Non-coding RNA-mediated gene regulation in Alzheimer's disease pathogenesis: molecular insights and emerging innovations

Abstract

The accumulation of pathological markers, such as tau tangles and amyloid-beta (Aβ) plaques, and progressive cognitive dysfunction are the markers of Alzheimer's disease (AD). The development of successful therapeutic plans requires exposure to the molecular mechanisms underlying AD development. The importance of non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs), microRNAs (miRNAs), long ncRNAs (lncRNAs), and PIWI-interacting RNAs (piRNAs), in controlling gene expression and influencing the pathophysiology of disease has been brought to light by recent studies. With a focus on their role in important processes such tau hyperphosphorylation, neuroinflammation, and amyloid-beta formation, this study attempts to give a thorough overview of the several types of ncRNAs and their dysregulation in AD. The genetic variants that are associated with the function of ncRNA including single nucleotide polymorphisms (SNPs) may influence ncRNA expression and activity, thereby impacting the susceptibility of individual towards AD. Furthermore, the impact of biomarkers of ncRNAs for early diagnosis and therapeutic option for intervention, highlighting most recent advancement in high-throughput technologies and bioinformatics facilitating ncRNA profiling has also being discussed. The integration of multi-omics approaches and artificial intelligence, new advancement for the complex relationship among ncRNAs and AD pathology are also discussed. The enhancement and understanding of ncRNAs could lead to the door for novel therapeutic concepts for the mitigation of AD progression, offering effective interventions in a disease that currently starves the curative treatments.

Introduction

Alzheimer's disease (AD) is the leading cause of dementia worldwide, accounting for 60–80% of all cases (Ferrari and Sorbi 2021). The 2022 AD Facts and Figures publications predict that by 2050, there will be more than 150 million AD patients globally (Peng et al. 2023). The progressive decline in cognitive abilities is the hallmark of AD, and the atrophy in the brain region is caused by neuron loss and the breakdown of synapses inside the hippocampus which is responsible for spatial orientation, learning, emotions, and memory formation (Teleanu et al. 2022). A complex interplay of environmental, genetic, and behavioural risk factors that stem from pathogenic pathways makes up the aetiology of AD (Plascencia-Villa and Perry 2021). The main risk factor for AD is thought to be getting aged. Epigenetic changes, macromolecular damage, genomic instability, adaptive sensing of nutrients, impaired functioning of mitochondria, cellular decline, stem cell fatigue, altered communication between cells, chronic inflammation, and dysbiosis are the signs of ageing that contribute to AD (Liu et al. 2024). The buildup of aberrantly folded Tau and Aβ proteins in neuronal tangles and amyloid plaques, respectively, leads to neurodegeneration in the brain and forms the basis for AD histopathology. Memory loss and a lowering in executive function are common clinical observations of dementia that interfere with everyday activities and reduce the independence of the elderly population, necessitating the need for support services. A more serious memory deprive that results in visual, verbal, and executive concerns is known as an atypical presentation of dementia (YeLancHezian et al. 2022). One of the signs of AD is the production of massive clumps of amyloid, which is thought to be the primary cause of neurodegeneration and, consequently, cognitive impairment (Rammes 2023). It is believed that a large portion of the cognitive impairment seen early in the course of AD is caused by dysfunction of the hippocampus and entorhinal cortex (EC). The EC's susceptibility to AD has been linked to the dysregulation of the ARMS/Kidins220 scaffold protein and brain-derived neurotrophic factor (BDNF), which are crucial for providing the EC with neurotrophic support (Olajide et al. 2021).

Three important genetic mutations linked to the genes that encodes presenilin 2 (PSEN2), presenilin 1 (PSEN1), and amyloid precursor protein (APP), are found by the genetic and molecular research among the AD patients. The APOEε4 allele is found to be the primary risk factor of gene responsible for AD, specifically in cases of sporadic AD. CD33 is a top-ranked genetic risk factor for late-onset AD (Zhao 2019). The variations in CD33 splicing are important in the modification and their impact in genetic propensity (Singh et al. 2024). There is a strong genetic link between the immune system and the risk of developing AD Extensive research has sparked into the function of immune molecules and cells in AD and expanded our understanding of the pathophysiological chain in AD. As a result, an updated version of the amyloid cascade hypothesis now includes a"cellular phase,"in which pathological curriculum is triggered by protein aggregates that are exacerbated by the responses to the immune system aimed at those aggregates. It is essential to establish standardized methods for analyzing processes like astrocyte activation (astrogliosis) and microglial activity, which play key roles in the progression of AD (Trejo-Lopez et al. 2022). There have been reports of aberrant-activated microglia and neurotoxic astrocytes, as well as the complement system's role in synaptic pruning processes and mitochondrial dysfunction, which seem to be significant mediators and could all lead to synapse loss and cognitive impairments (Rammes 2023). Non-coding RNAs (ncRNAs) appear to play a vital role in maintaining the proper function of both nuclear-encoded mitochondrial genes and mitochondrial DNA. A growing body of research has explored how these regulatory RNAs influence gene expression in both cellular compartments. Studies increasingly highlight their effects on molecular pathways linked to mitochondrial dysfunction, a key contributor to AD progression. Notably, ncRNAs modulate critical processes such as oxidative stress, energy metabolism, and mitophagy (the selective clearance of damaged mitochondria). Disruptions in these mechanisms are tightly connected to AD pathology, with evidence suggesting that ncRNA dysregulation may impair mitophagy, further aggravating neurodegenerative processes (Abed et al. 2024).

