Comprehensive analysis of PM20D1 QTL in Alzheimer’s disease

Abstract

Background: Alzheimer's disease (AD) is a complex disorder caused by a combination of genetic and non-genetic risk factors. In addition, an increasing evidence suggests that epigenetic mechanisms also accompany AD. Genetic and epigenetic factors are not independent, but multiple loci show genetic-epigenetic interactions, the so-called quantitative trait loci (QTLs). Recently, we identified the first QTL association with AD, namely Peptidase M20 Domain Containing 1 (PM20D1). We observed that PM20D1 DNA methylation, RNA expression, and genetic background are correlated and, in turn, associated with AD. We provided mechanistic insights for these correlations and had shown that by genetically increasing and decreasing PM20D1 levels, AD-related pathologies were decreased and accelerated, respectively. However, since the PM20D1 QTL region encompasses also other genes, namely Nuclear Casein Kinase and Cyclin Dependent Kinase Substrate 1 (NUCKS1); RAB7, member RAS oncogene family-like 1 (RAB7L1); and Solute Carrier Family 41 Member 1 (SLC41A1), we investigated whether these genes might also contribute to the described AD association. Results: Here, we report a comprehensive analysis of these QTL genes using a repertoire of in silico methods as well as in vivo and in vitro experimental approaches. First, we analyzed publicly available databases to pinpoint the major QTL correlations. Then, we validated these correlations using a well-characterized set of samples and locusspecific approaches-i.e., Sanger sequencing for the genotype, cloning/sequencing and pyrosequencing for the DNA methylation, and allele-specific and real-time PCR for the RNA expression. Finally, we defined the functional relevance of the observed alterations in the context of AD in vitro. Using this approach, we show that only PM20D1 DNA methylation and expression are significantly correlated with the AD-risk associated background. We find that the expression of SLC41A1 and PM20D1-but not NUCKS1 and RAB7L1-is increased in mouse models and human samples of AD, respectively. However, SLC41A1 and PM20D1 are differentially regulated by AD-related stressors, with only PM20D1 being upregulated by amyloid-β and reactive oxygen species, and with only PM20D1 being neuroprotective when overexpressed in cell and primary cultures. Conclusions: Our findings reinforce PM20D1 as the most likely gene responsible of the previously reported PM20D1 QTL association with AD.

Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

“…Although not most common, such effect size of a QTL has been reported in multiple studies, e.g., [ 24 , 25 ]. In fact, this agrees almost perfectly with what is been observed in brain tissues as reported in the aforementioned work of Sanchez-Mut et al [ 13 , 22 ]. Interestingly, although rs960603 is reported to be co-segregated as a haplotype in nearly 85% of cases in the 1000 Genomes Project, its allelic dosage is not as significant in multiple tests within our analysis.…”

“…In contrast, in samples with hypermethylated PM20D1 (high risk, homozygous alternate allele haplotype carriers, AA/TT), the promoter region is not contacted by the enhancer and transcription does not occur, which results in low PM20D1 expression, and there is no protective effect against Aβ. The role of PM20D1 in AD has since then been further explored [ 22 , 23 ], showing that it is the sole risk gene with consistently enriched promoter hypermethylation in AD patients, and upregulated by Aβ and reactive oxygen species, and being neuroprotective when overexpressed in cell and primary cultures.…”

Epigenome-wide association study of COVID-19 severity with respiratory failure

“…Only one gene, in addition to AIM2 and HLA-C, was represented by two CpG sites in our COVID-19 EWAS: PM20D1 (peptidase M20 domain-containing 1). PM20D1 has most often been categorized as a metabolic disease-associated gene, particularly in relation to obesity and diabetes [41] , but genetic and epigenetic variants have also emerged as being a risk factor for neurodegenerative disorders such as Parkinson's [42] and Alzheimer's disease [ 43 , 44 ]. Thus, its additional link as a potential modulator of the severity of SARS-CoV-2 infection, described here, suggests that this peptidase lies at the crossroads of many cellular and pathological pathways.…”

Association of peripheral blood DNA methylation level with Alzheimer’s disease progression

“…The most significant DMR was identified in the AD-associated gene PM20D1 [ 46 , 47 ], which was associated with both the slope of CDR-SB (called by comb-p) and the MCI to AD conversion status (called by both comb-p and DMRcate). While variants associated with AD have been characterized as both meQTL and eQTL for PM20D1 , the differential methylation of PM20D1 promoters in human samples of AD and differential expression of PM20D1 in mouse models and human samples of AD were reported [ 47 ].…”

“…While variants associated with AD have been characterized as both meQTL and eQTL for PM20D1 , the differential methylation of PM20D1 promoters in human samples of AD and differential expression of PM20D1 in mouse models and human samples of AD were reported [ 47 ]. PM20D1 expression is upregulated by AD-related stressors, amyloid-β and reactive oxygen species, and overexpression of PM20D1 was neuroprotective in cell and primary cultures [ 46 ]. DUSP22 promoter hypermethylation and mRNA downregulation in the hippocampus of AD patients were reported previously [ 48 ].…”