Multiomic Analyses of Dopaminergic Neurons Isolated from Human Substantia Nigra in Parkinson’s Disease: A Descriptive and Exploratory Study

Abstract

Dopaminergic neurons (DA) of the substantia nigra pars compacta (SNpc) selectively and progressively degenerate in Parkinson’s disease (PD). Until now, molecular analyses of DA in PD have been limited to genomic or transcriptomic approaches, whereas, to the best of our knowledge, no proteomic or combined multiomic study examining the protein profile of these neurons is currently available. In this exploratory study, we used laser capture microdissection to extract regions from DA in 10 human SNpc obtained at autopsy in PD patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nanoliquid chromatography–mass spectrometry, respectively, and the differential expression between PD and control group was assessed. Qualitative analyses confirmed that the microdissection protocol preserves the integrity of our samples and offers access to specific molecular pathways. This multiomic analysis highlighted differential expression of 52 genes and 33 proteins, including molecules of interest already known to be dysregulated in PD, such as LRP2, PNMT, CXCR4, MAOA and CBLN1 genes, or the Aldehyde dehydrogenase 1 protein. On the other hand, despite the same samples were used for both analyses, correlation between RNA and protein expression was low, as exemplified by the CST3 gene encoding for the cystatin C protein. This is the first exploratory study analyzing both gene and protein expression of laser-dissected neuronal parts from SNpc in PD. Data are available via ProteomeXchange with identifier PXD024748 and via GEO with identifier GSE 169755.

Single-cell transcriptomic atlas of the human substantia nigra in Parkinson’s disease

“…CST3, TMEFF2, and CRYAB are increased in at least two DA neuron subtypes of PD. CST3 is an inhibitor of cathepsin B and was shown increased in the DA neurons of PD through laser capture analysis 43 , and it plays a role in protecting DA neurons 44 . TMEFF2 is a transmembrane protein with EGF like and two follistatin like domains 2 and considered a survival factor for hippocampal and dopaminergic mesencephalic neurons 45 .…”

Unveiling the genes and pathways that are dysregulated in dopaminergic neurons during both familial and sporadic Parkinson’s disease

“…Using powerful tools like high throughput RNA sequencing, attempts have been made to identify dysregulated genes in the disease state by comparing gene expression patterns in healthy versus PD-afflicted DA neurons 4–10 . Analyzing the postmortem brain tissue from PD patients provides a direct view of gene expression patterns in affected DA neurons 4–6 . Induced Pluripotent Stem Cells (iPSCs) derived from PD patients can be differentiated into DA neurons 7–10 .…”

High-Quality Nuclei Isolation from Postmortem Human Heart Muscle Tissues for Single-Cell Studies

“…These recent technological developments have led to increased capability, and the accessibility of information obtainable from a single biological sample has been expanded 6,7 . Omics technologies, such as genomics, epigenomics, and transcriptomics, are increasingly employed in parallel to construct a more comprehensive picture of development and disease 8,9 .…”