Approximately 98–99% of all RNAs synthesized by mammalian genomes are ncRNAs, which are defined as RNA that lacks the ability to code for proteins (Sun et al. 2022). As epigenetic regulators implicated in CNS diseases, ncRNAs have garnered a lot of interest (Xu and Zhang 2022). Due to the fact that ncRNAs may identify and selectively bind with complementary sequences, they can either control the expression of the gene at the time of transcription or operate as modulators of epigenetics through chromatin remodelling. ncRNAs can act as modulators of epigenetics by the remodelling of chromatin or control gene expression at transcriptional and post-transcriptional stages due to their ability to identify and selectively interact with complimentary sequences (Ilieva 2024). AD is predominantly characterized by two hallmark neuropathological changes: extracellular amyloid plaque accumulation and aggregation of neurofibrillary tangles (NFTs) containing hyperphosphorylated tau proteins (Idda et al. 2018). In AD, both factors are closely related to cognitive decline, although their exact roles in disease progression remain unclear. There is growing evidence that ncRNAs including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play crucial regulatory roles in these pathogenic processes, influencing gene expression at transcriptional, post-transcriptional, and epigenetic levels. Aβ peptides are produced by abnormal cleavage of amyloid precursor protein (APP) by β-secretase (BACE1) and γ-secretase enzymes. The resulting Aβ42 peptide aggregation disrupts synaptic function and promotes neurotoxicity through the formation of oligomers and plaques. A number of ncRNAs have been found to regulate the expression and activity of these secretases. In AD brains, miR-29a/b-1 and miR-107 are known to negatively regulate BACE1 expression, and their reduced levels lead to increased Aβ production (Olufunmilayo and Holsinger 2023; Wang et al. 2008; Nelson and Wang 2010). Similarly, lncRNA BACE1-antisense transcript (BACE1-AS), an antisense transcript of the BACE1 gene, stabilizes BACE1 mRNA and promotes its translation, thereby enhancing Aβ generation (Faghihi et al. 2008). According to the article by Wu et al. (2024), one of the key findings is that long ncRNAs (lncRNA) MIR600HG can regulate mitochondrial function by modulating PINK1, a protein essential for mitochondrial quality control and repair. In AD, MIR600HG promotes the degradation of PINK1 via the ubiquitin ligase NEDD4L, which results in impaired mitochondrial activity. Inhibiting MIR600HG blocks PINK1 degradation, enhances mitochondrial function, and alleviates cognitive impairment in AD mouse models (Wu et al. 2024). A study conducted by Huang et al. showed that simvastatin ameliorated memory deficits in both clinical AD patients and the animal model, reduced inflammatory cytokines, decreased amyloid plaque burden, improved neuronal survival, and downregulated miR-106b-mediated apoptosis, suggesting its potential as a lead drug for further anti-AD treatment development (Huang et al. 2017).

Conversely, tau protein, which normally stabilizes microtubules, undergoes hyperphosphorylation in AD, resulting in insoluble NFTs. The progression of cognitive symptoms and neuronal loss is strongly correlated with tau pathology. It has been shown that certain ncRNAs are involved in tau phosphorylation. In AD, miR-132, a neuron-enriched miRNAs, is significantly downregulated and has been shown to regulate tau phosphorylation enzymes, such as glycogen synthase kinase-3β (GSK-3β) and PTEN (Smith et al. 2011). Tau accumulation and neuronal vulnerability are therefore caused by the loss of miR-132 expression. The lncRNA MAPT-AS1, which is transcribed antisense to the MAPT gene that encodes tau, has also been associated with epigenetic regulation of tau expression, possibly affecting tau-related diseases. Further, ncRNAs are involved in cellular processes exacerbated by Aβ and tau, including oxidative stress, neuroinflammation, mitochondrial dysfunction, and impaired autophagy. circRNAs like ciRS-7, for instance, act as sponges for miR-7, a miRNAs that targets many genes involved in inflammation and Aβ metabolism. It has been shown that circRNA–miRNA dysregulation can exacerbate neurodegenerative processes (Zhang and Bian 2021).

