• Generation of single-nucleus RNA sequencing data from the neocortex of 424 aged individuals, analyzing 1.5 million transcriptomes from seven cell types and 64 subtypes.
• Identification of 10,004 genes influenced by genetic variants (eGenes) at the cell-type level with additional 8,099 eGenes found at cell-subtype level.
• Novel single nucleotide polymorphism (SNP) discovered that regulates APOE expression in microglia, thereby affecting cerebral amyloid angiopathy, but not Alzheimer’s Disease
• Colocalization studies confirmed established results and found new quantitative trait loci (QTLs) with SNPs that increase the risk for Alzheimer’s and Parkinson’s Disease, as well as schizophrenia.

In the history of Alzheimer’s research, several gene discovery studies, such as reference epigenomic atlases from patients and cell lines, set a foundation for genetic research approaches ^[1]. These studies, while of high importance, remained mostly suggestive yet insufficient for further functional analyses. Aiming for a more comprehensive approach, Fujita et al. (20249 combined quantitative trait loci (QTL) studies with cytometry-based single-nucleus RNA sequencing data sets. They selected tissue from the neocortex of 424 individuals from two long-term studies (Religious Order Study, 1994 & Memory Aging Project, 1997), 63% of whom were diagnosed with AD.

The study identified 10,004 eGenes across all seven major neocortical cell types, predominantly in excitatory and inhibitory neurons. This newly established single-nucleus based approach identified an additional 8,099 eGenes on a cell-subtype level including around 2,000 eGenes not found at the cell-type level. Interestingly, the authors were also able to reproduce parts of this approach by in vitro studies in iPSC-derived neurons and astrocytes.

Although the majority of eGenes was shared among different cell types, the study pinpointed some cell-type specific associations with AD risk. For instance, APP, a key player in AD pathogenesis was significantly affected by a SNP only in oligodendrocytes. APOE also showed a unique SNP regulation exclusively in microglia. Epigenetic modifications (acetylation and methylation) enhanced APOE expression independent of the AD-related APOEε4 phenotype and increased cerebral amyloid angiopathy (CAA) pathology. Furthermore, the authors found one SNP associated with TMEM106B in a subtype of excitatory neurons significantly linked to AD risk.

Lastly, colocalization studies with data sets from past genome-wide association studies (GWAS) allowed confirmation of already established results, such as the microglia-specific expression of BIN1 in AD-development ^[2]. In combination with a transcriptome-wide association study (TWAS) they additionally identified new colocalizations, e.g., a large excess of microglial genes associated with AD. The authors were able to expand this data on other neurological pathologies such as Parkinson’s Disease, amyotrophic lateral sclerosis (ALS), and schizophrenia.

By establishing a new, more specific single-nucleus based QTL study, Fujita et al. have catalogued cell-type and subtype-specific expression patterns associated with neurological pathologies, thereby improving the outcomes of previous association studies. This study demonstrates novel genetic interactions especially in AD development that exceed the tau and amyloid phenotype, setting a new direction for future research.

This article refers to:

Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, Green GS, Rozenblatt-Rosen O, Phillips D, Amir-Zilberstein L, Lee H, Pearse RV, Khan A, Vardarajan BN, Kiryluk K, Ye CJ, Klein H-U, Wang G, Regev A, Habib N, Schneider JA, Wang Y, Young-Pearse T, Mostafavi S, Bennett DA, Menon V, Jager PL de (2024) Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain. Nat Genet 56:605–614. DOI: 10.1038/s41588-024-01685-y

Further references:

[1] Stunnenberg HG, Hirst M (2016) The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery. Cell 167:1145–1149. DOI: 10.1016/j.cell.2016.11.007

[2] Lopes KdP, Snijders GJL, Humphrey J, Allan A, Sneeboer MAM, Navarro E, Schilder BM, Vialle RA, Parks M, Missall R, van Zuiden W, Gigase FAJ, Kübler R, van Berlekom AB, Hicks EM, Bӧttcher C, Priller J, Kahn RS, Witte LD de, Raj T (2022) Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies. Nat Genet 54:4–17. DOI: 10.1038/s41588-021-00976-y