Research of lncRNA expression signatures for four molecular subtype of breast cancer
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ABSTRACT:
PROVIDER: PRJNA779793 | ENA |
REPOSITORIES: ENA
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Project description:To screen promising serum-based lncRNA biomarkers for different molecular subtype of breast cancer,we uesed a genome-wide lncRNA microarray to identify differentially expressed lncRNAs from serum samples of patients with four different molecular subtype of BC and healthy controls.
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Project description:Frontotemporal dementia is characterized by progressive atrophy of frontal and/or temporal cortices and an early age of onset. The disorder is highly heterogenic, comprising several genetic causes as well as a diverse phenotypic landscape of sporadic cases. Here we investigated the proteomic signatures of human brain frontal and temporal cortical lobes to identify key pathways involved in the three most frequent genetic subtypes of frontotemporal dementia. We included 38 patients with either an autosomal dominant repeat expansion in the C9ORF72 gene (n = 16), or a mutation in the GRN gene (n = 9) or the MAPT gene (n = 13), and 11 non-demented controls. Using data-independent quantitative proteomic analysis on laser-dissected tissues we identified brain region-specific protein signatures for these genetic frontotemporal dementia subtypes compared to non-demented controls. Using published single cell RNA expression data for cell type enrichment we deduced the involvement of major brain cell types in driving these different protein signatures. Using gene ontology analysis, we identified distinct genetic subtype- and cell type-specific biological processes. In the GRN-mediated subtype, we observed higher protein expression related to immune processes, with a role for endothelial cells and astrocytes, and lower protein expression implicating mitochondrial dysregulation, primarily in neurons. In the MAPT-mediated subtype, we observed higher protein expression associated with dysregulation of RNA processing in multiple cell types, and lower protein expression implicating altered neuronal functioning via dysregulation of oligodendrocytes. Comparison of the MAPT-mediated frontotemporal dementia signature with one obtained from Alzheimer’s disease brains demonstrated only partial overlap in protein dysregulation, thus separating general neurodegenerative processes and highlighting the frontotemporal dementia-specific involvement of altered RNA processing and oligodendrocyte dysfunction. Taken together, our results indicate a role for different brain cell types and biological mechanisms in frontotemporal dementia, revealing both genetic subtype-specific processes, and processes shared with other neurodegenerative diseases such as Alzheimer’s disease.
2023-03-10 | PXD022872 | Pride
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Project description:Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. Long non-coding RNA (lncRNA) was discovered to play key roles in many diseases through regulating the gene expression. Here, using microarray assay, we investigated the expression profiles of mRNA and lncRNA in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 821 lncRNAs and 1,349 mRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype. Of them, all five types of lncRNAs were identified, including 302 of sense, 280 of antisense, 312 of intergenic, 44 of divergent, and 33 of intronic lncRNAs. Ten lncRNAs and ten mRNAs randomly selected were successfully confirmed the microarray results. The co-expression and target prediction analysis indicated 27 of mRNAs cis-regulated by 29 lncRNAs and 109 of coding genes trans-regulated by 114 lncRNAs. These predicted targets were enriched in pathways involved in the interaction between host and C. parvum, eg. hedgehog signaling pathway, Wnt signaling pathway and tight junction, suggesting that these aberrantly lncRNAs would play important regulating roles during infection of C. parvum IId subtype.
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Project description:To further development of our lncRNA and mRNA expression approach to pancreatic ductal adenocarcinoma(PDAC), we have employed lncRNA and mRNA microarray expression profiling as a discovery platform to identify lncRNA and mRNA expression in pancreatic ductal adenocarcinoma.Human pancreatic ductal adenocarcinoma tissues and normal pancreatic tissues from PDAC donors and other duodenum diseases donors. analyze mRNA and lncRNA expression in pancreatic ductal adenocarcinoma (PDAC) by microarray platform
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Project description:Investigation of lncRNA expression signatures in hypoxia-induced HCC cells
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Project description:In pancreatic ductal adenocarcinoma (PDAC), no recurrent metastasis-specific mutation has been found, suggesting that epigenetic mechanisms, such as DNA methylation, are the major contributors of late-stage disease progression. Here, we performed the first whole genome bisulfite sequencing (WGBS) on mouse and human PDAC organoid models to identify stage-specific and subtype-specific DNA methylation signatures in PDAC. With this approach, we identified thousands of DMRs that can distinguish between the stages and subtypes of PDAC. Stage-specific DMRs are associated with genes related to nervous system development and cell-cell adhesions and are enriched in promoters and bivalent enhancers. Subtype-specific DMRs showed hypermethylation of GATA6 transcriptional networks in the squamous subtype and hypermethylation of EMT transcriptional networks in the progenitor subtype. These results indicate that aberrant DNA methylation contributes to both PDAC progression and subtype differentiation, resulting in significant and reoccurring DNA methylation patterns with diagnostic and prognostic potential.
2024-01-29 | GSE243528 | GEO