Comparative proteomics profiling through DIA-SWATH-MS analysis in WT vs PPT1 KO "neuron-like" human cell lines as CLN1 model

The project DEM-AGING (DEMentias with AutophaGy from Infancy to AgiNG) aims to investigate common autophagy-dependent biomarkers between NCLs (neuronal ceroid-lipofuscinoses), the leading cause of childhood dementia, and senile dementias in order to design original therapeutic interventions to fight cognitive impairments throughout the lifespan. In this frame, we are currently involved in a proteomics study on "neuron-like" human cell lines as CLN1 model. CLN1 disease, belonging to NCLs group, is a lysosomal storage disorder characterized by mutations in PPT1 gene coding for Palmitoyl-Protein Thioesterase-1, a lysosomal enzyme which affects the recycling and degradation of lipid-modified proteins by removing palmitate residues. The deficiency of this enzyme causes the progressive death of cortical neurons leading to epileptic seizures, visual failure and neurocognitive decline. Although many advances have been made in genetic diagnosis and counseling for families, treatment options that delay or halt disease progression are still missing. In order to identify new treatment opportunities for NCLs, as well as for monitoring disease progression and treatment response, mass spectrometry-based proteomics studies [1-5] have been undertaken to better understand molecular mechanisms related to lysosomal disfunctions of dementia in childhood and to point out clinically useful biomarkers. In particular we carried out proteomics analyses, exploiting DIA-SWATH-MS (Data Independent Acquisition-Sequential Window Acquisition of all THeoretical fragment ion-Mass Spectrometry) technique on an ESI-TripleTOF 5600 (ABSciex), on "neuron-like" human cell lines, that is SH-SY5Y wild type (WT) vs SH-SY5Y PPT1 knockout (KO), with the aim to highlight possible protein dysregulations and differentially activated metabolic pathways between the two conditions. Among the 1322 proteins quantified, we found ten significantly dysregulated and specifically related to the contrast PPT1 KO vs WT. A functional analysis (DAVID tool) showed three down-regulated proteins (ANXA2, ANXA11, CPNE3) to be involved in calcium binding processes, biological pathway already mentioned in genomics [6] and transcriptomics [7] investigations on CLN1 disease. Our preliminary proteomics findings on CLN1 investigated in "neuron-like" cell model through MS thus agree with the results already reported in literature and, combined with the future outcomes deriving from transcriptomics/proteomics studies planned in DEM-AGING Project for other NCLs variants, will provide a more detailed and complete vision on this group of rare infantile neurodegenerative disorders.