An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations

Abstract

Parietal cortex RNA-sequencing (RNA-seq) data were generated from individuals with and without Alzheimer disease (AD; n_control = 13; n_AD = 83) from the Knight Alzheimer Disease Research Center (Knight ADRC). Using this and an independent (Mount Sinai Brain Bank (MSBB)) AD RNA-seq dataset, cortical circular RNA (circRNA) expression was quantified in the context of AD. Significant associations were identified between circRNA expression and AD diagnosis, clinical dementia severity and neuropathological severity. It was demonstrated that most circRNA-AD associations are independent of changes in cognate linear messenger RNA expression or estimated brain cell-type proportions. Evidence was provided for circRNA expression changes occurring early in presymptomatic AD and in autosomal dominant AD. It was also observed that AD-associated circRNAs co-expressed with known AD genes. Finally, potential microRNA-binding sites were identified in AD-associated circRNAs for miRNAs predicted to target AD genes. Together, these results highlight the importance of analyzing non-linear RNAs and support future studies exploring the potential roles of circRNAs in AD pathogenesis.

Figure 1:. Cortical circRNAs are associated with AD traits.

Each circular Manhattan plot presents the results from a meta-analysis of circRNA AD-association results from discovery (parietal cortex) and replication (inferior frontal gyrus (Brodmann Area 44)) datasets. In order from outermost to innermost circular plot, the AD traits include: clinical dementia rating at expiration/death (CDR), Braak neuropathological severity score, and AD case-control status (AD case). Study-wide significance threshold is based on a false discovery rate of 0.05 and depicted by the red, dashed line. circRNAs that passed this threshold are displayed with star symbols. Lines extending through all three plots identify circRNAs that are significantly associated with multiple AD traits – dotted line: 2 traits; solid line: 3 traits.

Figure 2:. Changes in cortical circRNA expression tracks with AD clinical severity.

Presented are boxplots of library-size normalized, differential expression covariate-adjusted counts for two AD-associated circRNAs: circHOMER1 and circCORO1C in the Knight ADRC parietal dataset. AD: Alzheimer disease. PreSympAD (Pre-symptomatic AD: neuropathological evidence of AD but, at most, very mild dementia (Clinical dementia rating <= 0.5). Box plot elements: center line (median), box (first and third quartiles), whiskers (quartile ± 1.5×interquartile range), dots (outlier points as defined by falling outside of whiskers).

Figure 3:. AD-associated circRNAs explain more of the observed variation in clinical dementia rating compared to number of APOE4 alleles or the estimated proportion of neurons.

Percent of variation in clinical dementia rating (CDR) explained by the top 10, most meta-analysis significant CDR-associated circRNAs compared to two known contributors number of APOE4 alleles – the most common genetic risk factor for AD – and the estimated proportion of neurons. Knight ADRC: PCtx – parietal discovery dataset (n_CDR = 96); MSBB BM44 – inferior frontal gyrus replication dataset (n_CDR = 195).

Figure 4:. AD-associated circRNAs co-express with AD-relevant genes.

Spearman correlation-based network co-expression module c1_46 (module association with clinical dementia rating (CDR), p-value: 1.52×10⁻⁰⁷) in the MSBB BM44 dataset (n = 195). Module association with CDR was determined from a multivariate linear regression with module eigengene and differential expression covariates. Significance of the module eigengene association with CDR was determined using a two-tailed t-test. KEGG, Kyoto Encyclopedia of Genes and Genomes.