Discovery of toxic and protective short RNAs associated with Alzheimer's disease and superior memory capacity

By Vijay Kumar MalesuReviewed by Danielle Ellis, B.Sc.Jan 22 2024

In a recent study published in Nature Communications, a group of researchers explored how Death Induced by Survival gene Elimination (DISE) through the analysis of ribonucleic acid (RNA)-induced silencing complex (RISC)-bound short RNAs (R-sRNAs)  in Alzheimer's disease (AD) models, influences neuronal survival and correlates with neurotoxicity in AD.

Background 

AD is marked by neurodegeneration with poorly understood causes. Key features include Amyloid Beta (Aβ) plaques, hyper-phosphorylated tau protein (p-tau) accumulation, and multiple cell death pathways. Aβ42 toxicity and genetic links in familial AD are established. Aging accelerates deoxyribonucleic acid (DNA) damage, contributing to AD.

In RNA interference (RNAi), micro (mi)RNAs regulate gene expression post-transcriptionally, with seed regions targeting messenger RNA (mRNA) 3' untranslated regions (3'UTR). R-sRNAs with guanine (G)-rich 6mer seeds can activate multiple cell death pathways via DISE. Further research is needed to fully understand the mechanisms by which modifying nontoxic miRNAs could potentially be utilized as a treatment for AD.

About the study 

In the present study, a variety of methods were employed to investigate the mechanisms underlying AD. Mouse and human brain tissues were utilized for analysis. Key reagents and antibodies were prepared alongside the synthesis of Aβ peptides.

The study involved extensive cell culture work, including the generation of knockout (k.o.) cells and the assessment of cell growth and viability. SH-SY5Y (SH) cells were differentiated for specific experiments. Treatments with Aurintricarboxylic acid and Enoxacin were applied in certain contexts. RNA extraction, reverse transcription, and quantitative real-time polymerase chain reaction (PCR) were conducted for genetic analysis. Western blot analysis was used to study protein levels and interactions. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was employed to detect DNA fragmentation in mouse brains.

The study also incorporated induced pluripotent stem cell (iPSC)-derived excitatory forebrain neurons from AD patients and iPSC-derived midbrain dopamine neurons for in vitro aging studies. An important aspect of the methodology was the Argonaute (Ago) pull-down and subsequent small RNA sequencing (Ago-RP-Seq), which played a crucial role in understanding the RNA components involved in the disease process.

Study results

The results of the study highlight the significant role of R-sRNAs in AD. With aging, there is a notable shift in the balance of R-sRNAs towards those with toxic 6mer seeds, which are less viable and more likely to induce neuronal cell death through DISE. This shift is attributed to the reduced ability of aging neurons to produce sufficient nontoxic miRNAs. Key enzymes like Dicer and Drosha, crucial for miRNA expression, are affected during AD and aging, with their stability being compromised by reactive oxygen species and interferons, which are common in AD. The phosphorylation and subsequent translocation of Drosha from the nucleus to the cytosol, for instance, result in the loss of most miRNAs.

Two primary cellular responses to Aβ42 involving RISC activity are identified: cell death/DISE and DNA damage. DISE integrates various cell death pathways, and the specific pathway activated depends on the affected cell's transcriptome. This finding aligns with multiple cell death pathways implicated in AD. The DISE mechanism might contribute not only to neuronal cell death but also to neurodegeneration by inducing DNA damage, suggesting a need for further research to understand its full impact on synaptic dysfunction and AD pathology.

The study also points to the possibility that the increase in toxic sRNAs and the concurrent loss of nontoxic miRNAs during aging might be central to other neurodegenerative diseases like Parkinson's disease, Huntington's disease, and Amyotrophic Lateral Sclerosis (ALS). The study's molecular profiling suggests a collective contribution of genetic modifiers, mutations, and the balance of toxic versus nontoxic miRNAs to the onset and progression of AD. In terms of therapeutic implications, the results challenge the primary focus of AD drug discovery, which has been predominantly on reducing amyloid plaque load and preventing tau phosphorylation. 

Conclusions 

The study presents a novel perspective on AD, suggesting that the balance of R-sRNAs, specifically the ratio of toxic to nontoxic miRNAs, plays a crucial role in neuronal survival and neurodegeneration. It concluded that with aging and AD, there is a shift towards more toxic sRNAs in the RISC, leading to increased neuronal susceptibility to DISE and DNA damage. This shift could be due to aging-related decreases in key miRNA processing enzymes like Dicer and Drosha.

The study also indicates that DISE, involving various cell death pathways, may contribute significantly to AD pathology, including synaptic dysfunction and neurodegeneration. Moreover, this mechanism might extend to other neurodegenerative diseases like Parkinson's, Huntington's, and ALS. The findings challenge the conventional focus on amyloid and tau in AD treatment, proposing instead that enhancing nontoxic miRNA levels could be a more effective therapeutic strategy.