Moreover, these ncRNAs play a role in AD pathology by altering the expression patterns of specific ncRNAs, which further deregulate genes involved in Aβ and tau metabolism. As a result of this dynamic interaction, ncRNAs may be active players in the progression of disease, rather than passive markers. Importantly, the role of ncRNAs in AD pathogenesis is not limited to neurons. There are distinct sets of ncRNAs expressed by glial cells, such as microglia and astrocytes, that regulate inflammatory responses, contributing to the neuroinflammatory environment associated with AD. The miR-155 gene, known for its pro-inflammatory effects, is elevated in microglia in AD, which has been implicated in chronic neuroinflammation (Cardoso et al. 2021).

Functionally, housekeeping and regulatory ncRNAs are two functional subtypes of ncRNAs. Ribosomal (r) RNA, transfer (t) RNA, and small nuclear (sn) RNA are examples of housekeeping ncRNAs that are crucial for routine cellular upkeep. Conversely, certain cell types express regulatory ncRNAs, which respond to environmental stimuli, internal circumstances, and developmental signals by exhibiting regulatory functions (Fig. 1) (He et al. 2023).

Fig. 1.

Pathophysiology of Alzheimer’s disease

Understanding molecular mechanisms is essential for advancing diagnostic tools, developing targeted therapies, and improving patient outcomes in AD. Our understanding of genomics, epigenetics, and ncRNA biology continues to advance, bringing us closer to breaking the cycle of trial-and-error drug development and offering real hope for AD patients. The objective of this manuscript is to provide a review of the growing roles of ncRNAs in AD pathogenesis. This review categorizes the various types of ncRNAs that includes miRNAs (miRNAs), long lncRNAs, PIWI-interacting RNAs (piRNAs), and circRNAs, while elucidating their biogenesis, functions, and mechanisms of action in gene regulation. A primary focus will be on examining the dysregulation of ncRNAs in AD pathology, particularly their involvement in critical processes such as Aβ accumulation, tau phosphorylation, and neuroinflammation.

Search strategy

To assess the available evidence, a literature search from two primary international sources of data, PubMed and Embase, were conducted. The references for the papers that were included in the study were procured from the years 2019–2025 and the keywords like Alzheimer's disease, biomarkers, long non-coding RNAs, microRNAs, non-coding RNAs, circular RNAs and therapeutic targets were used for the effective literature search. The research and review articles that were added were also verified to prevent missing information (Fig. 2).

Fig. 2.

Selection criteria

Molecular genetic landscape of ncrnas in alzheimer's disease

Variations in the location, expression, and proportion of the isoforms of the RBPs and the sequence of the genes regulated by them are the main causes of RNA processing abnormalities in AD. Proteomic techniques and high-throughput transcriptomic techniques are employed to evaluate these alterations (Rybak-Wolf and Plass 2021). Once thought to be transcriptional"noise,"ncRNAs are now shown to be important transcriptional, post-transcriptional, and epigenetic regulators of gene expression. Among the most researched groups of ncRNAs linked to brain disorders are circRNAs, lncRNAs, and miRNAs. Numerous facets of CNS development, function, and pathology have been linked to the dysregulation of these ncRNAs (Ilieva 2024). By influencing the expression of transcripts that code for proteins, ncRNAs help to produce functional proteins. After RNA polymerases II (Pol II) and III transcribes for miRNA precursors, a sequence of cleavage actions results in mature miRNAs. Pol II transcribes lncRNAs that have a poly (A) terminus at 3′ and a 5′ methyl-cytosine cap. With a few exceptions, the biogenesis of lncRNAs is comparable with mRNA. The back-splicing process produces endogenous ncRNAs known as circRNAs. While some circRNAs include one or more exons with significant positions in the cytoplasm, others are composed of introns that start in the nucleus. A circRNA lacks a 5–3′ direction and a polyadenylated tail. As ncRNAs have a persistent loop of covalent connections, these properties make them more stable in tissues and plasma (Talebi Taheri et al. 2024). The impact of genetic variants on ncRNA function is described in Table 1.

