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Correlated metabolomic, genomic, and histologic phenotypes in histologically normal breast tissue

ABSTRACT: By the integrated analyses of histological, metabolomic and transcriptional data, we characterized two distinct subtypes of non-malignant breast tissue

ORGANISM(S): Homo sapiens

PROVIDER: GSE111601 | GEO | 2018/04/05

REPOSITORIES: GEO

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Project description: Not available

| S-EPMC5905995 | biostudies-literature

Project description:Correlated metabolomic, genomic, and histologic phenotypes in histologically normal breast tissue

| PRJNA437646 | ENA

Metabolomic Evidence for a Field Effect in Histologically Normal and Metaplastic Tissues in Patients with Esophageal Adenocarcinoma.

Project description: Not available

| S-EPMC5288314 | biostudies-literature

Metabolomic heterogeneity of severe pulmonary arterial hypertension

Project description:Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH), the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the severe human PAH lung. The results suggest that PAH has specific metabolic pathways contributing to increased ATP synthesis for the vascular remodeling process in severe pulmonary hypertension. These identified metabolites may serve as potential biomarkers for the diagnosis of severe PAH. By profiling metabolomic alterations of the PAH lung, we reveal new pathogenic mechanisms of PAH in its later stage, which may differ from the earlier stage of PAH, opening an avenue of exploration for therapeutics that target metabolic pathway alterations in the progression of PAH. Global profiles were determined in human lung tissue and compared across 11 normal and 12 severe pulmonary arterial hypertension patients. Using a combination of microarray and high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the severe human PAH lung.

2014-11-14 | E-GEOD-53408 | biostudies-arrayexpress

Unexpected frequency of genomic alterations in histologically normal colonic tissue from colon cancer patients.

Project description: Not available

| S-EPMC5097093 | biostudies-literature

Validation study of colorectal cancer treatment effect prediction by metabolomic markers

Project description:Primary outcome(s): Best clinical response (RECIST 1.1) Serum concentration of metabolomic markers

| 2652805 | ecrin-mdr-crc

Integrative Transcriptomic, Lipidomic, and Metabolomic Analysis Reveals Potential Biomarkers of Basal and Luminal Muscle Invasive Bladder Cancer Subtypes

Project description:Muscle invasive bladder cancer (MIBC) is a heterogeneous disease with a high recurrence rate and poor clinical outcomes. Molecular subtype provides a new framework for the study of MIBC heterogeneity. Clinically, MIBC can be classified as basal and luminal subtypes, they display different clinical and pathological characteristics, but the molecular mechanism is still unclear. Lipidomic and metabolomic molecules have recently been considered to play an important role in the genesis and development of tumors, especially as potential biomarkers. Their different expression profiles in basal and luminal subtypes provide clues for the molecular mechanism of basal and luminal subtypes and the discovery of new biomarkers. Herein, we stratified MIBC patients into basal and luminal subtype using a MIBC classifier based on transcriptome expression profiles. We qualitatively and quantitatively analyzed the lipids and metabolites of basal and luminal MIBC subtypes, and identified differential lipid and metabolite profiles of them. Our results suggest that free fatty acids (FFA) and sulfatides (SL), which are closely associated with immune and stromal cell types, can contribute to the diagnosis of basal and luminal subtypes of MIBC. Moreover, we showe that glycerophosphocholine (GCP)/imidazoles and nucleosides/imidazoles ratios can accurately distinguish the basal and luminal tumors. Overall, by integrating transcriptomic, lipidomic, and metabolomic data, our study reveals specific biomarkers to differentially diagnose basal and luminal MIBC subtypes and may provide a basis for precision therapy of MIBC.

2021-07-08 | GSE179440 | GEO

Genomic And Metabolomic Profiling Of Finnish Familial Dyslipidemia Families

Project description:Genomic And Metabolomic Profiling Of Finnish Familial Dyslipidemia Families

| PRJNA324461 | ENA

The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics

Project description:Histology plays an essential role in therapeutic decision-making for lung cancer patients. However, the molecular determinants of lung cancer histology are largely unknown. We conducted whole-exome sequencing (WES) and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histology. A median of 68.9% of point mutations and 83% of copy number aberrations were shared between different histologic components within the same tumors. Furthermore, different histologic components within the tumors demonstrated similar subclonal architecture. On the other hand, transcriptomic profiling revealed shared pathways between the same histologic subtypes from different patients, which was supported by the analyses of the transcriptomic data from 141 cell lines and 343 lung cancers of different histologic subtypes. These data derived from mixed histologic subtypes in the setting of identical genetic background and exposure history support that the histologic fate of lung cancer cells is associated with transcriptomic features rather than the genomic profiles. The in-house clariom.s.human microarray data were analyzed using Bioconductor packages Oligo, pd.clariom.s.human, and limma following standard workflow. Gene set enrichment analysis using Hallmark dataset was carried out using fgsea Bioconductor package and the genes are pre-ranked by (signed log2FoldChange) * -log10(p-value) for all the public datasets. For the in-house microarray data, we computed the fold change between distinct histologies within the same patient and rank the genes by the fold change.

2021-11-13 | GSE188665 | GEO

Metabolomic heterogeneity of severe pulmonary arterial hypertension

2014-11-14 | GSE53408 | GEO

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