Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 22
Filtrar
Más filtros

Banco de datos
País/Región como asunto
Tipo del documento
País de afiliación
Intervalo de año de publicación
1.
Blood ; 135(5): 360-370, 2020 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-31774495

RESUMEN

The oncogenic events involved in breast implant-associated anaplastic large cell lymphoma (BI-ALCL) remain elusive. To clarify this point, we have characterized the genomic landscape of 34 BI-ALCLs (15 tumor and 19 in situ subtypes) collected from 54 BI-ALCL patients diagnosed through the French Lymphopath network. Whole-exome sequencing (n = 22, with paired tumor/germline DNA) and/or targeted deep sequencing (n = 24) showed recurrent mutations of epigenetic modifiers in 74% of cases, involving notably KMT2C (26%), KMT2D (9%), CHD2 (15%), and CREBBP (15%). KMT2D and KMT2C mutations correlated with a loss of H3K4 mono- and trimethylation by immunohistochemistry. Twenty cases (59%) showed mutations in ≥1 member of the JAK/STAT pathway, including STAT3 (38%), JAK1 (18%), and STAT5B (3%), and in negative regulators, including SOCS3 (6%), SOCS1 (3%), and PTPN1 (3%). These mutations were more frequent in tumor-type samples than in situ samples (P = .038). All BI-ALCLs expressed pSTAT3, regardless of the mutational status of genes in the JAK/STAT pathway. Mutations in the EOMES gene (12%) involved in lymphocyte development, PI3K-AKT/mTOR (6%), and loss-of-function mutations in TP53 (12%) were also identified. Copy-number aberration (CNA) analysis identified recurrent alterations, including gains on chromosomes 2, 9p, 12p, and 21 and losses on 4q, 8p, 15, 16, and 20. Regions of CNA encompassed genes involved in the JAK/STAT pathway and epigenetic regulators. Our results show that the BI-ALCL genomic landscape is characterized by not only JAK/STAT activating mutations but also loss-of-function alterations of epigenetic modifiers.


Asunto(s)
Implantes de Mama/efectos adversos , Epigénesis Genética , Quinasas Janus/metabolismo , Linfoma Anaplásico de Células Grandes/etiología , Linfoma Anaplásico de Células Grandes/genética , Factores de Transcripción STAT/metabolismo , Transducción de Señal , Adulto , Anciano , Anciano de 80 o más Años , Variaciones en el Número de Copia de ADN , Femenino , Genoma Humano , Humanos , Linfoma Anaplásico de Células Grandes/patología , Persona de Mediana Edad , Mutación/genética
2.
Bioinformatics ; 2019 Oct 24.
Artículo en Inglés | MEDLINE | ID: mdl-31647522

RESUMEN

MOTIVATION: Microsatellite instability (MSI) is a molecular marker of DNA mismatch repair deficiency frequently at play in oncogenesis. MSI testing is used for diagnostic, prognostic and therapeutic purposes in several cancers. The current gold standard analysis for microsatellite status is based on length distribution analysis of multiplex-PCR generated DNA fragments from tumor samples which is a laborious and time consuming method. Next generation sequencing (NGS) using amplicon panels is an easy, accurate and scalable technique to determine both the microsatellite status and tumor genome mutations at the same time. Here, we describe MIAmS, an application designed to tag microsatellite status from amplicon NGS of tumor samples. Interestingly, this tool does not require paired normal tissue for comparison. In addition, this scalable application provides a user-friendly report for the interpretation of the results by biologists and exhibits a strong accuracy and robustness for determination of the MSI status. AVAILABILITY: https://github.com/bialimed/miams. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online, evaluation data are available at http://www.ebi.ac.uk/ena/data/view/PRJEB31725.

3.
Bioinformatics ; 34(8): 1287-1294, 2018 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-29228191

RESUMEN

Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME. Availability and implementation: Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr. Contact: geraldine.pascal@inra.fr. Supplementary information: Supplementary data are available at Bioinformatics online.


