Mitochondrial DNA somatic Mutation Analysis in Breast Cancer
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40354 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4590700_1.fastq.gz | Fastqsanger.gz | |||
| ERR4590700_2.fastq.gz | Fastqsanger.gz | |||
| ERR4590710_1.fastq.gz | Fastqsanger.gz | |||
| ERR4590710_2.fastq.gz | Fastqsanger.gz | |||
| ERR4590720_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 368 |
Similar Datasets
Project description:We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which translation was inhibited or the mRNA binding protein context altered (Delta puf3). We used cell fractionation protocols together with microarray to assess the distribution of mRNAs between free and mitochondrion-bound polysomes. Keywords: Mitochondrial-associated RNA localization in cells GSM239122-GSM239127: mitochondrial associated RNA (three biological replicates each in dye swap) GSM239128-GSM239131: mitochondrial associated RNA in presence of 200µg/ml cycloheximide (two biological replicates each in dye swap) GSM239132-GSM239135: mitochondrial associated RNA in presence of 2.1mM puromycin (two biological replicates each in dye swap) GSM239136-GSM239139: mitochondrial associated RNA in Delta Puf3 strain (two biological replicates each in dye swap)
2008-06-01 | E-GEOD-9393 | biostudies-arrayexpress
Project description:<p> Human disorders of mitochondrial oxidative phosphorylation (OXPHOS) represent a devastating collection of inherited diseases. These disorders impact at least 1:5000 live births, and are characterized by multi-organ system involvement. They are characterized by remarkable locus heterogeneity, with mutations in the mtDNA as well as in over 77 nuclear genes identified to date. It is estimated that additional genes may be mutated in these disorders. </p> <p>To discover the genetic causes of mitochondrial OXPHOS diseases, we performed targeted, deep sequencing of the entire mitochondrial genome (mtDNA) and the coding exons of over 1000 nuclear genes encoding the mitochondrial proteome. We applied this 'MitoExome' sequencing to 124 unrelated patients with a wide range of OXPHOS disease presentations from the Massachusetts General Hospital Mitochondrial Disorders Clinic. </p> <p>The 2.3Mb targeted region was captured by hybrid selection and Illumina sequenced with paired 76bp reads. The total set of 1605 targeted nuclear genes included 1013 genes with strong evidence of mitochondrial localization from the MitoCarta database, 377 genes with weaker evidence of mitochondrial localization from the MitoP2 database and other sources, and 215 genes known to cause other inborn errors of metabolism. Approximately 88% of targeted bases were well-covered (>20X), with mean 200X coverage per targeted base. </p>
| phs000339 | dbGaP
Project description:Altered mitochondrial function in prostate cancer was characterized using paired malignant/non-malignant (benign) tissue samples. Mitochondrial DNA heteroplasmies (mtDNA-NGS) and mitochondria associated gene transcript levels (RNAseq-NGS) were analyzed and correlated to mitochondrial respiration (high-resolution respirometry), to each other and to the tumor stage and grade.
| EGAS00001004186 | EGA
Project description:Mitochondrial metabolism plays a central role in promoting cancer growth and metastatic progression. The transition between a hyperfused and fragmented mitochondrial network is termed mitochondrial dynamics and is important for many mitochondria-associated functions; however, little is known regarding how this process influences metastasis. Here, we show that breast cancer cells with low metastatic potential exhibit a more fused mitochondrial network compared to highly metastatic breast cancer cells. To examine whether a fused mitochondrial network could impair metastasis, we inhibited mitochondrial fission in metastatic breast cancer cells by individual genetic deletion of three key regulators of mitochondrial fission (Drp1, Fis1 and Mff) or pharmacological intervention using leflunomide, an anti-rheumatic drug. These cells displayed a fused mitochondrial network and limited survival under anoikis conditions, consistent with mitochondrial fusion limiting metastasis. Transcriptomics and metabolomics analyses revealed that mitochondrial fusion causes significant alterations in metabolic pathways and processes related to cell adhesion. Functional bioenergetics assays demonstrated that mitochondrial fusion limited the mitochondrial capacity of cancer cells. Mitochondrial fusion in breast cancer cells had no significant effect on primary tumor growth but almost completely ablated lung metastasis in vivo. Furthermore, the transcriptomics signature associated with enhanced mitochondrial fusion correlated with improved survival in patients with breast cancer. Overall, our findings highlight mitochondrial fusion as a therapeutic opportunity for breast cancer.
2024-09-25 | GSE245216 | GEO
Project description:The PDE12 gene codes for the poly(A)-specific exoribonuclease, involved in the quality control of mitochondrial non-coding RNAs. Here, we report that disease-causing PDE12 variants in three unrelated families are associated with mitochondrial respiratory chain deficiencies. Clinically, they presented in utero and within the neonatal period with muscle and brain involvement leading to marked cytochrome c oxidase (COX) deficiency in muscle and severe lactic acidosis. To analyze perturbations in specific cellular pathways contributing to pathogenesis in our patient cohort, we used Affymetrix Clariom D transcriptome arrays to study the RNA levels in fibroblasts derived from two patient (Patient 2 and patient 3), comparing these to age-matched controls.
2024-09-29 | E-MTAB-14251 | biostudies-arrayexpress
Project description:Gene expression profiling in peripheral blood cells from monozygotic twin pairs with various sytemic autoimmune diseases revealed 92 genes that could discriminate between MZ twin pairs and unrelated-matched controls. No genes were found that could discriminate between proband and unaffected twin pairs, or between the various disease phenotypes.
2010-12-30 | GSE24060 | GEO
Project description:In our study, we applied high-throughput mass spectrometry, bioinformatic, and machine learning approaches to investigate the proteome, including noncoding RNA (ncRNA)–derived micropeptides, of different breast cancer subtypes. In total, 19 tumor and 18 paired nontumor samples were used to obtain the proteome and peptidome. Among these, 5 samples were classified as LABC (plus 5 paired nontumor samples), 4 as LBBC (HER2−) (plus 4 paired nontumor samples), 4 as HER2+ breast cancer (plus 3 paired nontumor samples), and 6 as TNBC (plus 6 paired nontumor samples). We identified that each subtype depends on different protein expression patterns to sustain its malignancy,and also alterations in pathways and processes that can be associated with each subtype and its biological and clinical behaviors. Regarding subtype biomarkers, our panels achieved performances with at least 75% of sensibility and 92% of specificity. In the validation cohort, the panels obtained acceptable to outstanding performances (AUC = 0.740 to 1.00). We identified 58 peptides expressed on breast tissue, including 27 differentially expressed MPs in tumor compared with nontumor samples and MPs exhibiting tumor or subtype specificity. These peptides presented physicochemical features compatible with the canonical proteome and were predicted to influence the tumor immune environment and participate in cell communication, metabolism, and signaling processes. In addition, some MPs presented potential as anticancer, antiinflammatory, and antiangiogenic molecules.
2024-11-12 | PXD057759 | Pride
Project description:Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.
| S-EPMC4987284 | biostudies-literature
Project description:We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues. 10 breast tumor samples (8 invasive, 2 pre-invasive) and 10 normal breast tissues, paired randomly (except Array 10: matched pair)
2012-09-14 | E-GEOD-35263 | biostudies-arrayexpress
Project description:Gene expression profiles were used to identify coordinately regulated gene sets and pathways actuvated in tumors occuring in IL10R2-/- patients. Frozen tumor biopsies and paired peripheral blood from 2 children with IBD and 2 age-matched tonsil were obtained. Cases were ascertained at the Necker hospital. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on all cases.
2012-07-22 | E-GEOD-39503 | biostudies-arrayexpress