MiRNA profiling by high throughput sequencing of 60 malignant pleural mesothelioma
ABSTRACT: A Cartes d'Identite des Tumeurs (CIT) : Total RNAs are purified with miRNeasy kit which allows the selection of the small RNA fraction less than 100b. From these samples enriched in small RNAs, libraries are performed according to previously established protocols [Vigneault, F. et al. High-throughput multiplex sequencing of miRNA. Curr Protoc Hum Genet Chapter 11, Unit 11.12.1–10 (2012).].
Project description:In this study, a series of 102 cartilage tumors was used to uncover the molecular diversity of chondrosarcomas through the profiling of mRNA, miRNA, DNA methylation, DNA copy number aberrations and point mutations. An integrated classification using multiple molecular dimensions revealed three major molecular features unraveling the diversity in clinical outcome of chondrosarcoma: a high mitotic state, regional 14q32 loss of expression and IDH mutations leading to genome-wide hypermethylation. These three robust and simple molecular features classify chondrosarcoma in subtypes with superior clinical value as compared to the current grading system.
Project description:A Carte d'Identitite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net): Pheochromocytomas (PCC) and paragangliomas (PGL) are neural crest-derived tumors. We performed the integrated genomic analysis of a collection of PCC/PGL from the French COMETE network using SNP arrays, whole-exome sequencing, DNA methylation arrays, mRNA expression arrays and miRNA sequencing. We found that PCC/PGL are characterized by a low mutation rate, with few recurrent somatic mutations and focal copy number alterations (CNAs). In contrast, we detected recurrent broad CNAs strongly associated with known molecular groups, often leading to the biallelic inactivation of the known susceptibility genes of PCC/PGL. We also identified DNA methylation changes and miRNA expression clusters strongly associated with molecular groups. Of note, overexpression of the miRNA cluster 182/96/183 is specific of SDHB-mutated tumors and induces invasive traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster due to a loss of heterozygosity of the 14q32.2 locus is a potential driver in a subset of sporadic tumors. This comprehensive analysis illustrates the functional interdependence between genomic and epigenomic dysregulations underlying PCC/PGL.
Project description:A Cartes d'Identit des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net): Pancreatic adenocarcinoma (PDAC) is one of the most lethal human malignancies and a major health problem. Patient-derived xenografts (PDX) are appearing as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. We generated subcutaneous PDX from PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). The extensive multiomics characterization of the xenografts demonstrated that PDX is a suitable model for preclinical studies, representing the diversity of the primary cancers. the MultiOmicClassification variable indicates groups resulting from the analysis, and the CIMPclass, the CpG Island Methylator Phenotype as estimated by the methylation analysis. This dataset, describes the miRNA-Seq data used in the multiOmics analysis.
Project description:Small RNAs (<100 bases in length) were purified from total RNA samples using the miRNeasy kit (Qiagen), and multiplexed miRNA libraries were prepared using a previously described protocol and sequenced on a HiSeq 2000 (Illumina). Image analysis, base calling, demultiplexing and conversion of BCL to FASTQ format were carried out using CASAVA 1.8.2 software (Illumina). Adaptor sequences were removed using mirExpress software. Fastq were 3p-adaptor trimmed. The sequences were then aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a), allowing no mismatch with reference. Reads were counted using HTSeq-count (HTSeq v 0.6.1p1 Python package) using “intersection-strict” mode, to count mature miRNA abundance according to miRbase v.20.
Project description:Micro-RNA sequencing of adrenocortical tumors and normal adrenal samples. miRNA sequencing of 45 adrenocortical carcinomas (ACC), 30 adrenocortical adenomas (ACA) and 3 normal adrenal samples.
Project description:Coq9R239X mice, a model of mitochondrial encephalopathy due to Coenzyme Q deficiency, were treated with Rapamycin administered in the chow at two different concentrations, i.e. 28 ppm and 225 ppm. The results are compared to those obtained in untreated Coq9R239X mice and untreated Coq9+/+ mice.
Project description:Epigenetic changes such as DNA methylations regulate gene expression patterns in response to environmental cues including infections. Microbial infections induced DNA methylation may play a potential role in modulating host-immune response. In the present study, we sought to determine DNA methylation changes induced by the mastitis causing Escherichia coli (E coli) in porcine mammary epithelial cells (PMEC). Two time points (3hr and 24 hr) were selected based on the specific transcriptomic changes as early and late phase immune responses. Genome-wide methylation information was obtained to identify significant differential methylation patterns in E coli infected PMEC.
Project description:We used a machine-learning framework to systematically discover prognostic long non-coding RNAs (lncRNAs) in 9,446 patient tumors of 30 types. We identified 166 prognostic lncRNAs whose transcript abundance correlated with patient risk and improved the performance of common clinical variables and molecular tumor subtypes. In lower-grade gliomas, discrete activation of HOXA10-AS indicated poor patient prognosis, neurodevelopmental pathway activation and a transcriptomic similarity to glioblastomas. To understand the role of HOXA10-AS in the hallmark pathways of glioma, we used RNA-seq to profile the patient-derived G797 glioma cells with siRNA-mediated HOXA10-AS knockdown (KD) and pcDNA3.1-Neomycin-mediated overexpression (OE) phenotypes. Both KD and OE were validated using RT-PCR. We found a pronounced transcriptional response to HOXA10-AS deregulation with 1,715 and 408 differentially expressed protein-coding genes detected in KD and OE cells, respectively (FDR < 0.05, absolute FC > 1.2), including 23 genes detected in both experiments, as well as known genes involved in glioma biology and Hippo signaling. Our study underscores the pan-cancer potential of the non-coding transcriptome for developing molecular biomarkers and innovative therapeutic strategies.