Asunto(s)
Metagenómica/métodos , Programas Informáticos , Bacterias/genética , Análisis por Conglomerados
4.
Genes Chromosomes Cancer ; 57(4): 203-210, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29266774

RESUMEN

An increasing number of sarcomas displaying a primitive, monomorphic spindle cell phenotype have been shown to harbor recurrent gene fusions, including biphenotypic sinonasal sarcoma (SNS). Occurring in the sinonasal area of middle-aged patients, SNS is a locally aggressive tumor harboring in 90% of cases recurrent gene fusions involving the PAX3 gene, in which the chimeric transcription factor induces an aberrant dual myogenic and neural phenotype. Here, we report an unusual oropharyngeal monomorphic spindle cell sarcoma in a 53-year-old man that revealed a novel RREB1-MKL2 gene fusion by RNA sequencing with the Illumina TruSight RNA Fusion Panel. The gene fusion was validated by RT-PCR. Although the tumor location is unusual (but head and neck seated), most of the other clinical, morphologic, immunophenotypic (focal combined expression of S100 protein, SMA, desmin, and myogenin) and oncogenic data suggest that this biphenotypic "oropharyngeal" sarcoma is closely related to the biphenotypic SNS spectrum. Notably, the RREB1-MKL2 chimeric transcription factor encoded by this fusion gene produced an increase in MKL2 expression, which regulates both neural and myogenic differentiation, mimicking the crucial role of PAX3 reported in SNS oncogenesis. NGS and especially RNA sequencing may be used to identify new candidate fusion oncogenes in soft tissue tumors, which would help in updating the existing classification. In turn, this would lead to better therapeutic management of patients.


Asunto(s)
Proteínas de Unión al ADN/genética , Neoplasias de los Senos Paranasales/genética , Factores de Transcripción/genética , Biomarcadores de Tumor/genética , Proteínas de Unión al ADN/metabolismo , Fusión Génica , Humanos , Masculino , Persona de Mediana Edad , Fusión de Oncogenes , Proteínas de Fusión Oncogénica/genética , Neoplasias Orofaríngeas/genética , Sarcoma/genética , Neoplasias de los Tejidos Blandos/genética , Factores de Transcripción/metabolismo
5.
Bioinformatics ; 32(3): 456-8, 2016 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-26454273

RESUMEN

SUMMARY: Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows. AVAILABILITY AND IMPLEMENTATION: Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal. CONTACT: Jerome.Mariette@toulouse.inra.fr.


Asunto(s)
Biología Computacional/métodos , Sistemas de Administración de Bases de Datos , Almacenamiento y Recuperación de la Información , Internet , Programas Informáticos , Bases de Datos Factuales , Humanos , Flujo de Trabajo
6.
J Exp Bot ; 68(15): 4339-4355, 2017 07 10.
Artículo en Inglés | MEDLINE | ID: mdl-28922755

RESUMEN

In many fruit species, including grapevine, grafting is used to improve scion productivity and quality and to adapt the plant to environmental conditions. However, the mechanisms underlying the rootstock control of scion development are still poorly understood. The ability of rootstocks to regulate nitrogen uptake and assimilation may contribute to this control. A split-root system was used to grow heterografted grapevines and to investigate the molecular responses to changes in nitrate availability of two rootstocks known to affect scion growth differently. Transcriptome profiling by RNA sequencing was performed on root samples collected 3 and 24 h after nitrogen supply. The results demonstrated a common response involving nitrogen-related genes, as well as a more pronounced transcriptomic reprogramming in the genotype conferring the lower scion growth. A weighted gene co-expression network analysis allowed the identification of co-regulated gene modules, suggesting a role for nitrate transporter 2 family genes and some transcription factors as main actors controlling this genotype-dependent response to heterogeneous nitrogen supply. The relationship between nitrate, ethylene, and strigolactone hormonal pathways was found to differ between the two genotypes. These findings indicated that the genotypes responded differently to heterogeneous nitrogen availability, and this may contribute to their contrasting effect on scion growth.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Nitratos/metabolismo , Raíces de Plantas/fisiología , Transducción de Señal , Transcriptoma , Vitis/fisiología , Perfilación de la Expresión Génica , Nitrógeno/metabolismo , Raíces de Plantas/genética , Vitis/genética
7.
BMC Bioinformatics ; 15: 293, 2014 Aug 29.
Artículo en Inglés | MEDLINE | ID: mdl-25176396

RESUMEN

BACKGROUND: Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. RESULTS: jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. CONCLUSIONS: jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.