Table 1.

Impact of genetic variants on ncRNA function

Type of Variant	Effect on ncRNA Function	References
Single Nucleotide Polymorphisms	Alterations in regulatory processes affecting gene expression; can disrupt secondary structures of long non-coding RNAs	Mirza et al. 2014; Aznaourova et al. 2020)
Copy Number Variants	Can lead to aberrant expression of ncRNAs, impacting transcriptional regulation and chromatin remodeling	Aznaourova et al. 2020; Tyagi et al. 2024)
Enhancer Variants	Modulate enhancer activity, influencing the expression of nearby genes through ncRNA interactions	Bhatti et al. 2021; López-Jiménez and Andrés-León 2021)
Long Non-Coding RNA Variants	Disruption of lncRNA functions can disturb key transcriptional circuits, affecting gene regulation at multiple levels	Aznaourova et al. 2020; Yang et al. 2021)
Regulatory Element Variants	Affect the site of binding for transcription factors and other regulatory proteins, leading to altered gene expression profiles	Wang et al. 2024; Degtyareva et al. 2021)

Single nucleotide polymorphisms (SNPs) in ncRNA genes

The role of single nucleotide polymorphisms (SNPs) in the genes of ncRNA have a remarkable impact due to their potential effect on the regulation of gene and disease susceptibility. SNPs are classified into functional and neutral categories, where functional SNPs are known to influence biological processes and prevent the risks for multifactorial diseases. Specifically, SNPs located in the regulatory regions of ncRNAs, such as miRNAs, can alter their expression levels and functional capabilities, thereby affecting target mRNA interactions and downstream gene expression (Ramírez-Bello and Jiménez-Morales 2017). Research indicates that SNPs in the 3'untranslated regions (UTRs) of mRNAs can disrupt miRNA binding sites, leading to altered gene expression profiles linked to various cancers (Deng et al. 2017; Gebert et al. 2020). For instance, the rs6983267 SNP has been identified as a remarkable risk agent for colorectal cancer, potentially through its effect on the lncRNA CCAT2 (Li et al. 2020). Additionally, SNPs can affect the splicing of precursor mRNAs which affects the stability and translation of mature transcripts. This interaction marks the relationship between genetic variation in ncRNA genes and their regulatory inputs in cellular processes (Robert and Pelletier 2018). Also, the presence of SNPs within ncRNA genes impacts the RNA secondary structures, which are important for their function. Changes in these structures may lead to variations in translational stability or efficiency of the associated proteins (Talaat et al. 2023). The AD-associated SNPs rs190982 and rs11771145 are located within the lncRNA genes for MEF2C (MEFC2-AS1) and EPHA1 (EPHA1-AS1). Likewise, rs3935067 has been identified at the EPHA1-AS1 locus. Several AD GWAS detected the rs2632516 variant and annotated it to both a miRNA (MIR142) and a lncRNA (TSPOAP1-AS1) (Policarpo and d'Ydewalle 2021). In another study by Chen and colleagues, a SNP (rs7990916) located at a brain-specific lncRNA showed a distinct distribution among cognitively normal elderly, people with mild cognitive impairment, and those with AD (Chen et al. 2013).Genetic regulation of AD is depicted in Fig. 3.

Fig. 3.

Genetic regulation of Alzheimer’s disease

Mechanistic roles of ncRNAs in AD pathophysiology

ncRNAs are genetic regulators that have been thoroughly studied in the brains of neurological disease patients and peripheral tissues. The functions of miRNAs among the many ncRNA types were highly valued. In light of their sequence complementarity with genes linked to AD, the target miRNAs were mostly chosen for association studies. The brain tissues of AD patients showed deregulation of miR-34, miR-107, and miR-219, three miRNAs that post-transcriptionally suppress tau production. As potential AD biomarkers, miR-146a, miR125, and miR-155 are implicated in neuroinflammation (Wang et al. 2020). Studies have shown that miR-146a levels are upregulated in the brains of AD patients and correlate with disease severity, cognitive decline, and neuroinflammation. It targets genes like IRAK1, CFH, and TLR2, which are involved in immune responses and amyloid-beta pathology (Maffioletti et al. 2019; Liang et al. 2021; Lukiw 2020). miR-125 is involved in synaptic plasticity and neuronal function, processes that are disrupted in AD. Dysregulation of miR-125 has been linked to tau hyperphosphorylation and neurodegeneration (Kumar and Reddy 2016). Chromatin is a complex multilevel packing of the DNA double-helix folded around histone proteins in conjunction with several regulatory components that make up the cellular genome. The transcriptional activity of chromatin is influenced by the extent of its condensation (Ilina et al. 2022).

