Multi‐omic landscaping of human midbrains identifies disease‐relevant molecular targets and pathways in advanced‐stage Parkinson's disease

• Published in: Clinical and translational medicine Vol. 12; no. 1; pp. e692 - n/a
• Main Authors: Caldi Gomes, Lucas, Galhoz, Ana, Jain, Gaurav, Roser, Anna‐Elisa, Maass, Fabian, Carboni, Eleonora, Barski, Elisabeth, Lenz, Christof, Lohmann, Katja, Klein, Christine, Bähr, Mathias, Fischer, André, Menden, Michael P., Lingor, Paul
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01-01-2022; John Wiley and Sons Inc; Wiley
• Subjects: Aged; Aged, 80 and over; Brain diseases; Brain research; Chromatography; Clinical medicine; data integration; Female; Gene expression; Genomes; Humans; Male; Mesencephalon - anatomy & histology; Mesencephalon - drug effects; Mesencephalon - pathology; Middle Aged; miRNAs; Molecular Targeted Therapy - methods; Molecular Targeted Therapy - statistics & numerical data; multi‐omics; Nervous system; Parkinson disease; Parkinson Disease - genetics; Parkinson Disease - mortality; Parkinson Disease - therapy; Parkinson's disease; Pathogenesis; Proteins; Real-Time Polymerase Chain Reaction - methods; Real-Time Polymerase Chain Reaction - statistics & numerical data; United Kingdom; United Kingdom; Parkinson disease; multi-omics; miRNAs; data integration
• ISSN: 2001-1326; 2001-1326
• DOI: 10.1002/ctm2.692

Background
Parkinson's disease (PD) is the second most common neurodegenerative disorder whose prevalence is rapidly increasing worldwide. The molecular mechanisms underpinning the pathophysiology of sporadic PD remain incompletely understood. Therefore, causative therapies are still elusive. To obtain a more integrative view of disease‐mediated alterations, we investigated the molecular landscape of PD in human post‐mortem midbrains, a region that is highly affected during the disease process.
Methods
Tissue from 19 PD patients and 12 controls were obtained from the Parkinson's UK Brain Bank and subjected to multi‐omic analyses: small and total RNA sequencing was performed on an Illumina's HiSeq4000, while proteomics experiments were performed in a hybrid triple quadrupole‐time of flight mass spectrometer (TripleTOF5600+) following quantitative sequential window acquisition of all theoretical mass spectra. Differential expression analyses were performed with customized frameworks based on DESeq2 (for RNA sequencing) and with Perseus v.1.5.6.0 (for proteomics). Custom pipelines in R were used for integrative studies.
Results
Our analyses revealed multiple deregulated molecular targets linked to known disease mechanisms in PD as well as to novel processes. We have identified and experimentally validated (quantitative real‐time polymerase chain reaction/western blotting) several PD‐deregulated molecular candidates, including miR‐539‐3p, miR‐376a‐5p, miR‐218‐5p and miR‐369‐3p, the valid miRNA‐mRNA interacting pairs miR‐218‐5p/RAB6C and miR‐369‐3p/GTF2H3, as well as multiple proteins, such as CHI3L1, HSPA1B, FNIP2 and TH. Vertical integration of multi‐omic analyses allowed validating disease‐mediated alterations across different molecular layers. Next to the identification of individual molecular targets in all explored omics layers, functional annotation of differentially expressed molecules showed an enrichment of pathways related to neuroinflammation, mitochondrial dysfunction and defects in synaptic function.
Conclusions
This comprehensive assessment of PD‐affected and control human midbrains revealed multiple molecular targets and networks that are relevant to the disease mechanism of advanced PD. The integrative analyses of multiple omics layers underscore the importance of neuroinflammation, immune response activation, mitochondrial and synaptic dysfunction as putative therapeutic targets for advanced PD.
Midbrain samples of Parkinson's disease (PD) and control (CTR) patients were subjected to a multi‐omic analysis. The expression of miRNAs, transcripts and proteins was explored, followed by data integration and functional analyses. This comprehensive assessment of PD‐affected and CTR human midbrains revealed multiple molecular targets and networks that are relevant to the disease mechanism of advanced PD.