Study Overview
Study selection method:
A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) criteria, whose main objectives are standardization and reproducibility. First, we searched public repositories such as GEO (Gene Expression Omnibus), ArrayExpress, BioStudies, ENCODE, UCSC Cell Browser, Human Cell Atlas and Single Cell Expression Atla using the keywords: “Parkinson’s”, “Parkinson’s disease” or “PD”. To identify suitable datasets, we set the following inclusion criteria: i) organism: Homo sapiens and, ii) study type: single-cell or single nuclei RNA sequencing (scRNA-seq and snRNA-seq). Among the selected studies, we discarded those that met any of the established exclusion criteria: i) experimental design not involving individuals with PD versus controls, ii) not focused on PD, iii) lack of information on patient sex, iv) lack of representation of both sexes in all conditions, and v) samples not from post-mortem brain tissue (fetal, organoid, etc.).
We identified seven studies after applying the established inclusion and exclusion criteria. After quality control analyses, one of these datasets was discarded due to the high expression of mitochondrial genes in the majority of the cells, which is indicative of poor cell viability. Therefore, six studies were included in the final analysis, with a total of 110 samples. Of these six studies, four were from the substantia nigra (GSE148434, GSE178265, GSE243639, GSE157783) and two from anterior cortical areas (1 from the anterior cingulate cortex and 1 from the prefrontal cortex) (GSE202210, GSE178146).
PRISMA diagram of study selection