The miR-106b overexpression in human hepatocyte HepG2 cells increases Aβ release and hinders its clearance by targeting the 3'UTR of the ATP-binding cassette transporter A1 (ABCA1). This process inhibits the production of Aβ release. Dysregulation of ABCA1, which is necessary to maintain lipidation and APOE levels, has been linked to AD and other inflammatory illnesses. BACE1 mRNA levels are upregulated in AD, potentially due to the downregulation of miR-124 and miR-107, which are miRNAs known to negatively regulate BACE1 expression is a transmembrane aspartyl protease that plays a critical role in the pathogenesis of AD. Similarly, the miR-29 family, particularly miR-29a/b-1 and miR-29c, is decreased in AD brains, resulting in higher BACE1 protein levels. Other miRNAs such as miR-188-3p, miR-339-5p, miR-195, and miR-186 also negatively regulate BACE1, and their downregulation in AD contributes to amyloid pathology. miRNAs like miR-27a-3p and miR-34a target components of the γ-secretase complex, influencing Aβ production, while miR-144, elevated in AD patients, suppresses ADAM10 (α-secretase), favoring amyloidogenic APP processing (Idda et al. 2018).

Other miRNAs, including miR-222, are reduced early in AD and may serve as potential biomarkers due to their involvement in neuronal proliferation and cell cycle regulation (Olufunmilayo and Holsinger 2023). Tight junction-related proteins were induced by miR-107 overexpression in human brain microvascular endothelial cell co-cultures that mimicked the BBB in order to restore BBB permeability. The most typical role of circRNAs is that of miRNA sponges, in which they attach to a miRNA in a sequence-specific way to stop it from binding to the downstream target proteins and genes. It was hypothesized that mmu_circRNA_017963, a highly dysregulated circRNA, would sponge mmu_miR_7033-3p and impact downstream AD signalling pathways such as RNA splicing, vesicular transport, and autophagy (Martinez-Feduchi et al. 2024). Dysregulated RNA splicing contributes to aberrant tau isoforms and amyloid precursor protein (APP) processing, both of which are critical in AD pathology. Upregulation of circHDAC9 reduces Aβ-induced neuroinflammation by sequestering miR-142-5p, leading to decreased pro-inflammatory cytokines and apoptosis markers (Olufunmilayo and Holsinger 2023). Circulating ncRNAs (e.g., miR-132, miR-206) may serve as biomarkers for monitoring AD progression or cholinesterase inhibitor responses (Kovarik et al. 2024). ncRNAs, including miRNAs, lncRNAs, and tRFs, play a crucial role in modulating cholinergic signaling in AD (Chen et al. 2022). Many human diseases, including AD, have been linked to epigenetic changes in their development. Histone posttranslational modifications, ncRNA regulation, DNA methylation, and hydroxymethylation are also influenced by epigenetic changes implicated in AD aetiology. Although ncRNAs do not translate into proteins, they play a critical role in controlling many physiological processes by binding proteins, RNA, and DNA. This affects gene expression, translation of mRNA, and the formation of protein complexes. Translational suppression and degradation of the targeted mRNA are the ultimate outcomes of miRNA action. More than 2000 distinct miRNAs are currently known to control human gene expression; each miRNA may control the expression of distinct genes and interact with diverse histone modifications and DNA methylation (Nikolac Perkovic et al. 2021). Certain lncRNAs also modulate neuroinflammation and oxidative stress, with studies showing that knockdown of lncRNA ANRIL decreases apoptosis and inflammatory cytokines. These ncRNAs are emerging as promising biomarkers and therapeutic targets for AD, offering insights into disease mechanisms and avenues for personalized treatment approaches (Fig. 4).

Fig. 4.

Molecular Mechanism ncRNA in AD

Categories of Non-coding RNAs in gene Regulation

miRNAs, lncRNAs, circRNAs, short interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), vault RNA (vtRNA) and a small nucleolar RNA (snoRNA) are regulatory ncRNAs implicated in AD pathogenesis.

