Micro-RNA profiles of pathology and resilience in posterior cingulate cortex of cognitively intact elders

Abstract

The posterior cingulate cortex (PCC) is a key hub of the default mode network underlying autobiographical memory retrieval, which falters early in the progression of Alzheimer's disease (AD). We recently performed RNA sequencing of post-mortem PCC tissue samples from 26 elderly Rush Religious Orders Study participants who came to autopsy with an ante-mortem diagnosis of no cognitive impairment but who collectively displayed a range of Braak I-IV neurofibrillary tangle stages. Notably, cognitively unimpaired subjects displaying high Braak stages may represent cognitive resilience to AD pathology. Transcriptomic data revealed elevated synaptic and ATP-related gene expression in Braak Stages III/IV compared with Stages I/II, suggesting these pathways may be related to PCC resilience. We also mined expression profiles for small non-coding micro-RNAs (miRNAs), which regulate mRNA stability and may represent an underexplored potential mechanism of resilience through the fine-tuning of gene expression within complex cellular networks. Twelve miRNAs were identified as differentially expressed between Braak Stages I/II and III/IV. However, the extent to which the levels of all identified miRNAs were associated with subject demographics, neuropsychological test performance and/or neuropathological diagnostic criteria within this cohort was not explored. Here, we report that a total of 667 miRNAs are significantly associated (rho > 0.38, P < 0.05) with subject variables. There were significant positive correlations between miRNA expression levels and age, perceptual orientation and perceptual speed. By contrast, higher miRNA levels correlated negatively with semantic and episodic memory. Higher expression of 15 miRNAs associated with lower Braak Stages I-II and 47 miRNAs were associated with higher Braak Stages III-IV, suggesting additional mechanistic influences of PCC miRNA expression with resilience. Pathway analysis showed enrichment for miRNAs operating in pathways related to lysine degradation and fatty acid synthesis and metabolism. Finally, we demonstrated that the 12 resilience-related miRNAs differentially expressed in Braak Stages I/II versus Braak Stages III/IV were predicted to regulate mRNAs related to amyloid processing, tau and inflammation. In summary, we demonstrate a dynamic state wherein differential PCC miRNA levels are associated with cognitive performance and post-mortem neuropathological AD diagnostic criteria in cognitively intact elders. We posit these relationships may inform miRNA transcriptional alterations within the PCC relevant to potential early protective (resilience) or pathogenic (pre-clinical or prodromal) responses to disease pathogenesis and thus may be therapeutic targets.

Keywords: cognition; micro-RNA; posterior cingulate cortex; resilience; transcriptomics.

Graphical Abstract

Figure 1

Network plot of micro-RNA expression level associations with subject data. A plot was generated using a force-directed algorithm that orders nodes (circles) based on overlap in shared micro-RNA (miRNA). Size of nodes represent number of connections ranging from 5 (perc.sp_neg) to 50 (age_pos). Each edge (line) represents a significant (P < 0.05) correlation (Spearman rho) between a miRNA and a hub. Edges are colour-coded to represent positive or negative miRNA expression level correlation with demographics age or education, pathology Braak or NIA-Reagan and patient test scores: screening (MMSE or GCS), episodic memory, semantic memory, working memory, perceptual orientation, or perceptual speed. Details on associations can be found in Supplementary Tables 1 and 2. ∼, miR; _neg, negative correlation with miRNA; _pos, positive correlation with miRNA; age, age at death; braak, Braak score; cerad, Consortium to Establish a Registry for Alzheimer’s Disease pathology score; educ, years of education; epis.mem, episodic memory score; glob.cog, global cognitive score; mmse, Mini-Mental Status Examination; niaregan, National Institute of Aging-Reagan score; perc.or, perceptual orientation score; perc.sp, perceptual speed score; sem.mem, semantic memory score; sex_neg, biological sex male; sex_pos, biological sex female; work.mem, working memory score.

Figure 2

Network plot of micro-RNA expression level associations with ante-mortem performance on individual neuropsychological tests. A plot was generated to order nodes (circles) based on overlap to shared micro-RNA (miRNA, smaller blue nodes). Size of nodes represent number of connections, ranging from 5 (perc.sp_neg) to 50 (age_pos). Each edge (line) represents a significant (P < 0.05) correlation (Spearman rho) between an miRNA and a hub. Nodes denoting cognitive domains are coloured by cognitive domain and labelled to indicate specific neuropsychological tests within each domain, and edges are coloured to represent positive (purple) or negative (aqua) correlations. Abbreviations: _neg, negative correlation with miRNA; _pos, positive correlation with miRNA; alph.span, alpha span; att, attention; bost.nam, Boston naming 15 items; cat.fluenc, category fluency fruits; chr, chromosome; cog, cognitive test; compl.ideat.matr, complex ideational matrix; dig.forw, digits forward; dig.order, digit ordering; east.bost.del.recall, East Boston delayed recall; epi, episodic memory; ext.rang.voc, extended range vocabulary; lan, language; log.mem.del, logical memory II delayed; log.mem.imm, logical memory I immediate; MIR, micro-RNA; MMSE, Mini-Mental State Exam; numb.comp, number comparison; ori, perceptual orientation; progr.matr, progressive matrices 16 items; progr.matr.subs, progressive matrices subset 9 items; read.test, Reading test 10 items; sem, semantic memory; spe, perceptual speed; symb.dig.oral, symbol digits modality oral; wor, working memory.

Figure 3

Network plot of micro-RNA expression level associations with post-mortem neuropathological diagnostic variables. Plot was generated as noted in Figs 1 and 2 using significant Spearman rho correlations (P < 0.05) correlations between higher micro-RNA expression levels and either higher (positive association) or lower (negative association) pathological stage, as indicated (see key). CERAD, Consortium to Establish a Registry for Alzheimer’s Disease; NIA-Reagan, National Institute on Aging-Reagan.

Figure 4

Co-regulatory network predicted for resilience-related PCC micro-RNAs and AD-related genes. Micro-RNA (miRNA) sequences related to resiliency in PCC were used to probe the StarMir database for potential mRNA targets known to have influence on AD pathogenesis and progression. Sixteen mRNA targets related to amyloidosis (ADAM19, BACE1, PSEN1, MME, ADAM17, APP, PSEN2), tau and its aggregation (GSKB, MAPK13, MAPT, CDK5, GSKA), a transcription factor (REST) and cytokines (IL1A, IL1B, IL6) appeared in the search, each potentially regulated by 4–15 miRNA species.

Figure 5

qRT-PCR validation of select micro-RNAs and predicted mRNA targets (A) miR-12118 and (B) ADAM10 transcript expression levels measured in PCC samples from NCI cases, subdivided into Braak Stages II/II, Braak Stage III or Braak Stage IV. **, P < 0.01 via Kruskal–Wallis ANOVA with post hoc Dunn’s test for multiple comparisons.