Asunto(s)
Gráficos por Computador , Programas Informáticos , Biología Computacional , Internet
8.
BMC Evol Biol ; 14: 259, 2014 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-25527898

RESUMEN

BACKGROUND: Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform. RESULTS: The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA (Met) and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations. CONCLUSIONS: Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.


Asunto(s)
Bivalvos/citología , Bivalvos/genética , Núcleo Celular , Genoma Mitocondrial , Mitocondrias , Animales , ADN Intergénico , Evolución Molecular , Proteínas de la Membrana/genética , Anotación de Secuencia Molecular , ARN Ribosómico/genética , ARN de Transferencia/genética
10.
Eur J Hum Genet ; 31(5): 526-530, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36404347

RESUMEN

Microphthalmia, Anophthalmia and Coloboma (MAC) form a spectrum of congenital eye malformations responsible for severe visual impairment. Despite the exploration of hundreds of genes by High-Throughput Sequencing (HTS), most of the patients remain without genetic diagnosis. One explanation could be the not yet demonstrated involvement of somatic mosaicism (undetected by conventional analysis pipelines) in those patients. Furthermore, the proportion of parental germline mosaicism in presumed de novo variations is still unknown in ocular malformations. Thus, using dedicated bioinformatics pipeline designed to detect mosaic variants, we reanalysed the sequencing data obtained from a 119 ocular development genes panel performed on blood samples of 78 probands with sporadic MAC without genetic diagnosis. Using the same HTS strategy, we sequenced 80 asymptomatic parents of 41 probands carrying a disease-causing variant in an ocular development gene considered de novo after Sanger sequencing of both parents. Reanalysis of the previously sequencing data did not find any mosaic variant in probands without genetic diagnosis. However, HTS of parents revealed undetected SOX2 and PAX6 mosaic variants in two parents. Finally, this work, performed on two large cohorts of patients with MAC spectrum, provides for the first time an overview of the interest of looking for mosaicism in ocular development disorders. Somatic mosaicism does not appear to be frequent in MAC spectrum and might explain only few diagnoses. Thus, other approaches such as whole genome sequencing should be considered in those patients. Parental mosaicism is however not that rare (around 5%) and challenging for genetic counselling.


Asunto(s)
Oftalmopatías , Mosaicismo , Humanos , Masculino , Femenino , Oftalmopatías/genética , Pruebas Genéticas , Linaje
11.
NAR Cancer ; 5(2): zcad011, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-36915289

RESUMEN

The exonuclease domain of DNA polymerases epsilon's catalytic subunit (POLE) removes misincorporated nucleotides, called proofreading. POLE-exonuclease mutations cause colorectal- and endometrial cancers with an extreme burden of single nucleotide substitutions. We recently reported that particularly the hereditary POLE exonuclease mutation N363K predisposes in addition to aggressive giant cell glioblastomas. We knocked-in this mutation homozygously into human cell lines and compared its properties to knock-ins of the likewise hereditary POLE L424V mutation and to a complete proofreading-inactivating mutation (exo-null). We found that N363K cells have higher mutation rates as both L424V- or exo-null mutant cells. In contrast to L424V cells, N363K cells expose a growth defect, replication stress and DNA damage. In non-transformed cells, these burdens lead to aneuploidy but macroscopically normal nuclei. In contrast, transformed N363K cells phenocopy the enlarged and disorganized nuclei of giant cell glioblastomas. Taken together, our data characterize a POLE exonuclease domain mutant that not only causes single nucleotide hypermutation, but in addition DNA damage and chromosome instability, leading to an extended tumor spectrum. Our results expand the understanding of the polymerase exonuclease domain and suggest that an assessment of both the mutational potential and the genetic instability might refine classification and treatment of POLE-mutated tumors.