MicroRNAs (miRNAs)

Longer primary miRNA transcripts with one or more hairpins are the source of miRNAs, which are ~ 22 nucleotide (nt) RNAs (Shang et al. 2023). Effective post-transcriptional controllers of gene expression are miRNAs (Komatsu et al. 2023). The regulation of let-7 family development by Lin-28 RBPs is one of the earliest examples of controlled miRNA biogenesis. A protected loop motif in pre-let-7 is recognized by these, and terminal uridyltransferase (TUTase, TUT4/7) is recruited to oligouridylate pre-let-7118,119, causing its breakdown through Dis3L2. Group I members of the vast mammal family let-7 miRNA loci are the one that are blocked by Lin-28/TUTase/Dis3L2. Other let-7 members are poor Dicer substrates (Group II) due to their substandard 1-nt 3'pre-miRNA overhang after the cleavage of microprocessor. However, TUT4/7 can monouridylate such pre-let-7 hairpins in the absence of Lin-28, restoring a 2-nt overhang that improves Dicer processing. Pre-miRNA 3'-tailing also modifies the location of Dicer cleavage, altering the sequence of miRNA seed or potentially switches the dominant functional product of the miRNA duplex arm (Shang et al. 2023). The role of miRNA in post-transcriptional regulation is detailed in Table 2.

Table 2.

Role of miRNA in post-transcriptional regulation

Mechanism	Description	Implications	References
Target mRNA Binding	miRNAs primarily bind to the 3'UTR of target mRNAs, which leads to the translational repression and mRNA degradation	Essential for regulating the expression of gene in various biological processes	Michlewski and Cáceres 2019; O'Brien et al. 2018)
Nuclear Functions	miRISC (miRNA-induced silencing complex) can localize in the nucleus and regulate transcription and mRNA splicing	Suggests a dual role of miRNAs in both transcriptional and post-transcriptional regulation	O'Brien et al. 2018; Shalgi et al. 2009)
Subcellular Localization	miRNAs and their target mRNAs are found in P-bodies and stress granules, influencing their stability and translation	Localization affects the efficiency of miRNA-mediated regulation	O'Brien et al. 2018; Panni and Pizzolotto 2025)
Regulation by RNA-Binding Proteins (RBPs)	RBPs can enhance or inhibit miRNA processing and function by interacting with precursor or mature miRNAs	Highlights a complex regulatory network involving RBPs in miRNA biogenesis and action	Michlewski and Cáceres 2019; Mello et al. 2024)
Feedback Mechanisms	Some miRNAs can control the expression of their own biogenesis factors, creating feedback loops that modulate their activity	Important for maintaining cellular homeostasis and responding to environmental changes	Michlewski and Cáceres 2019; ViLimova and Pfeffer 2023)

Numerous biological processes, including immune cell formation, distinction, activation, growth, metabolism, apoptosis, and autophagy, have been demonstrated to be critically dependent on miRNAs. Multiple research investigations have examined the dysregulation of miRNA expression in autoimmune diseases, cancer, neurological and cardiovascular disorders, and obesity (Kimura et al. 2023). miRNAs regulate the activity of the osteoblast–osteoclast axis, which is essential for maintaining bone homeostasis during skeletal development. The control of the growth, differentiation, apoptosis, and starvation of osteoblasts, osteocytes, and osteoclasts, aided miRNAs in bone metabolism (Iantomasi et al. 2023). By suppressing proteins involved in cytoskeletal reorganization, miR-7 also reduces the quantity of insulin produced by β-cells (Agbu and Carthew 2021). Specific miRNAs, known as"CholinomiRs,"such as miR-132, miR-124, and miR-608, regulate key components of the cholinergic pathway. miR-132 targets the synaptic variant of acetylcholinesterase (AChE-S), increasing synaptic ACh and reducing inflammation, while miR-124, induced by α7 nicotinic ACh receptor activation, downregulates inflammatory mediators like STAT3 and TACE. miR-608 targets both AChE and inflammatory genes, with certain genetic variants affecting its regulatory potential. Additionally, lncRNAs like Gm21284 influence cholinergic neuron differentiation by sponging miRNAs, and transfer RNA fragments (tRFs), which can function similarly to miRNAs, have been shown to shift dynamically in aging and disease, targeting cholinergic transcripts particularly after brain injury (Winek et al. 2021). Specific tRFs bind to cholinergic transcripts like CHRNA7 (encoding α7 nicotinic receptors), altering receptor availability. Reduced α7 nAChR activity in AD impairs anti-inflammatory responses and amyloid-β (Aβ) clearance.

