Replication of HLA‐DRB1*04:04 allele subtype protective effect against Alzheimer’s Disease in cognitively healthy centenarians using long‐read sequencing

Abstract

AbstractBackgroundGenomic‐Wide Association Studies (GWAS) of Alzheimer’s Disease (AD) have identified several single‐nucleotide‐polymorphisms (SNPs) in the Human Leukocyte Antigens (HLA) gene cluster. Fine mapping of the genetic signals, by means of model‐based HLA allele imputation from SNP‐array‐based genotyping data, was linked to a protective effect of three HLA‐DRB1*04 allele subtypes. These alleles would favor the binding of an aggregation‐prone Tau peptide by T‐cells, promoting early clearance of toxic Tau aggregate seeds, and reducing neurodegeneration. Here, we aim to replicate this association by means of HLA genotyping with long‐read sequencing.MethodWe used an HLA genotyping assay, [NGS‐go MX11‐3, GenDx], coupled with [PacBio] long‐read sequencing. This allows for genotyping of HLA genes at their full resolution of polymorphism. So far, we have genotyped HLA genes in 129 AD cases from the Amsterdam Dementia Cohort (ADC, mean age = 67.4 with SD = 7.56, N females = 85, N males = 44) and 138 cognitively healthy centenarians from the 100‐plus Study (mean age = 101.1 with SD = 3.33, N females = 92, N males = 46), thereby maximizing the analysis power. We then focused on the comparison of previously identified protective HLA‐DRB1*04 allele subtypes (DRB1*04:01, DRB1*04:04 and DRB1*04:07) between AD cases and centenarians.ResultFor all three HLA‐DRB1*04 allele subtypes, we observed no additional genetic variation concerning synonymous DNA substitutions in coding regions and changes in non‐coding regions. DRB1*04:04:01:02 had a frequency of 0.116 in centenarians, as compared to a 0.054 in AD cases (one‐sided Fisher’s exact test, p = 0.04). The frequency in centenarians was higher than the previously reported joint frequency of carriers in AD and controls, frequency = 0.073. DRB1*04:01:01:01 had similar frequencies in centenarians (0.174) and AD cases (0.178) (p>0.05). Similarly, DRB1*04:07:01:01 had a frequency of 0.014 in centenarians and 0.015 in AD (p>0.05).ConclusionWe confirmed a protective HLA‐DRB1*04:04 allele subtype, previously described by HLA imputation, with the use of long read sequencing. Genotyped at full resolution as DRB1*04:04:01:02, we observed an enrichment in cognitively healthy centenarians compared to the original AD vs controls setting. The HLA system could play a role in the enhanced immunity of centenarians, and how they are able to escape neurodegenerative diseases.