12.
BMC Genomics ; 13: 462, 2012 Sep 09.
Artículo en Inglés | MEDLINE | ID: mdl-22958229

RESUMEN

BACKGROUND: Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. RESULTS: We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. CONCLUSIONS: NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data.


Asunto(s)
Programas Informáticos , Análisis de Secuencia de ADN , Interfaz Usuario-Computador
13.
Am J Surg Pathol ; 46(6): 742-753, 2022 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-34799485

RESUMEN

Despite the impressive efficacy of chimeric antigen receptor (CAR) T-cell therapy (CART) in B-cell non-Hodgkin lymphomas, durable responses are uncommon. The histopathologic and molecular features associated with treatment failure are still largely unknown. Therefore, we have analyzed 19 sequential tumor samples from 9 patients, prior anti-CD19 CART (pre-CART) and at relapse (post-CART), using immunohistochemistry, fluorescence in situ hybridization, array comparative genomic hybridization, next-generation DNA and RNA sequencing, and genome-scale DNA methylation. The initial diagnosis was diffuse large B-cell lymphoma (n=6), double-hit high-grade B-cell lymphoma (n=1), and Burkitt lymphoma (n=2). Histopathologic features were mostly retained at relapse in 7/9 patients, except the frequent loss of 1 or several B-cell markers. The remaining 2 cases (1 diffuse large B-cell lymphoma and 1 Burkitt lymphoma) displayed a dramatic phenotypic shift in post-CART tumors, with the drastic downfall of B-cell markers and emergence of T-cell or histiocytic markers, despite the persistence of identical clonal immunoglobulin gene rearrangements. The post-CART tumor with aberrant T-cell phenotype showed reduced mRNA expression of most B-cell genes with increased methylation of their promoter. Fluorescence in situ hybridization and comparative genomic hybridization showed global stability of chromosomal alterations in all paired samples, including 17p/TP53 deletions. New pathogenic variants acquired in post-CART samples included mutations triggering the PI3K pathway (PIK3R1, PIK3R2, PIK3C2G) or associated with tumor aggressiveness (KRAS, INPP4B, SF3B1, SYNE1, TBL1XR1). These results indicate that CART-resistant B-cell non-Hodgkin lymphomas display genetic remodeling, which may result in profound dysregulation of B-cell differentiation. Acquired mutations in the PI3K and KRAS pathways suggest that some targeted therapies could be useful to overcome CART resistance.


Asunto(s)
Linfoma de Burkitt , Linfoma de Células B Grandes Difuso , Transdiferenciación Celular , Hibridación Genómica Comparativa , Genómica , Humanos , Inmunoterapia Adoptiva/métodos , Hibridación Fluorescente in Situ , Linfoma de Células B Grandes Difuso/genética , Linfoma de Células B Grandes Difuso/terapia , Recurrencia Local de Neoplasia , Fosfatidilinositol 3-Quinasas/genética , Proteínas Proto-Oncogénicas p21(ras)/genética , Factores de Transcripción/genética
14.
Cancers (Basel) ; 13(12)2021 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-34208034

RESUMEN

T-cell lymphomas (TCL) represent a very heterogeneous group of lymphoid tumors which are clearly distinct from B-cell neoplasms [...].

