Basic Science and Pathogenesis.

Background: Determining the precise genetic mechanisms that contribute to LOAD, both in coding and noncoding variants, will enable a deeper understanding of pathogenesis and advance preclinical models for the testing of targeted therapeutics.

Methods: We have introduced candidate genetic variants in the EPHA1, BIN1, CD2AP, SCIMP, KLOTHO, PTK2B, ADAMTS4, IL1RAP, IL34, and PTPRB loci into a sensitized mouse model already harboring humanized amyloid-beta, APOE4, and Trem2.R47H alleles knocked in to a C57BL/6J background. Variants were selected based on predicted function, cross-species conservation, increased risk of LOAD, and allele frequency. Coding variants were chosen in PTPRB, IL34, and KLOTHO while promoter and/or enhancer variants were modeled for the remaining loci. Genome editing with CRISPR-Cas9 was performed and mouse cohorts were aged to four and 12 months. Homogenized brain hemispheres were assayed from both male and female mice with RNA-seq. Transcriptomic changes were compared to postmortem human brain data to determine disease relevance.

Results: Transcriptomic effects from these genetic variants recapitulated a variety of human gene expression patterns observed in LOAD study cohorts, particularly when signatures were partitioned into Alzheimer's relevant biodomains. By 12 months of age, PTPRB*D57N mice exhibited neuroimmune signatures that correlate with postmortem LOAD cases relative to controls. A noncoding variant in the EPHA1 region primarily altered apoptotic processes, potentially driven by expression changes in CASP2 at the locus. The BIN1 promoter variant exhibited both neuroimmune and oligodendrocyte-related changes that correlated with LOAD modules. These changes were more pronounced with age, supporting their role in age-related dementia.

Conclusions: We have characterized in vivo signatures of nine genetic candidates for LOAD, identifying alterations in specific LOAD-related pathways in each variant on a sensitized genetic background. These results provide animal models for preclinical testing of therapeutics designed to correct specific molecular alterations that contribute to LOAD pathology and progression.