Characterization of a pathogenic variant in GBA for Parkinson’s disease with mild cognitive impairment patients

Abstract

Parkinson's disease (PD) is the second most common neurodegenerative disease, and mild cognitive impairment (MCI) is a well-established risk factor for the development of dementia in PD. A growing body of evidence suggests that low expression of glucocerebrosidase (GBA) promotes the transmission of α-synuclein (α-Syn) interpolymers and the progression of PD. However, how GBA mutations affect the pathogenesis of PD via abnormal aggregation of α-Syn is unclear, and no clinically valid PD-MCI genetic markers have been identified. Here, we first located a GBA eQTL, rs12411216, by analysing DHS, eQTL SNP, and transcription factor binding site data using the UCSC database. Subsequently, we found that rs12411216 was significantly associated with PD-MCI (P < 0.05) in 306 PD patients by genotyping. In exploring the relationship between rs12411216 and GBA expression, the SNP was found to be associated with GBA expression in 50 PD patients through qPCR verification. In a further CRISPR/Cas9-mediated genome editing module, the SNP was identified to cause a decrease in GBA expression, weaken enzymatic activity and enhance the abnormal aggregation of α-Syn in SH-SY5Y cells. Additionally, using an electrophoretic mobility shift assay, we confirmed that the binding efficiency of transcription factor E2F4 was affected by the rs12411216 SNP. In conclusion, our results showed that rs12411216 regulated GBA expression, supporting its potential role as a PD-MCI genetic biomarker and highlighting novel mechanisms underlying Parkinson's disease.

Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases

“…However, the expressed sets of TFs in different tissues are significantly different [ 11 ]; correspondingly, it is most desirable in such experiments to use several cell lines [ 3 , 23 , 51 ]. It is especially important that the EMSA with specific antibodies or purified TFs is able to reliably identify the TF with its binding site affected by a nucleotide substitution [ 23 , 28 , 30 , 40 , 41 ] and numerous other papers ( Table 1 ). In a similar manner, such TF can be identified, although somewhat less unambiguously, in the reporter assays with cotransfection by the plasmids expressing suspected TFs [ 52 , 53 , 54 ].…”

“…If ChIP-seq peaks are numerous, this suggests a potential enhancer function, which is further verified by an increase in the luciferase reporter activity with recording of allele-specific effects [ 23 , 26 , 77 , 78 ]. To find out which particular genes are influenced by the studied region, it is inactivated using siRNA-mediated transcriptional gene silencing [ 23 ] or CRISPR interference (CRISPRi) involving recruitment of a KRAB repressor domain fused to catalytically dead Cas9 [ 18 , 79 ] or just via deletion of this region with CRISPR/Cas9 technology [ 28 , 78 , 80 ]. Then the transcription levels of the selected genes are assayed [ 23 , 28 , 79 , 80 ] or a whole transcriptome analysis is performed [ 78 , 80 ].…”

“…To find out which particular genes are influenced by the studied region, it is inactivated using siRNA-mediated transcriptional gene silencing [ 23 ] or CRISPR interference (CRISPRi) involving recruitment of a KRAB repressor domain fused to catalytically dead Cas9 [ 18 , 79 ] or just via deletion of this region with CRISPR/Cas9 technology [ 28 , 78 , 80 ]. Then the transcription levels of the selected genes are assayed [ 23 , 28 , 79 , 80 ] or a whole transcriptome analysis is performed [ 78 , 80 ]. A physical interaction between the region carrying an SNP and the potential target genes is usually confirmed with the help of Hi-C methods [ 26 , 28 , 59 , 80 ], including allele-specific chromosome conformation capture assays [ 74 ], or using available Hi-C data [ 59 , 79 , 81 ].…”

“…Starting from the 1990s, numerous studies have been performed focusing on the noncoding SNPs that perturb the TF binding and are associated with various pathologies. As has been shown, risk alleles can (i) destroy a binding site for a TF [ 16 , 17 , 18 , 19 ]; (ii) create a binding site for a TF [ 20 , 21 , 22 ]; or alter the binding affinities towards an increase [ 23 , 24 , 25 ] or a decrease [ 25 , 26 , 27 , 28 ]. In addition, several cases have been observed when a damage/destruction of a binding site for a TF leads to a concurrent formation of another/other TFBS(s) [ 19 , 29 , 30 ].…”

Arylsulfatase A (ASA) in Parkinson’s Disease: From Pathogenesis to Biomarker Potential

“…Interestingly, early cognitive impairment has been associated with GBA1 -related PD [ 23 , 24 , 49 ], postural and action tremor has been reported in asymptomatic carriers of LRRK2 mutations [ 50 ], and PD patients with SNCA mutations display early dementia [ 51 ]. These clinical observations suggest that mixed tremor and early cognitive decline may characterize PD cases related to genes associated with lysosomal function.…”