Stratified cohorts for biomarker assessment and trial readiness: TMEM175, SCARB2 and CTSB in Parkinson's disease

Technical Summary: Stratified Cohorts for Biomarker Assessment and Trial Readiness in Parkinson's Disease

Problem Statement
Lysosomal dysfunction is a central mechanism in Parkinson's disease (PD) pathogenesis, most notably established through GBA1 mutations. However, genome-wide association studies (GWAS) have identified additional lysosomal-related risk genes—TMEM175, SCARB2, and CTSB—whose functional impact on patient biomarker profiles remains unclear. While these genes are implicated in lysosomal pathways and have been explored as therapeutic targets in experimental models, there is a lack of comprehensive data linking their genetic variants to clinical outcomes, $\alpha$-synuclein seeding activity, lysosomal protein levels, and sphingolipid profiles in human PD cohorts. This gap hinders the ability to stratify patients for clinical trials and to identify biomarkers for monitoring target engagement and treatment efficacy.

Methodology
The study employed a discovery-validation design utilizing three cohorts:

1. Discovery Cohort: A combined German dataset (TUEPAC-DESCRIBE-PD) comprising 2,629 PD patients from the University of Tübingen and various German DZNE sites.
2. Validation Cohort: The Accelerating Medicines Partnership® Parkinson's Disease (AMP-PD) dataset, comprising 2,172 PD patients.

Genetic Stratification:
Patients were stratified by GBA1 mutation status (PD$_{GBA1\_wildtype}$ and PD$_{GBA1}$) and by risk alleles in three lysosomal genes:

• TMEM175: p.M393T (rs34311866) and p.Q65P (rs34884217).
• SCARB2: rs6812193 and rs6825004.
• CTSB: rs1293298.
  Patients with rare mutations in LRRK2, Parkin, PINK1, and SNCA were excluded to reduce genetic confounding.

Biomarker Assessment:
The study evaluated a multi-dimensional biomarker profile:

• Clinical: Motor function (UPDRS-III), cognition (MoCA), and depression (BDI-II).
• $\alpha$-Synuclein: Cerebrospinal fluid (CSF) $\alpha$-syn seeding activity via seed amplification assay (SAA).
• Lysosomal Proteins: CSF levels of LIMP2 (SCARB2), Cathepsin B (CTSB), and LAMP2.
• Enzymatic Activity: Blood-based glucocerebrosidase (GCase) enzyme activity.
• Sphingolipidomics: CSF and plasma levels of glucosylceramides (GlcCer), ceramides (Cer), sphingomyelin (SM), and related metabolites.

Statistical Analysis:
Associations were assessed using multivariable linear and logistic regression, adjusted for sex, age, disease duration, and GBA1 status. Analyses were conducted both in the overall PD cohort and within GBA1-stratified subgroups. Multiple testing was corrected using the Benjamini–Hochberg (BH) method to control the false discovery rate (FDR).

Key Results

• Clinical Outcomes: In the discovery cohort, the TMEM175 p.M393T risk variant was nominally associated with decreased cognitive function (MoCA) when adjusted for GBA1 status, though this did not survive multiple testing correction. No significant associations were found between the studied variants and UPDRS-III or BDI-II scores in either cohort.
• $\alpha$-Syn Seeding: Carriers of the TMEM175 p.Q65P risk allele showed a higher proportion of positive $\alpha$-syn seeding activity compared to non-carriers in the discovery cohort (79% vs 95%, $P=0.053$), but this did not reach statistical significance after correction.
• Lysosomal Proteins:
  • CTSB: In the discovery cohort, carriers of the CTSB rs1293298 risk allele had nominally lower CSF CTSB levels. Significantly lower CSF LAMP2 levels were observed in risk allele carriers compared to protective allele carriers in the overall PD cohort and specifically in the PD$_{GBA1\_wildtype}$ subgroup.
  • SCARB2: No significant differences in CSF LIMP2 levels were observed based on SCARB2 genotype.
• GCase Activity: In the discovery cohort, SCARB2 rs6812193 risk allele carriers exhibited significantly lower GCase activity in the PD$_{GBA1\_wildtype}$ subgroup ($P=0.027$ after correction), with a similar non-significant trend in the validation cohort. No significant differences were found for TMEM175 variants regarding GCase activity.
• Sphingolipid Profiles:
  • TMEM175 p.M393T risk allele carriers showed nominally lower CSF levels of GCase downstream products (various Ceramides) and higher plasma sphingomyelin (SM) levels compared to protective allele carriers.
  • SCARB2 rs6825004 risk allele carriers showed nominally higher CSF GlcCer C24:0 levels.

Significance and Claims
The authors claim that this study provides the first integration of these specific lysosomal genetic variants with a broad spectrum of clinical and fluid biomarkers in PD. The findings demonstrate that genetic variants in TMEM175, SCARB2, and CTSB have a functional impact on biomarker profiles, particularly regarding lysosomal protein levels, GCase activity, and sphingolipid metabolism.

The paper posits that integrating genetic characterization with biochemical profiling offers a framework for patient stratification. Specifically, the observed associations suggest that these biomarkers could serve as translational readouts for target engagement and treatment efficacy in future clinical trials targeting lysosomal pathways. The authors emphasize that while some associations were nominal and did not survive strict multiple testing correction, the data supports the biological heterogeneity of PD driven by lysosomal genetics and warrants further investigation in independent cohorts and experimental studies. The study concludes that these findings provide exploratory reference data to support the design of future trials focused on patient stratification and lysosomal pathway-targeted therapies.