Functional Network Profiles in ARSACS Disclosed by Aptamer-Based Proteomic Technology.

Federica Morani,Enrico Silvio Bertini,Elisa Sciarrillo,Stephan Züchner,Fabiana Fattori,Stefano Doccini,Daniele Galatolo,Federica Gemignani,Giovanna Chiorino,Filippo Maria Santorelli

doi:10.3389/fneur.2020.603774

Abstract

Although the genetic basis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) has been uncovered, our poor understanding of disease mechanisms requires new light on functional pathways and modifying factors to improve early diagnostic strategies and offer alternative treatment options in a rare condition with no cure. Investigation of the pathologic state combining disease models and quantitative omic approach might improve biomarkers discovery with possible implications in patients' diagnoses. In this study, we analyzed proteomics data obtained using the SomaLogic technology, comparing cell lysates from ARSACS patients and from a SACS KO SH-SY5Y neuroblastoma cell model. Single-stranded deoxyoligonucleotides, selected in vitro from large random libraries, bound and quantified molecular targets related to the neuroinflammation signaling pathway and to neuronal development. Changes in protein levels were further analyzed by bioinformatics and network approaches to identify biomarkers of ARSACS and functional pathways impaired in the disease. We identified novel significantly dysregulated biological processes related to neuroinflammation, synaptogenesis, and engulfment of cells in patients and in KO cells compared with controls. Among the differential expressed proteins found in this work, we identified several proteins encoded by genes already known to be mutated in other forms of neurodegeneration. This finding suggests that common dysfunctional networks could be therapeutic targets for future investigations.

Highlights

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare disease caused by mutations in SACS, the gene encoding sacsin [1]
To discover whether significant differentially expressed proteins (DEPs) found in ARSACS might have a potential causative or modifier role in other forms of spastic ataxia or neurodegenerative conditions, we explored the genomic collection of the Prepare-Ataxia research network and queried the GENESIS 2.0 platform [19], an affordable genome-scale analysis and data management solution for medical research containing genomic data of over 9,000 individuals with rare neurological diseases
We ran three technical replicates per sample on the multiplexed proteomic platform using the SOMAScan Assay technology to investigate a targeted set of 1,300 proteins and compare their expression in skin fibroblasts from ARSACS patients and healthy subjects and in neuroblastoma WT and KO cell lines, either untreated or treated with FCCP, the uncoupler of mitochondrial oxidation and phosphorylation leading to impaired mitochondrial fragmentation [11]

Summary

Introduction

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare disease caused by mutations in SACS, the gene encoding sacsin [1]. ARSACS is characterized by early-onset spasticity in the lower limbs, axonal-demyelinating sensorimotor peripheral neuropathy, and cerebellar ataxia [2,3,4]. Proteomics, the massive analysis of proteins, is feasible using various technologies, such as mass spectrometry, gelbased techniques, antibody-based arrays, and recently developed aptamer-based technologies [6,7,8]. Despite these technological advances, the extraction of knowledge from generated data is still challenging and requires significant bioinformatics expertise.

Methods

Results

Conclusion