Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules

Abstract

Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural features and biochemical compositions. The molecular mechanisms causing progressive neurodegeneration and common molecular pathways linking expression of different NCL genes are largely unknown. We analyzed proteome alterations in the brains of a mouse model of human infantile CLN1 disease-palmitoyl-protein thioesterase 1 (Ppt1) gene knockout and its wild-type age-matched counterpart at different stages: pre-symptomatic, symptomatic and advanced. For this purpose, we utilized a combination of laser capture microdissection-based quantitative liquid chromatography tandem mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight MS imaging to quantify/visualize the changes in protein expression in disease-affected brain thalamus and cerebral cortex tissue slices, respectively. Proteomic profiling of the pre-symptomatic stage thalamus revealed alterations mostly in metabolic processes and inhibition of various neuronal functions, i.e., neuritogenesis. Down-regulation in dynamics associated with growth of plasma projections and cellular protrusions was further corroborated by findings from RNA sequencing of CLN1 patients' fibroblasts. Changes detected at the symptomatic stage included: mitochondrial functions, synaptic vesicle transport, myelin proteome and signaling cascades, such as RhoA signaling. Considerable dysregulation of processes related to mitochondrial cell death, RhoA/Huntington's disease signaling and myelin sheath breakdown were observed at the advanced stage of the disease. The identified changes in protein levels were further substantiated by bioinformatics and network approaches, immunohistochemistry on brain tissues and literature knowledge, thus identifying various functional modules affected in the CLN1 childhood encephalopathy.

Phenotype and natural history of variant late infantile ceroid‐lipofuscinosis 5

“…Dysregulated thalamic proteins to a variety of signalling pathways, including Huntington disease signalling, have been detected in the PPT1-deficient thalamus and supported by RNA sequencing data in the fibroblasts of patients with CLN1. 25 In conclusion, the cohort of patients described herein raises to 40 the number of reported patients affected with CLN5 disease, late infantile. Analysis of data obtained by this study has provided some new evidence and confirmed previous experience.…”

“…A systems biology approach might identify which pathways are dysregulated in the NCLs, and possibly explain the gradient of neural system involvement. Dysregulated thalamic proteins to a variety of signalling pathways, including Huntington disease signalling, have been detected in the PPT1‐deficient thalamus and supported by RNA sequencing data in the fibroblasts of patients with CLN1 …”

Brain RNA-Seq Profiling of the Mucopolysaccharidosis Type II Mouse Model

“…An alteration of the axon guidance processes has been so far supposed only for other three LSDs: In the drosophila model for Batten disease [30], in the brain of the MPS VII mouse [8] and in the brain of a mouse model for CLN1 disease [31]. …”

“…Proteins linked to Rho GTPase family are also relevant for axon guidance, and aberration of the neuronal outgrowth was observed at the pre-symptomatic stage in the brain of CLN1 mouse model [31]. Cytoskeletal alterations have been observed also in Krabbe, Pompe and Niemann–Pick type C diseases [40,41,42] and in other adult-onset disorders of the nervous system, such as Charcot–Marie–Tooth, Alzheimer’s disease, Parkinson’s disease [26].…”

Decreased sensitivity of palmitoyl protein thioesterase 1-deficient neurons to chemical anoxia

“…In fibroblasts from patients with infantile CLN1 disease, fragmented mitochondrial reticulum was observed, and reduced activities of ATP synthase and respiratory chain complexes II and IV were reported (32, 33). A recent proteomic analysis of the thalamus and cerebral cortex of symptomatic Ppt1 −/− mice found changes in the expression level of mitochondrial proteins, including decreased levels of cytochrome c oxidase subunit 7C and 2 proteins in the Fo complex of ATP synthase (34). Notably, the F1 complex of ATP synthase interacts with PPT1 (35).…”