Identification of cerebral spinal fluid protein biomarkers in Niemann-Pick disease, type C1

Abstract

Background Niemann-Pick disease, type C1 (NPC1) is an ultrarare, recessive, lethal, lysosomal disease characterized by progressive cerebellar ataxia and cognitive impairment. Although the NPC1 phenotype is heterogeneous with variable age of onset, classical NPC1 is a pediatric disorder. Currently there are no therapies approved by the FDA and therapeutics trials for NPC1 are complicated by disease rarity, heterogeneity, and the relatively slow rate of neurological decline. Thus, identification of disease relevant biomarkers is necessary to provide tools that can support drug development efforts for this devastating neurological disease. Methods Proximal extension assays (O-link® Explore 1536) were used to compare cerebrospinal fluid (CSF) samples from individuals with NPC1 enrolled in a natural history study and non-NPC1 comparison samples. Relative expression levels of 1467 proteins were determined, and candidate protein biomarkers were identified by evaluating fold-change and adjusted Kruskal–Wallis test p-values. Selected proteins were orthogonally confirmed using ELISA. To gain insight into disease progression and severity we evaluated the altered protein expression with respect to clinically relevant phenotypic aspects: NPC Neurological Severity Score (NPC1 NSS), Annual Severity Increment Score (ASIS) and age of neurological onset. Results This study identified multiple proteins with altered levels in CSF from individuals with NPC1 compared to non-NPC1 samples. These included proteins previously shown to be elevated in NPC1 (NEFL, MAPT, CHIT1, CALB1) and additional proteins confirmed by orthogonal assays (PARK7, CALB2/calretinin, CHI3L1/YKL-40, MIF, CCL18 and ENO2). Correlations with clinically relevant phenotypic parameters demonstrated moderate negative (p = 0.0210, r = -0.41) and possible moderate positive (p = 0.0631, r = 0.33) correlation of CSF CALB2 levels with age of neurological onset and ASIS, respectively. CSF CHI3L1 levels showed a moderate positive (p = 0.0183, r = 0.40) correlation with the concurrent NPC1 NSS. A strong negative correlation (p = 0.0016, r = -0.648) was observed between CSF CCL18 and age of neurological onset for childhood/adolescent cases. CSF CCL18 levels also showed a strong positive correlation (p = 0.0017, r = 0.61) with ASIS. Conclusion Our study identified and validated multiple proteins in CSF from individuals with NPC1 that are candidates for further investigation in a larger cohort. These analytes may prove to be useful as supportive data in therapeutic trials. Trial registrations NCT00344331, NCT00001721, NCT02931682.

Cerebrospinal Fluid Protein Biomarker Discovery in CLN3

“…Of the 146 proteins, 54 were 1.5-fold or more (i.e., absolute log2 fold change > 0.585) differentially expressed between the two cohorts, with 49 (33%) higher and 5 (3%) lower in CLN3 (Supporting Table 8). The top proteins with differential expression at p < 0.1 and absolute log2 fold change ≥ 1 in CLN3 compared to non-CLN3 (Table A, Figure A) include several previously identified in models of other neurodegenerative and neurometabolic conditions or processes: NEFL (neurofilament light chain and previously identified in CLN3), CHIT1 (chitinase 1) and CHI3L1 (chitinase 3-like 1), CTSH (cathepsin H), CPVL (carboxypeptidase vitellogenic-like , ), LEP (leptin), EFEMP1 (EGF containing fibulin extracellular matrix protein 1), CD302 (C-type lectin domain family 13, member A , ). A protein with ≥2-fold differential expression, and per our Pubmed search [(complete protein name OR symbol) AND (nerv* OR neuro*)] not previously associated with other neurological conditions, was CLPS (colipase).…”

“…Anonymized PLC samples from a pediatric emergency care facility would have been collected using a standard clinical procedure via lumbar puncture, though we do not have access to the clinical records for verification. PLC, SLOS, and CTD samples were simultaneously used as non-NPC comparison samples in the study of Niemann-Pick disease, type C1 biomarker discovery . Additional healthy adult lumbar CSF samples were obtained from PrecisionMed ().…”

“…PLC, SLOS, and CTD samples were simultaneously used as non-NPC comparison samples in the study of Niemann-Pick disease, type C1 biomarker discovery. 14 Additional healthy adult lumbar CSF samples were obtained from PrecisionMed (https://www. precisionmed.com).…”

Addressing inter-individual variability in CSF levels of brain-derived proteins across neurodegenerative diseases

“…The increase in CSF levels of MARCKSL1 and GAP43 may thus be related. CALB2, a calcium-binding protein highly expressed in neurons, has previously been found elevated in CSF from individuals with Niemann-Pick disease, along with NEFL and tau [50-52], suggesting a potential association to neuronal damage. The considerable overlap in altered proteins across the studied diseases indicates that changes in the levels of many CSF proteins may stem from common mechanisms to the diseases, potentially reflecting general neurodegenerative processes and/or neuronal loss.…”

Npc1 gene mutation abnormally activates the classical Wnt signalling pathway in mouse kidneys and promotes renal fibrosis

“…The human recessive genetic disease caused by the mutation of the NPC1 or NPC2 gene is called NPC. Currently, the incidence of NPC in the world is approximately 1 in 100 000, 95% of which are NPC1, and the rest are NPC2 (Campbell et al., 2023; Seker Yilmaz et al., 2020; Wassif et al., 2016). The symptoms of NPC are heterogeneous.…”