Analyzing Cerebrospinal Fluid Proteomes to Characterize Central Nervous System Disorders: A Highly Automated Mass Spectrometry-Based Pipeline for Biomarker Discovery

Methods to capture proteomic and metabolomic signatures from cerebrospinal fluid and serum of healthy individuals

Discovery of reliable signatures for the empirical diagnosis of neurological diseases-both infectious and non-infectious-remains unrealized. One of the primary challenges encountered in such studies is the lack of a comprehensive database representative of a signature background that exists in healthy individuals, and against which an aberrant event can be assessed. For neurological insults and injuries, it is important to understand the normal profile in the neuronal (cerebrospinal fluid) and systemic fluids (e.g., blood). Here, we present the first comparative multi-omic human database of signatures derived from a population of 30 individuals (15 males, 15 females, 23-74 years) of serum and cerebrospinal fluid. In addition to empirical signatures, we also assigned common pathways between serum and CSF. Together, our findings provide a cohort against which aberrant signature profiles in individuals with neurological injuries/disease can be assessed-providing a pathway for comprehensive diagnostics and therapeutics discovery.

Analytical Chemistry in the 21st Century: Challenges, Solutions, and Future Perspectives of Complex Matrices Quantitative Analyses in Biological/Clinical Field

Nowadays, the challenges in analytical chemistry, and mostly in quantitative analysis, include the development and validation of new materials, strategies and procedures to meet the growing need for rapid, sensitive, selective and green methods. In this context, considering the constantly updated International Guidelines, constant innovation is mandatory both in the pre-treatment procedures and in the instrumental configurations to obtain reliable, true, and reproducible information. In this context, additionally to the classic plasma (or serum) matrices, biopsies, whole blood, and urine have seen an increase in the works that also consider non-conventional matrices. Obviously, all these studies have shown that there is a correlation between the blood levels and those found in the new matrix, in order to be able to correlate and compare the results in a robust way and reduce any bias problems. This review provides an update of the most recent developments currently in use in the sample pre-treatment and instrument configurations in the biological/clinical fields. Furthermore, the review concludes with a series of considerations regarding the role and future developments of Analytical Chemistry in light of the forthcoming challenges and new goals to be achieved.

Quantitative proteomic characterization of microvesicles/exosomes from the cerebrospinal fluid of patients with acute bilirubin encephalopathy

Severe hyperbilirubinemia causes neurotoxicity and may lead to acute bilirubin encephalopathy (ABE) during the critical period of central nervous system development. The aim of the present study was to identify differentially expressed proteins (DEPs) in microvesicles/exosomes (MV/E) isolated from the cerebrospinal fluid (CSF) of patients with ABE. Co-precipitation was used to isolate the MV/E from the CSF of patients with ABE and age-matched controls. Isobaric tagging for relative and absolute quantification-based proteomic technology combined with liquid chromatography/tandem mass spectrometry was used to identify DEPs in the MV/E. Bioinformatics analysis was subsequently performed to investigate Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes enriched signaling pathways of these DEPs. A total of four proteins were selected for further validation via western blotting. A total of 291 dysregulated proteins were identified by comparing the patients with ABE with the controls. Bioinformatics analysis indicated the involvement of immune-inflammation-associated cellular processes and signaling pathways in the pathophysiology of ABE. In conclusion, the present study identified the proteomic profile of MV/E isolated from the CSF of patients with ABE. These results may provide an improved understanding of the pathogenesis of ABE and may help to identify early diagnostic biomarkers and therapeutic targets.

A systems biology approach for studying neurodegenerative diseases

Neurodegenerative diseases (NDDs), such as Alzheimer's (AD) and Parkinson's (PD), are among the leading causes of lost years of healthy life and exert a great strain on public healthcare systems. Despite being first described more than a century ago, no effective cure exists for AD or PD. Although extensively characterised at the molecular level, traditional neurodegeneration research remains marred by narrow-sense approaches surrounding amyloid β (Aβ), tau, and α-synuclein (α-syn). A systems biology approach enables the integration of multi-omics data and informs discovery of biomarkers, drug targets, and treatment strategies. Here, we present a comprehensive timeline of high-throughput data collection, and associated biotechnological advancements and computational analysis related to AD and PD. We hereby propose that a philosophical change in the definitions of AD and PD is now needed.

Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry

Cerebrospinal fluid (CSF) is a biofluid in direct contact with the brain and as such constitutes a sample of choice in neurological disorder research, including neurodegenerative diseases such as Alzheimer or Parkinson. Human CSF has still been less studied using proteomic technologies compared to other biological fluids such as blood plasma or serum. In this work, a pool of "normal" human CSF samples was analysed using a shotgun proteomic workflow that combined removal of highly abundant proteins by immunoaffinity depletion and isoelectric focussing fractionation of tryptic peptides to alleviate the complexity of the biofluid. The resulting 24 fractions were analysed using liquid chromatography coupled to a high-resolution and high-accuracy timsTOF Pro mass spectrometer. This state-of-the-art mass spectrometry-based proteomic workflow allowed the identification of 3'174 proteins in CSF. The dataset reported herein completes the pool of the most comprehensive human CSF proteomes obtained so far. An overview of the identified proteins is provided based on gene ontology annotation. Mass and tandem mass spectra are made available as a possible starting point for further studies exploring the human CSF proteome.