Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease

Abstract

Objectives. This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 72 samples comprising 22 healthy control blood samples and 50 PD blood samples for further analysis. Later, we used Limma to screen DEGs and differentially expressed lncRNAs (DElncRNAs) and estimated their functions by the Gene Ontology (GO). Besides, the competing endogenous RNA (ceRNA) network, including microRNAs, lncRNAs, and mRNAs, was constructed to elucidate the regulatory mechanism. Furthermore, we performed the KEGG pathway enrichment with mRNAs in the ceRNA regulatory network and constructed a final network, including pathways, mRNAs, microRNAs, and lncRNAs. Results. Overall, we obtained 394 DEGs, including 207 upregulated DEGs and 187 downregulated DEGs, and 7 DElncRNAs, including 2 upregulated DElncRNAs and 5 downregulated DElncRNAs. Insulin-like growth factor-1 receptor (IGF1R) was considerably enriched in the endocytosis pathway. In the ceRNA regulation network, IGF1R was the target of hsa-miR-133b and lncRNAs of XIST, and PART1 could also be the target of hsa-miR-133b. While the upregulated DEGs were enriched in the GO terms of the cytoskeleton, cytoskeletal part, and microtubule cytoskeleton, the downregulated DEGs were enriched in the immune response. PRKACA was markedly enriched in numerous pathways, including the MAPK and insulin signaling pathways. Conclusions. IGF1R, PRKACA, and lncRNA-XIST could be potentially involved in PD, and these diverse molecular mechanisms could support the development of the similar treatment for PD.

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“… 7 , 8 Additionally, the interaction network of lncRNAs and mRNAs has been examined in context of the pivotal mechanisms underlying PD. 9 …”

Inflammation and regulatory T cell genes are differentially expressed in peripheral blood mononuclear cells of Parkinson’s disease patients

“…IL23A is involved in Th17-type immune response Tan et al 19 Drug-naïve sporadic PD Microarray (Affymetrix) KEGG, STRING 40 PD, 19 HC CD40, GATA3 (upregulated) ICAM1 (downregulated) Chemokine signaling pathway, Cytokine–cytokine receptor interaction, Cell adhesion molecules, NF-kappa B signaling pathway ICAM1, other cell adhesion molecules and chemokines are involved in persistent neuroinflammation. GATA3 is a regulator of T-cell development Chi et al 84 Early-stage idiopathic PD Microarray (Affymetrix) KEGG 50 PD, 22 HC HLADQB1, IFI27 (downregulated) The downregulated DEGs were enriched in the immune response HLADQB1 is related with T cell activation Calligaris et al 16 Drug-naïve sporadic PD Microarray (Affymetrix) GO, DAVID, GSEA 40 PD, 20 HC TCF3, DOCK10, MAN1C1 (downregulated) Lymphocyte activation, leukocyte activation TCF3 is involved in development and differentiation of B and T cells. DOCK10 is involved in IL-4 receptor signaling.…”

Dysregulated Long Non-coding RNAs in Parkinson’s Disease Contribute to the Apoptosis of Human Neuroblastoma Cells

“…reanalyzing the microarray datasets GSE6613 (Chi et al, 2019). A possible reason for the more identified DE lncRNAs in our study is that the array platform GPL21047 (Agilent-074348 Human lncRNA v6 4 × 180K probe) used in our study focused on the lncRNA expression, whereas the platform GPL96 (Affymetrix Human Genome U133A Array) for GSE6613 focused on mRNA expression.…”