Early downregulation of hsa-miR-144-3p in serum from drug-naïve Parkinson's disease patients

Abstract

Advanced age represents one of the major risk factors for Parkinson's Disease. Recent biomedical studies posit a role for microRNAs, also known to be remodelled during ageing. However, the relationship between microRNA remodelling and ageing in Parkinson's Disease, has not been fully elucidated. Therefore, the aim of the present study is to unravel the relevance of microRNAs as biomarkers of Parkinson's Disease within the ageing framework. We employed Next Generation Sequencing to profile serum microRNAs from samples informative for Parkinson's Disease (recently diagnosed, drug-naïve) and healthy ageing (centenarians) plus healthy controls, age-matched with Parkinson's Disease patients. Potential microRNA candidates markers, emerging from the combination of differential expression and network analyses, were further validated in an independent cohort including both drug-naïve and advanced Parkinson's Disease patients, and healthy siblings of Parkinson's Disease patients at higher genetic risk for developing the disease. While we did not find evidences of microRNAs co-regulated in Parkinson's Disease and ageing, we report that hsa-miR-144-3p is consistently down-regulated in early Parkinson's Disease patients. Moreover, interestingly, functional analysis revealed that hsa-miR-144-3p is involved in the regulation of coagulation, a process known to be altered in Parkinson's Disease. Our results consistently show the down-regulation of hsa-mir144-3p in early Parkinson's Disease, robustly confirmed across a variety of analytical and experimental analyses. These promising results ask for further research to unveil the functional details of the involvement of hsa-mir144-3p in Parkinson's Disease.

Figure 1

Intersection plot reporting the number of shared DEMs. The matrix at the bottom represents a table whose rows are the DESeq2 contrasts (names on the left and size on the right end), and whose columns represent the results of selected contrasts’ intersections (solid black circle). The sizes of each intersection is visually depicted by the bars color-coded by statistical significance (p-value), and sizes reported on top. The minimum number of shared DEMs in the plot is 10. The plot was created using the R package upset v. 1.4.0 (https://cran.r-project.org/web/packages/UpSetR/index.html), R software version 3.5.1.

Figure 2

Network analysis. Graphical process of the network analysis implemented for the two cohorts of dnPDs and CENT. Nodes per community are listed by the adjacency matrix box, and the final numbers of communities are shown below each cohort. The figure was created using PowerPoint software Version 16.30, 2019, (https://www.microsoft.com/).

Figure 3

RQ (Relative Quantitation) plot. The plot displays the results of the RT-qPCR relative quantification (dnPDs, adPDs and PDsibs with respect to CTR_ALL) of the gene expression profile of hsa-miR-150-5p, hsa-miR-215-5p and hsa-miR-144-3p, in the validation. Standard asterisks notations indicates **for P-value < 0.01, and Fold Change (RQ) > 2 or < 0.5, and ***for P-value < 0.001 and Fold Change (RQ) > 2 or < 0.5. The image was obtained and downloaded from the software ThermoFisher Applied Biosystems™ Analysis Software web application (apps.thermofisher.com), Relative Quantitation Analysis Module (2020.2.1-Q2-20-build4 of 2020-04-27). The image was afterwards edited with LibreOffice Draw, Libre Office version 5 (https://www.libreoffice.org/).

Figure 4

MiRIntegrator analysis for hsa-miR-144-3p. Graphical representation of the miRNA-augmented KEGG pathway hsa04610 “Complement and coagulation cascades” obtained using MiRIntegrator (R package version 1.22, http://datad.github.io/mirIntegrator/, and R software version 3.5.1). The repression activity of hsa-miR-144-3p to its targets FGG, FGA and FGB genes is highlighted with a black oval.

Figure 5

Summary of the overall experimental design and results pipeline. The figure was drawn using Microsoft Office 2016, Power Point. (https://www.microsoft.com/).