LncRNAs

LncRNAs are longer than 200 nucleotides, avoid the overlapping of any coding RNAs, and have a variety of functions in the regulation of genes at different levels, making a significant fraction of transcriptomes (Anver et al. 2024). Enhancer lncRNAs, antisense lncRNAs, promoter lncRNAs, intergenic lncRNAs, and circRNAs originating from excised and religated introns and/or exons are among the various types of lncRNAs that are frequently categorized according to their transcription site in relation to protein-coding genes (Herman et al. 2022). lncRNAs have been found to regulate transcription by the interaction with transcriptional machinery, either activating or repressing it. Examples include Airn, which pauses transcription at the Igf2r promoter, and GNG12-AS1, which represses DIRAS3 transcription. DIRAS3 is a tumor suppressor gene inducing autophagy that is a critical cellular process for clearing damaged proteins and organelles, and its dysfunction is implicated in AD, where accumulation of misfolded proteins like amyloid-beta and tau occurs (Uddin et al. 2018). Additionally, lncRNAs such as PANDA, PVT1, and LincRNAp21 modulate transcription by binding transcription factors or related proteins (Herman et al. 2022). LncRNA act as molecular sponges by binding miRNAs through miRNA response elements (MREs), preventing them from interacting with their target mRNAs. It can stabilize or destabilize miRNAs by forming RNA duplexes or altering their degradation pathways (López-Urrutia et al. 2019).

Epigenetic changes to the chromatin supervise complex organisms'differentiation and development. In fungi and animals, the RNAi pathway is crucial for the establishment of silencing of epigenetic gene and heterochromatin. LncRNAs recruit chromatin-modifying enzymes to miRNA loci, influencing their transcription. Dysregulated lncRNA-miRNA interactions contribute to processes like neuroinflammation and synaptic dysfunction (Gareev, et al. 2023; Mattick et al. 2023). Cholinesterase inhibitors are the current standard of care for AD, which prevents acetylcholine breakdown. While donepezil, rivastigmine, and galantamine drugs improve symptoms, they do not address the underlying pathology. There is also emerging evidence that lncRNAs are involved in cholinergic signaling pathways, suggesting potential new therapeutic avenues (Kurt et al. 2020).

Circular RNAs

CircRNAs are a unique class of ncRNAs identified by their covalent structure that is closed, which makes them resistant to exonuclease degradation. This stability allows circRNAs to function effectively as molecular sponges for miRNAs and thus regulates the availability of these miRNAs to their target mRNAs. CircRNA CDR1 as serves as a key sponge for miR-7 that leads to the miR-7 targets dysregulation and implicating circRNAs in varied biological processes that includes neurodegeneration. Also, circRNAs it is identified as scaffolds for RNA-binding proteins (RBPs) that facilitates the assembly of protein complexes regulating gene expression and cellular signaling pathways. In the AD, circRNAs such as circTRPC6 has showed to interact with APP, influencing Aβ production and synaptic function. CircRNAs are dynamically expressed in neurons and play remarkable roles in synaptic plasticity, making them key biomarkers and therapeutic aim for the neurodegenerative disorders. Their tendency to modulate the expression of genes by miRNA sponging and RBP scaffolding underscores their significance in both normal brain function and disease pathology. A prominent circRNA in the human and mouse brain, located on chromosome Xq27.1. It is about 1500 nucleotides long and contains over 70 highly conserved microRNA binding sites. circRNAs can bind and sequester miRNAs, affecting miRNA activity and stability. For example, ciRS-7 can bind up to 20,000 miR-7 miRNAs per cell, leading to their degradation, and influencing the regulation of gene expression (Olufunmilayo and Holsinger 2023). Figure 5 illustrates the involvement of ncRNAs in cholinergic dysfunction and the progression of AD.

Fig. 5.

Role of ncRNAs in cholinergic dysfunction and AD

Small Interfering RNAs (siRNAs)

Small interfering RNAs (siRNAs) and piRNAs are two classes of small ncRNAs that have garnered focus for their emerging roles in the brain. siRNAs are involved in the pathway of RNA interference that guides the degradation of complementary mRNA sequences and regulates the expression of genes at the post-transcriptional level. High-affinity siRNA binding is exhibited by the de novo DNA (cytosine 5) methyltransferase 3 A (DNMT3A) and DNMT3B of mammalian, but not by the maintenance DNA methylase DNMT1. The growing study have demonstrated that siRNAs can modulate synaptic plasticity along with neuronal survival and suggest their involvement in cognitive functions and neuroprotection (Ilieva 2024).

Piwi-interacting RNAs

piRNAs are primarily known for their role in transposon silencing in germ cells; however, recent evidence indicates that they may also have functions in somatic tissues, including the brain. In particular, piRNAs have functioned in gene expression regulation during neuronal development and differentiation. Emerging research suggests that both siRNAs and piRNAs contribute to the pathophysiology of neurodegenerative ailments by influencing processes such as apoptosis and neuroinflammation. The precise mechanisms through which these small RNAs operate in the brain help in finding new therapeutic domains for the treatment of neurological disorders (Chavda et al. 2022).

