Biomarkers in neurodegeneration: A beginner’s guide into curated analyses using publicly available datasets

Abstract The availability of bioassays for the discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains a significant challenge. With the advent of the next generation omics technologies and refinements in analytical algorithms, a substantial number of annotated datasets have recently been made available in the public domain. However, without sufficient background in programming or statistical analyses, many researchers find it a daunting task to parse such datasets and translate these data into impactful paradigms. It is also likely that several researchers, especially younger researchers, are not sufficiently aware of these resources. The purpose of this brief Method/Resource article is to demonstrate the utility of publicly available datasets for probing disease relevance of candidate markers in neurodegeneration. As a starting point, we introduce the readers to several open-access resources which contain genomics and proteomics datasets from human studies in common NDDs. Then, using a step-by-step approach- as well as without adopting any a priori hypothetical bias-, we present findings from curated gene expression analyses probing glutathione biogenesis, calcium signaling and autophagy related gene expression across select brain regions of four cohorts of PD patients (and from one study in common NDDs). This is accompanied by summary of reports on the detection of select markers in the cerebrospinal fluid (CSF). Lastly, we enclose a compilation of several annotated microarray studies and additional curated CSF protemics data in common NDDs, which the readers can utilize for translational purposes. We anticipate that this “beginner’s guide” will be of great benefit to the research community in neurodegenerative diseases, and can serve as a useful educational tool.