15.
Cancers (Basel) ; 13(13)2021 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-34282778

RESUMEN

Epstein-Barr virus (EBV) is a ubiquitous virus detected in up to 95% of the general population. Most people are asymptomatic, while some may develop a wide range of EBV-associated lymphoproliferative disorders (LPD). Among them, EBV-positive T/NK LPD are uncommon diseases defined by the proliferation of T- or NK-cells infected by EBV. The 2017 World Health Organization (WHO) classification recognizes the following entities characterized by different outcomes: chronic active EBV infection of T- or NK-cell types (cutaneous and systemic forms), systemic EBV-positive T-cell lymphoma of childhood, EBV-positive aggressive NK-cell leukemia, extra nodal NK/T-cell lymphoma nasal type, and the new provisional entity known as primary EBV-positive nodal T/NK-cell lymphoma. In addition, EBV associated-hemophagocytic lymphohistiocytosis is part of EBV-positive T/NK LPD, but has not been included in the WHO classification due to its reactive nature. Despite novel insights from high-throughput molecular studies, EBV-positive NK/T-cell LPD diagnoses remain challenging, especially because of their rarity and overlap. Until now, an accurate EBV-positive NK/T LPD diagnosis has been based on its clinical presentation and course correlated with its histological features. This review aims to summarize clinical, pathological and molecular features of EBV-positive T/NK LPD subtypes and to provide an overview of new understandings regarding these rare disorders.

16.
Blood Adv ; 5(22): 4590-4593, 2021 11 23.
Artículo en Inglés | MEDLINE | ID: mdl-34607351

RESUMEN

Immunomorphological diagnosis of T-cell lymphoma (TCL) may be challenging, especially on needle biopsies. Multiplex polymerase chain reaction (PCR) assays to assess T-cell receptor (TCR) gene rearrangements are now widely used to detect T-cell clones and provide diagnostic support. However, PCR assays detect only 80% of TCL, and clonal lymphocyte populations may also appear in nonneoplastic conditions. More recently, targeted next-generation sequencing (t-NGS) technologies have been deployed to improve lymphoma classification. To the best of our knowledge, the comparison of these techniques' performance in TCL diagnosis has not been reported yet. In this study, 82 TCL samples and 25 nonneoplastic T-cell infiltrates were divided into 2 cohorts (test and validation) and analyzed with both multiplex PCR and t-NGS to investigate TCR gene rearrangements and somatic mutations, respectively. The detection of mutations appeared to be more specific (100.0%) than T-cell clonality assessment (41.7%-45.5%), whereas no differences were observed in terms of sensitivity (95.1%-97.4%). Furthermore, t-NGS provided a reliable basis for TCL diagnosis in samples with partially degraded DNA that was impossible to assess with PCR. Finally, although multiplex PCR assays appeared to be less specific than t-NGS, both techniques remain complementary, as PCR recovered some t-NGS negative cases.


Asunto(s)
Linfoma de Células T , Linfocitos T , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Linfoma de Células T/diagnóstico , Linfoma de Células T/genética , Reacción en Cadena de la Polimerasa , Receptores de Antígenos de Linfocitos T/genética
17.
Am J Surg Pathol ; 45(10): 1324-1336, 2021 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-34334687

RESUMEN

Although follicular lymphoma (FL) is usually graded as FL1-2, FL3A, and FL3B, some borderline cases can be observed and led us to investigate the clinicopathologic diversity of grade 3 FL (FL3). Among 2449 FL patients enrolled in Lymphoma Study Association (LYSA) trials, 1921 cases with sufficient material underwent a central pathologic review. The resulting diagnoses comprised 89.6% FL1-2 (n=1723), 7.2% FL3A (n=138), and 0.5% purely follicular FL3B (n=9). The remaining 51 unclassifiable cases (2.7%) exhibited high-grade features but did not meet WHO criteria for either FL3A or FL3B; and were considered as "unconventional" high-grade FL (FL3U). FL3U morphological pattern consisted of nodular proliferation of large cleaved cells or small-sized to medium-sized blast cells. Compared with FL3A, FL3U exhibited higher MUM1 and Ki67 expression, less BCL2 breaks and more BCL6 rearrangements, together with a higher number of cases without any BCL2, BCL6 or MYC rearrangement. FL3U harbored less frequent mutations in BCL2, KMT2D, KMT2B, and CREBBP than FL3A. MYC and BCL2 were less frequently mutated in FL3U than FL3B. Rituximab cyclophosphamide, doxorubicin, vincristine, and prednisone treated FL3U patients had a worse survival than FL1-2 patients with similar follicular lymphoma international prognostic index and treatment. These results suggest that high-grade FLs encompass a heterogeneous spectrum of tumors with variable morphology and genomic alterations, including FL3U cases that do not strictly fit WHO criteria for either FL3A or FL3B, and display a worse outcome than FL1-2. The distinction of FL3U may be useful to allow a better comprehension of high-grade FLs and to design clinical trials.


