determined by transcriptional activity.


Subject(s)
Adenosine Triphosphatases/metabolism , Autoantigens/metabolism , Drosophila Proteins/metabolism , Heat-Shock Proteins/genetics , Heat-Shock Response/genetics , Transcription, Genetic , Animals , Cells, Cultured , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Genetic Loci , HSP70 Heat-Shock Proteins/genetics
8.
Am J Physiol Heart Circ Physiol ; 295(1): H21-8, 2008 Jul.
Article in English | MEDLINE | ID: mdl-18502908

ABSTRACT

Extracellular purines and pyrimidines have major effects on cardiac rhythm and contraction. ATP/UTP are released during various physiopathological conditions, such as ischemia, and despite degradation by ectonucleotidases, their interstitial concentrations can markedly increase, a fact that is clearly associated with arrhythmia. In the present whole cell patch-clamp analysis on ventricular cardiomyocytes isolated from various mammalian species, ATP and UTP elicited a sustained, nonselective cationic current, I(ATP). UDP was ineffective, whereas 2'(3')-O-(4-benzoylbenzoyl)-ATP was active, suggesting that P2Y(2) receptors are involved. I(ATP) resulted from the binding of ATP(4-) to P2Y(2) purinoceptors. I(ATP) was maintained after ATP removal in the presence of guanosine 5'-[gamma-thio]triphosphate and was inhibited by U-73122, a PLC inhibitor. Single-channel openings are rather infrequent under basal conditions. ATP markedly increased opening probability, an effect prevented by U-73122. Two main conductance levels of 14 and 23 pS were easily distinguished. Similarly, in fura-2-loaded cardiomyocytes, Mn(2+) quenching and Ba(2+) influx were significant only in the presence of ATP or UTP. Adult rat ventricular cardiomyocytes expressed transient receptor potential channel TRPC1, -3, -4, and -7 mRNA and the TRPC3 and TRPC7 proteins that coimmunoprecipitated. Finally, the anti-TRPC3 antibody added to the patch pipette solution inhibited I(ATP). In conclusion, activation of P2Y(2) receptors, via a G protein and stimulation of PLCbeta, induces the opening of heteromeric TRPC3/7 channels, leading to a sustained, nonspecific cationic current. Such a depolarizing current could induce cell automaticity and trigger the arrhythmic events during an early infarct when ATP/UTP release occurs. These results emphasize a new, potentially deleterious role of TRPC channel activation.


Subject(s)
Adenosine Triphosphate/metabolism , Myocytes, Cardiac/metabolism , Receptors, Purinergic P2/metabolism , Signal Transduction , TRPC Cation Channels/metabolism , Uridine Triphosphate/metabolism , Animals , Arrhythmias, Cardiac/etiology , Arrhythmias, Cardiac/metabolism , Cell Membrane Permeability , Disease Models, Animal , Dogs , Estrenes/pharmacology , Humans , Male , Membrane Potentials , Mice , Mice, Knockout , Myocardial Infarction/complications , Myocardial Infarction/metabolism , Myocytes, Cardiac/drug effects , Myocytes, Cardiac/enzymology , Patch-Clamp Techniques , Phosphodiesterase Inhibitors/pharmacology , Phospholipase C beta/antagonists & inhibitors , Phospholipase C beta/metabolism , Pyrrolidinones/pharmacology , Rats , Rats, Wistar , Receptors, Purinergic P2/genetics , Receptors, Purinergic P2X , Receptors, Purinergic P2X4 , Receptors, Purinergic P2Y2 , Signal Transduction/drug effects
9.
J Biol Chem ; 279(8): 7241-6, 2004 Feb 20.
Article in English | MEDLINE | ID: mdl-14662757

ABSTRACT

TRPC proteins are the mammalian homologues of the Drosophila transient receptor potential channel and are involved in calcium entry after agonist stimulation of non-excitable cells. Seven mammalian TRPCs have been cloned, and their mechanisms of activation and regulation are still the subject of intense research. TRPC proteins interact with the inositol 1,4,5-trisphosphate receptor, and the conformational coupling plays a critical role in the activation of calcium entry. Some evidence also supports an exocytotic mechanism as part of the activation of calcium entry. To investigate the possible involvement of exocytosis in TRPC6 activation, we evaluated the location of TRPC6 at the plasma membrane by biotinylation labeling of cell surface proteins and by indirect immunofluorescence marking of TRPC6 in stably transfected HEK 293 cells. We showed that when the muscarinic receptor was stimulated or the thapsigargin-induced intracellular calcium pool was depleted the level of TRPC6 at the plasma membrane increased. The carbachol concentration at which TRPC6 externalization occurred was lower than the concentration required to activate TRPC6. Externalization occurred within the first 30 s of stimulation, and TRPC6 remained at the plasma membrane as long as the stimulus was present. These results indicate that an exocytotic mechanism is involved in the activation of TRPC6.


Subject(s)
Calcium Channels/physiology , Cell Membrane/metabolism , Exocytosis , GTP-Binding Protein alpha Subunits, Gq-G11/physiology , Receptors, G-Protein-Coupled/metabolism , Biotinylation , Calcium/metabolism , Calcium Channels/metabolism , Cell Line , Cytosol/metabolism , Dose-Response Relationship, Drug , Fluorescent Antibody Technique, Indirect , GTP-Binding Protein alpha Subunits, Gq-G11/metabolism , Humans , Immunoblotting , Inositol 1,4,5-Trisphosphate Receptors , Protein Conformation , Receptors, Cytoplasmic and Nuclear/metabolism , TRPC Cation Channels , TRPC6 Cation Channel , Time Factors , Transfection
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