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. 2024 Jul 17:16:1437278.
doi: 10.3389/fnagi.2024.1437278. eCollection 2024.

Identification of deregulated lncRNAs in Alzheimer's disease: an integrated gene co-expression network analysis of hippocampus and fusiform gyrus RNA-seq datasets

Ermes Filomena  1 , Ernesto Picardi  1   2 , Apollonia Tullo  2 , Graziano Pesole  1   2 , Anna Maria D'Erchia  1   2
Affiliations

Identification of deregulated lncRNAs in Alzheimer's disease: an integrated gene co-expression network analysis of hippocampus and fusiform gyrus RNA-seq datasets

Ermes Filomena et al. Front Aging Neurosci. .

Abstract

Introduction: The deregulation of lncRNAs expression has been associated with neuronal damage in Alzheimer's disease (AD), but how or whether they can influence its onset is still unknown. We investigated 2 RNA-seq datasets consisting, respectively, of the hippocampal and fusiform gyrus transcriptomic profile of AD patients, matched with non-demented controls.

Methods: We performed a differential expression analysis, a gene correlation network analysis (WGCNA) and a pathway enrichment analysis of two RNA-seq datasets.

Results: We found deregulated lncRNAs in common between hippocampus and fusiform gyrus and deregulated gene groups associated to functional pathways related to neurotransmission and memory consolidation. lncRNAs, co-expressed with known AD-related coding genes, were identified from the prioritized modules of both brain regions.

Discussion: We found common deregulated lncRNAs in the AD hippocampus and fusiform gyrus, that could be considered common signatures of AD pathogenesis, providing an important source of information for understanding the molecular changes of AD.

Keywords: Alzheimer’s disease; RNA-Seq; WGCNA; differentially expressed genes; lncRNAs.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Flow chart of our study. AD, Alzheimer’s disease; WGCNA, weighted gene correlation network analysis; DE, differentially expressed; IPA, ingenuity pathway analysis; ddPCR, digital droplet PCR.
Figure 2
Figure 2
Analysis of lncRNAs expression from AD hippocampus RNA-seq data by ddPCR. Results are expressed as copies/μL of reaction mix values, normalized with respect to GAPDH copies/μL.
See this image and copyright information in PMC

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