Asunto(s)
Biomarcadores de Tumor/genética , Análisis Citogenético , Heterogeneidad Genética , Linfoma Folicular/genética , Linfoma Folicular/patología , Adulto , Anciano , Anciano de 80 o más Años , Antineoplásicos/uso terapéutico , Hibridación Genómica Comparativa , Femenino , Francia , Reordenamiento Génico , Predisposición Genética a la Enfermedad , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Inmunohistoquímica , Hibridación Fluorescente in Situ , Linfoma Folicular/tratamiento farmacológico , Linfoma Folicular/mortalidad , Masculino , Persona de Mediana Edad , Mutación , Clasificación del Tumor , Fenotipo , Valor Predictivo de las Pruebas , Factores de Tiempo , Resultado del Tratamiento , Adulto Joven
18.
Brain Pathol ; 29(1): 53-62, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-29679497

RESUMEN

We investigated the challenging diagnostic case of a ventricular cystic glioneuronal tumor with papillary features, by RNA sequencing using the Illumina TruSight RNA Fusion panel. We did not retrieve the SLC44A1-PRKCA fusion gene specific for papillary glioneuronal tumor, but an EWSR1-PATZ1 fusion transcript. RT-PCR followed by Sanger sequencing confirmed the EWSR1-PATZ1 fusion. It matched with canonic EWSR1 fusion oncogene, juxtaposing the entire N-terminal transcriptional activation domain of EWSR1 gene and the C-terminal DNA binding domain of a transcription factor gene, PATZ1. PATZ1 protein belongs to the BTB-ZF (broad-complex, tramtrack and bric-à-brac -zinc finger) family. It directly regulates Pou5f1 and Nanog and is essential to maintaining stemness by inhibiting neural differentiation. EWSR1-PATZ1 fusion is a rare event in tumors: it was only reported in six round cell sarcomas and in three gliomas of three exclusively molecular studies. The first reported glioma was a BRAFV600E negative ganglioglioma, the second a BRAFV600E negative glioneuronal tumor, not otherwise specified and the third, very recently reported, a high grade glioma, not otherwise specified. In our study, forty BRAFV600E negative gangliogliomas were screened by FISH using EWSR1 break-apart probes. We performed methylation profiling for the index case and for seven out of the ten FISH positive cases. The index case clustered apart from other pediatric low grade glioneuronal entities, and specifically from the well-defined ganglioglioma methylation group. An additional pediatric intraventricular ganglioglioma clustered slightly more closely with ganglioglioma, but showed differences from the main ganglioglioma group and similarities with the index case. Both cases harbored copy number variations at the PATZ1 locus. EWSR1-PATZ1 gene fusion might define a new type of glioneuronal tumors, distinct from gangliogliomas.


Asunto(s)
Ganglioglioma/genética , Factores de Transcripción de Tipo Kruppel/genética , Proteína EWS de Unión a ARN/genética , Proteínas Represoras/genética , Adulto , Biomarcadores de Tumor/genética , Neoplasias Encefálicas/patología , Niño , Variaciones en el Número de Copia de ADN , Metilación de ADN , Femenino , Ganglioglioma/metabolismo , Fusión Génica , Glioma/genética , Humanos , Hibridación Fluorescente in Situ , Factores de Transcripción de Tipo Kruppel/metabolismo , Masculino , Neoplasias Neuroepiteliales/genética , Proteína EWS de Unión a ARN/metabolismo , Proteínas Represoras/metabolismo
20.
PeerJ ; 5: e2988, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28224052

RESUMEN

BACKGROUND: De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. RESULTS: We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. CONCLUSION: Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA