Dataset Information

Transcriptome Analysis Reveals Significant Differences in Gene Expression of Malignant Pheochromocytoma or Paraganglioma.

ABSTRACT: Prediction of malignant behavior of pheochromocytoma (PC) or paraganglioma (PG) is of limited value. The Cancer Genome Atlas (TCGA) and the French 'Cortico et Médullosurrénale: les Tumeurs Endocrines' (COMETE) network in Paris (France) facilitate accurate differentiation of malignant PC/PG based on genetic information. Therefore, the objective of this transcriptome analysis is to identify the prognostic genes underlying the differentiation of malignant PC/PG in the TCGA and COMETE databases. TCGA carries data pertaining to multigenomic analysis of 173 PC/PG surgical resection samples while the COMETE cohort contains data involving 188 PC/PG surgical resection samples. Clinical information and mRNA expression datasets were downloaded from TCGA and COMETE databases. Based on eligibility criteria, 58 of 173 PC/PG samples in TCGA and 171 of 188 PC/PG samples collected by the COMETE network were selected. Using Ingenuity Pathway Analysis, the mRNA expression of malignant and benign PC/PG was compared. The 58 samples in TCGA included 11 malignant and 47 benign cases. Among the 171 samples obtained from the COMETE cohort, 19 were malignant and 152 were benign. A comparative analysis of the mRNA expression data of the two databases revealed that 11 up/downregulated pathways involved in malignant PC/PG were related to cancer signaling, metabolic alteration, and prominent mitosis, whereas 6 upregulated genes and 1 downregulated gene were significantly enriched in the functional annotation pathways. The TCGA and COMETE databases showed differences in mRNA expression associated with malignant and benign PC/PG. Improved recognition of prognostic genes facilitates the diagnosis and treatment of PC/PG.

SUBMITTER: Suh YJ

PROVIDER: S-EPMC6530119 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptome Analysis Reveals Significant Differences in Gene Expression of Malignant Pheochromocytoma or Paraganglioma.

Suh Yong Joon YJ Park Jung Ho JH Bilegsaikhan Sanchir-Erdene SE Lee Dong Jin DJ

International journal of endocrinology 20190508

Prediction of malignant behavior of pheochromocytoma (PC) or paraganglioma (PG) is of limited value. The Cancer Genome Atlas (TCGA) and the French 'Cortico et Médullosurrénale: les Tumeurs Endocrines' (COMETE) network in Paris (France) facilitate accurate differentiation of malignant PC/PG based on genetic information. Therefore, the objective of this transcriptome analysis is to identify the prognostic genes underlying the differentiation of malignant PC/PG in the TCGA and COMETE databases. TCG ...[more]

PMID: 31205467

Similar Datasets

Project description:Pheochromocytomas and paragangliomas (PPGLs) are neuroendocrine tumors arising from the chromaffin cells in the adrenal medulla and extra-adrenal paraganglia, respectively. Local invasion, concurrent disorders, and metastases prevent surgical removal, which is the most effective treatment to date. Given the current lack of effective medical treatment, there is a need for novel therapeutic strategies. To identify druggable pathways driving PPGL development, we performed RNA sequencing on PPGLs (n = 19) and normal adrenal medullas (NAMs; n = 10) of dogs. Principal component analysis (PCA) revealed that PPGLs clearly clustered apart from NAMs. In total, 4,218 genes were differentially expressed between PPGLs and NAMs. Of these, 232 had a log2 fold change of >3 or < -3, of which 149 were upregulated in PPGLs, and 83 were downregulated. Compared with NAMs, PPGLs had increased expression of genes related to the cell cycle, tumor development, progression and metastasis, hypoxia and angiogenesis, and the Wnt signaling pathway, and decreased expression of genes related to adrenal steroidogenesis. Our data revealed several overexpressed genes that could provide targets for novel therapeutics, such as Ret Proto-Oncogene (RET), Dopamine Receptor D2 (DRD2), and Secreted Frizzled Related Protein 2 (SFRP2). Based on the PCA, PPGLs were classified into 2 groups, of which group 1 had significantly higher Ki67 scores (p = 0.035) and shorter survival times (p = 0.04) than group 2. Increased expression of 1 of the differentially expressed genes between group 1 and 2, pleiotrophin (PTN), appeared to correlate with a more aggressive tumor phenotype. This study has shed light on the transcriptomic profile of canine PPGL, yielding new insights into the pathogenesis of these tumors in dogs, and revealed potential novel targets for therapy. In addition, we identified 2 transcriptionally distinct groups of PPGLs that had significantly different survival times.

Project description:BackgroundHydrogen cyanide (HCN) is a small gaseous molecule that is predominantly produced as an equimolar co-product of ethylene (ET) biosynthesis in plants. The function of ET is of great concern and is well studied; however, the function of HCN is largely unknown. Similar to ET, HCN is a simple and diffusible molecule that has been shown to play a regulatory role in the control of some metabolic processes in plants. Nevertheless, it is still controversial whether HCN should be regarded as a signalling molecule, and the cross-talk between HCN and ET in gene expression regulation remains unclear. In this study, RNA sequencing (RNA-seq) was performed to compare the differentially expressed genes (DEGs) between HCN and ET in Arabidopsis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were subsequently performed to investigate the function and pathway enrichment of DEGs. Parts of key genes were confirmed by quantitative real-time PCR.ResultsThe results showed that at least 1305 genes and 918 genes were significantly induced by HCN and ET, respectively. Interestingly, a total of 474 genes (|log2 FC| ≥1) were co-regulated by HCN and ET. GO and KEGG analyses indicated that the co-regulated genes by HCN and ET were enriched in plant responses to stress and plant hormone signal transduction pathways, indicating that HCN may cooperate with ET and participate in plant growth and development and stress responses. However, a total of 831 genes were significantly induced by HCN but not by ET, indicating that in addition to ET, HCN is in essence a key signalling molecule in plants. Importantly, our data showed that the possible regulatory role of a relatively low concentration of HCN does not depend on ET feedback induction, although there are some common downstream components were observed.ConclusionOur findings provide a valuable resource for further exploration and understanding of the molecular regulatory mechanisms of HCN in plants and provide novel insight into HCN cross-talk with ET and other hormones in the regulation of plant growth and plant responses to environmental stresses.

Dataset Information

Transcriptome Analysis Reveals Significant Differences in Gene Expression of Malignant Pheochromocytoma or Paraganglioma.

Publications

Transcriptome Analysis Reveals Significant Differences in Gene Expression of Malignant Pheochromocytoma or Paraganglioma.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets