Interpreting Gene Expression Effects of Disease-Associated Variants: A Lesson from SNCA rs356168

Abstract

The SNCA intronic single nucleotide polymorphism (SNP), rs356168, has been associated with Parkinson’s disease (PD) in large genome wide association studies (GWAS). Recently, the PD-risk allele, rs356168-G was shown to increase SNCA-mRNA expression using genome edited human induced pluripotent stem cells (iPSC)-derived neurons. In this study, as means of validation, we tested the effect of rs356168 on total SNCA-mRNA levels using brain tissues, temporal and frontal cortex, from healthy control donors. Carriers of the rs356168-G allele demonstrated a borderline significant decrease of SNCA-mRNA levels in temporal brain tissues (p = 0.02) compared to individuals homozygous for the ‘A’ allele. Similar trend, but weak, was observed in the analysis of frontal cortex samples, however, this analysis did not reach statistical significance. These results conflict with the recently reported effect of SNCA SNP rs356168 described above. Our study conveys the need to carefully interpret the precise molecular mechanism by which rs356168, or another tightly linked variant, affects the regulation of SNCA expression. The regulatory mechanisms that contribute to the observed associations between PD and the SNCA-3′ linkage disequilibrium region warrant further investigations.

A comprehensive analysis of SNCA‐related genetic risk in sporadic parkinson disease

“…2 SNCA GWAS hits have been investigated as potential brain eQTLs in a number of previous studies without convincing results, including the large Genotype Tissue Expression 34 and BRAINEAC 40 databases, as well as a recent negative follow-up study of the proposed functional variant rs356168. 41 This suggests that regulation is complex, and refined analyses may be needed to detect disease-relevant mechanisms. Previous studies have investigated SNCA splice variants affecting coding exons, 42 but variation in 5′UTR expression has to our knowledge not been studied in relation to PD susceptibility and risk SNPs.…”

“…Such an eQTL effect is particularly plausible in the case of SNCA , where the dose‐dependent pathogenic effect of increased expression has been demonstrated in monogenic PD caused by genomic multiplications . SNCA GWAS hits have been investigated as potential brain eQTLs in a number of previous studies without convincing results, including the large Genotype Tissue Expression and BRAINEAC databases, as well as a recent negative follow‐up study of the proposed functional variant rs356168 . This suggests that regulation is complex, and refined analyses may be needed to detect disease‐relevant mechanisms.…”

Advancing Stem Cell Models of Alpha-Synuclein Gene Regulation in Neurodegenerative Disease

“…The same SNP was subsequently tested for changes in SNCA expression in frontal and temporal cortex of a cohort of 134 healthy individuals. That study concluded the opposite effect for the G-allele with an ~20% decrease in alpha-synuclein mRNA in individuals homozygous for the G-allele (Glenn et al, 2017 ).…”

“…Out of 25 PD-associated SNPs, seven have been reported to influence alpha-synuclein levels, however, some findings are controversial (Supplemental Table 2 ). Six SNPs within intron 4 and 3′ region were studied for total alpha-synuclein mRNA levels in post-mortem brain samples, blood, or in vitro with variable findings for alpha-synuclein expression (Fuchs et al, 2007a , 2008 ; Westerlund et al, 2008 ; Sotiriou et al, 2009 ; Mata et al, 2010 ; Hu et al, 2012 ; Rhinn et al, 2012 ; Cardo et al, 2014 ; Glenn et al, 2017 ).…”

Uncovering the impact of noncoding variants in neurodegenerative brain diseases

“…Measurement of total SNCA mRNA levels showed a significant increase in the presence of the risk allele, which was complemented by eQTL analysis of SNCA mRNA in the brain of patients with PD and control subjects, conferring risk for PD [96]. An opposite effect of rs356168 on SNCA mRNA levels was reported in the brains of healthy individuals [97]. The contradicting results might be due to technical limitations or methodological differences.…”