Up-regulated Pro-inflammatory MicroRNAs (miRNAs) in Alzheimer's disease (AD) and Age-Related Macular Degeneration (AMD)

Abstract

Alzheimer's disease (AD) of the brain neocortex and age-related macular degeneration (AMD) of the retina are two complex neurodegenerative disorders, which (i) involve the progressive dysregulation and deterioration of multiple neurobiological signaling pathways, (ii) exhibit the temporal accumulation of pro-inflammatory lesions including the amyloid beta (Aβ) peptide-containing senile plaques of AD and the drusen of AMD, and (iii) culminate in an insidious inflammatory neurodegeneration ending, respectively, in neural cell atrophy and death and progressive loss of cognition and central visual function. Recent independent research studies have indicated that AD and AMD share common, pathological signaling defects and disease mechanisms at the molecular genetic level. Using high-integrity total RNA samples pooled from AD brain and AMD retina, microfluidic hybridization miRNA arrays, and bioinformatics, the current study was undertaken to quantify microRNA (miRNA) speciation and complexity common to both AD and AMD. These small non-coding (sncRNAs) are known to post-transcriptionally regulate multiple neurobiological pathways and an abundance of research information has already been generated on the roles of these miRNAs in pathological situations involving inflammatory neuropathology and neural cell decline. Here, for the first time, we report the sequence and abundance of a septet of sncRNAs including miRNA-7, miRNA-9-1, miRNA-23a/miRNA-27a, miRNA-34a, miRNA-125b-1, miRNA-146a, and miRNA-155 that are significantly increased in abundance and common to both AD-affected superior temporal lobe neocortex (Brodmann A22) and the AMD-affected macular region of the retina. Bioinformatics, miRNA-mRNA complementarity, next-gen RNA sequencing, and feature alignment analysis further indicate that these 7 up-regulated miRNAs have the potential to interact with and down-regulate ~ 9460 target messenger RNAs (mRNAs; about 3.5% of the genome) involved in the synchronization of amyloid production and clearance, phagocytosis, innate-immune, pro-inflammatory, and neurotrophic signaling and/or synaptogenesis in diseased tissues.

Keywords: Age-related macular degeneration; Alzheimer’s disease; MicroRNA–mRNA integration; Neurotrophic signaling; Phagocytosis; Prion disease; Synaptogenesis.

Fig. 1

a miRNA array-based analysis of the AD superior temporal lobe neocortex (Brodmann A22) and the macular region of the AMD retina compared to age-matched controls—the brain neocortex and the retina derive from the same anatomical regions—the neural ectoderm and neuroepithelium—during neurodevelopment—perhaps not surprisingly common miRNA species are abundant in both the normally aging brain and retina; samples for AD were pooled from 45 high-quality AD and control brain tissues; all female, mean post-mortem interval all less than 3 h (not significant); mean age of AD cases = 76.1 ± 9.3 years; mean age of control brain neocortex cases = 75.4 ± 8.5 years (not significant); similarly samples for AMD were pooled from 27 high-quality AMD and control retinal tissues; all female, mean post-mortem interval all less than 1 h (not significant); mean age of AMD cases = 74.2 ± 9.1 years; mean age of control brain neocortex cases = 72.1 ± 7.2 years (not significant); mean RNA integrity number (RIN) for AD and control cases were 8.05 and 8.1, respectively (not significant); mean RNA integrity number (RIN) for AMD and control cases was 8.1 and 8.15, respectively (not significant); therefore, there were no significant differences in age, gender, post-mortem interval (PMI), or RIN between the AD and control or AMD and control cases examined; b miRNA signals were quantified in bar graph format from the data in a; while the internal control sncRNA miRNA-183 and 5S RNA exhibited no change in relative signal strength (and were arbitrarily set to 2.0), all other miRNAs in a were increased from 1.5-fold (miRNA-9 in AD) to 6.1-fold (miRNA-146a in AD) over age-matched controls; a dashed horizontal line at 2.0 is included for ease of comparison; *p < 0.01 (ANOVA); (c) AD and AMD appear to share a highly interactive pathogenic pattern of at least 7 up-regulated miRNAs and 13 down-regulated mRNA targets that can explain much of the observed neuropathology in AD or AMD. For every black arrow in c, there has already been made a potential connection in the literature between that up-regulated miRNA and its corresponding down-regulated mRNA (see text); dashed line represents the predicted interaction from the literature; note that in the lower right corner decreases in IRAK-1 expression are linked to a massive compensatory increase in IRAK-2 expression (Cui et al. 2010); because all miRNA fractions were obtained from short post-mortem interval (PMI) human tissue samples and miRNAs have been reported to have a high depolymerization (degradation) rate under physiological and especially pathophysiological conditions, only up-regulated miRNAs were studied here; in fact, miRNA up-regulation and mRNA down-regulation appear to be very common post-translational genetic regulatory mechanisms in the human and murine CNS (see text; Guo et al. ; Clement et al. 2016). Note that parts of c have been considerably updated from a previous version (see Zhao et al. 2015a)