Gene replacement-Alzheimer's disease (GR-AD): Modeling the genetics of human dementias in mice

INTRODUCTION

Genetic studies conducted over the past four decades have provided us with a detailed catalog of genes that play critical roles in the etiology of Alzheimer's disease (AD) and related dementias (ADRDs). Despite this progress, as a field we have had only limited success in incorporating this rich complexity of human AD/ADRD genetics findings into our animal models of these diseases. Our primary goal for the gene replacement (GR)-AD project is to develop mouse lines that model the genetics of AD/ADRD as closely as possible.

METHODS

To do this, we are generating mouse lines in which the genes of interest are precisely and completely replaced in the mouse genome by their full human orthologs.

RESULTS

Each model set consists of a control line with a wild-type human allele and variant lines that precisely match the human genomic sequence in the control line except for a high-impact pathogenic mutation or risk variant.

Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants

Genome-wide association studies (GWASs) are instrumental in identifying loci harboring common single-nucleotide variants (SNVs) that affect human traits and diseases. GWAS hits emerge in clusters, but the focus is often on the most significant hit in each trait- or disease-associated locus. The remaining hits represent SNVs in linkage disequilibrium (LD) and are considered redundant and thus frequently marginally reported or exploited. Here, we interrogate the value of integrating the full set of GWAS hits in a locus repeatedly associated with cardiac conduction traits and arrhythmia, SCN5A-SCN10A. Our analysis reveals 5 common 7-SNV haplotypes (Hap1-5) with 2 combinations associated with life-threatening arrhythmia-Brugada syndrome (the risk Hap1/1 and protective Hap2/3 genotypes). Hap1 and Hap2 share 3 SNVs; thus, this analysis suggests that assuming redundancy among clustered GWAS hits can lead to confounding disease-risk associations and supports the need to deconstruct GWAS data in the context of haplotype composition.

Human adaptation to arsenic in Andean populations of the Atacama Desert

OBJECTIVES

Quebrada Camarones, in the Atacama Desert, has the highest arsenic levels in the Americas (>1,000 µg/L). However, the Camarones people have subsisted in this adverse environment during the last 7,000 years and have not presented any epidemiological emergencies. Therefore, to solve this conundrum we compared the frequencies of four protective genetic variants of the AS3MT gene associated with efficient arsenic metabolization, between the living populations of Camarones and two other populations historically exposed to lower levels of arsenic.

MATERIALS AND METHODS

The Chilean selected population samples come from Quebrada Camarones (n = 50) and the Azapa Valley (n = 47) in the north and San Juan de la Costa (n = 45) in southern Chile. The genotyping was conducted using PCR-RFLP. We compared the genotypic and allelic frequencies, and estimated the haplotype frequencies in the AS3MT gene.

RESULTS

We found higher frequencies of the protective variants in those people from Camarones than in the other two populations. The haplotype estimation showed that the combination of protective variants of CTTA is very frequent in Camarones (68%) and Azapa (48%), but extremely low in San Juan de la Costa (8%). Also, the C variant associated with toxicity risks in the SNP Met287Thr had a lower frequency in Camarones (1%) and is higher in the other populations.

DISCUSSION

The higher frequency of protective variants in both northern Chilean populations indicates a long exposure to naturally arsenic-contaminated water sources. Our data suggest that a high arsenic metabolization capacity has been selected as an adaptive mechanism in these populations in order to survive in an arsenic-laden environment.