Replication Data for: PROTEOME ANALYSIS REVEALS COMMON PLAYERS BETWEEN THE PHYSIOLOGICAL NEURODEGENERATION OF THE ASCIDIAN CIONA INTESTINALIS AND THE PATHOLOGICAL NEURODEGENERATION IN HUMANS

This dataset includes LC-MS/MS data of differentially expressed proteins in the Ciona intestinalis proteome generated in the study entitled “PROTEOME ANALYSIS REVEALS COMMON PLAYERS BETWEEN THE PHYSIOLOGICAL NEURODEGENERATION OF THE ASCIDIAN CIONA INTESTINALIS AND THE PATHOLOGICAL NEURODEGENERATION IN HUMANS", by Daniele Capitanio, Silvia Mercurio, Ettore Mosca, Cristina Battaglia, Marco Venturin, and Roberta Pennati.
Tunicates, including ascidians, are recognized as the true “sister group” of vertebrates and are emerging as models to study the development and degeneration of central nervous system (CNS). Ascidian larvae have the typical chordate body plan that includes a dorsal neural tube. During their metamorphosis, a deep tissue reorganization takes place, with some tissues that degenerate while others develop to become functional during the adult life. The larval CNS also degenerates and most neurons disappear, making room to the formation of adult CNS. The genome of the ascidian Ciona intestinalis has been sequenced and annotated, with several CNS specific genes that have been characterized, revealing specification mechanisms shared with humans. These features make ascidian metamorphosis a good model to study the mechanisms underlying physiological CNS degeneration and to compare them to the pathological condition typical of neurodegenerative diseases.
In order to shed light on the molecular determinants of C. intestinalis metamorphosis and neurodegeneration, we analyzed its proteome at three stages of development: swimming larva (SwL, Hotta stage 28), settled larva (SetL, Hotta stage 32) and metamorphosing larva (MetL, Hotta stage 34).
A total of 9 samples were collected from three stages of larval development of Ciona (3 biological replicates for each stage) and their proteins were extracted in lysis buffer (0.1 M Tris/HCl pH 7.6, 4% SDS, 0.1 M DTT and 0.001 M PMSF) through sonication. Proteins were denatured at 95°C for 3 min and lysates clarified by centrifugation at 16000 g for 15 min. Protein concentrations were determined using the 2D-Quant Kit (Cytiva) and 120 ug of each extract were processed following the Filter aided sample preparation (FASP) method. Proteins were identified to match with Ciona intestinalis UNIPROT reference proteome (UP000008144) and their peaks were quantified with MaxQuant software (version 2.7.0.0, Max Planck Institute of Biochemistry, Germany) (Cox and Mann 2008). Detection of differentially expressed proteins (DEPs) was performed with Perseus software (Tyanova et al. 2016) (version 2.0.11, Max Planck Institute of Biochemistry). ANOVA and Tukey post-hoc test (p-value < 0.05) were used to obtain DEPs with their corresponding log fold change (LFC) values for the pairwise comparisons between the three developmental stages. Proteins with less than 6 valid values in at least 1 group were filtered out. False positives were excluded utilizing the Benjamini–Hochberg false discovery rate test. STRING (Version 12.0, https://string-db.org/) annotation was also used to further characterize DE proteins.
405 modulated proteins were identified by mass spectrometry, 156 of which are also regulated at transcript level. Enrichment analysis showed the involvement of several processes/pathways, including authophagy, proteasome and mTOR pathway among the most significant terms.
This work will contribute to give a comprehensive picture of the molecular pathways and mechanisms underlying ascidian metamorphosis, also pointing to new possible actors involved in the neurodegeneration process in humans.