Vault RNAs (vtRNAs)

The pathology of AD may be influenced by vtRNAs. Vault RNAs are ncRNAs with well-preserved sequence patterns that interact with RNA-ligands, RNA-RNAs, or RNA-proteins to function as vault particles. The vault RNAs function as miRNA precursors and signaling pathways and are thought to play a variety of roles such as cell proliferation, nucleocytoplasmic transport, intracellular detoxification processes, drug resistance, apoptosis, and autophagy (Aghajani 2024).

small nucleolar RNAs (snoRNAs)

The small nucleolar RNAs (snoRNAs) are ncRNAs that are involved in the posttranscriptional modification of ubiquitously expressed ribosomal and small nuclear RNAs (Bratkovič and Rogelj 2011). There is also evidence that SnoRNAs play a role in AD pathology. Alzheimer's brains have altered levels of snoRNA, according to a study (Fitz et al. 2021). By affecting the expression or function of proteins involved in AD pathology, such as those involved in amyloid processing or neurodegeneration, SnoRNAs may contribute to AD pathology (Lauretti et al. 2021).

Recent innovations in ncRNA in AD

scRNA sequencing (scRNA-seq) has emerged as a pivotal process for revealing the roles of ncRNAs in various biological contexts. This technology helps the researchers analyze the genes at the individual cell level and reveals heterogeneity in ncRNA expression across different cell types and states. Recent studies have demonstrated that scRNA-seq can effectively identify distinct subpopulations of cells in complex tissues, facilitating the discovery of novel ncRNAs associated with specific cellular functions and disease states, including neurodegenerative disorders like AD. scRNA-seq enables the identification of distinct subpopulations of cells in complex tissues by profiling gene expression at the single-cell level (Huang et al. 2024; Satam et al. 2023).

Spatial transcriptomics provides a powerful approach to visualize and quantify ncRNA expression within the spatial context of tissues, particularly in the brains affected by AD. A recent study mapped the expression of over 7,600 lncRNAs across various brain regions, identifying spatially differentially expressed lncRNAs that correlate with AD pathology. This technique has revealed that certain lncRNAs are enriched in specific cortical subregions, implicating them in key processes such as synaptic signaling and neuroinflammation, which are critical in AD pathogenesis (Piwecka et al. 2023).

Advancements in bioinformatics have significantly enhanced the ability to predict targets of ncRNAs and analyze gene regulatory networks (GRNs). Recent computational tools leverage high-throughput sequencing data to identify potential interactions between ncRNAs and their target genes, providing insights into their regulatory mechanisms. By integrating various omics data, researchers can construct comprehensive GRNs that elucidate ncRNAs role in cellular processes and disease mechanisms, thereby facilitating the identification of novel therapeutic targets (Jorge et al. 2012; Bang et al. 2022). The integration of ncRNA data with other omics platforms, such as proteomics, genomics, and metabolomics, has become crucial for understanding complex biological systems. This approach leads to the detailed knowledge of cellular functions and disease states. Recent studies have shown that combining transcriptomic data with epigenomic and proteomic profiles can uncover intricate regulatory networks involving ncRNAs, enhancing understanding of their roles in diseases like cancer and neurodegeneration (Satam et al. 2023; Jorge et al. 2012).

RNAi and antisense oligonucleotides (ASOs) are prominent strategies for therapeutically targeting ncRNAs. ASOs can be designed to specifically bind to complementary RNA sequences that lead to the degradation or modulation of target ncRNAs. Similarly, RNAi utilizes siRNAs to silence specific genes at the post-transcriptional level. These approaches have shown promise in preclinical models for treating various conditions, including neurodegenerative diseases where dysregulated ncRNA expression plays a crucial role (Olufunmilayo and Holsinger 2023; Lan et al. 2021).

CRISPR/Cas technology has revolutionized gene editing and is now being adapted for targeting ncRNAs. The use of CRISPR/Cas systems, can help in achieving precise modulation of ncRNA expression levels for functional studies that depicits their roles in health and disease (Fig. 6).

Fig. 6.

Role of non-coding RNAs in Alzheimer’s disease

This innovative approach holds significant potential for developing novel therapeutic strategies aimed at correcting dysregulated ncRNA pathways in diseases such as AD (Table 3) (Olufunmilayo and Holsinger 2023; Bang et al. 2022).

Table 3.

RNA-Based Clinical Trials in AD

Therapy	Target	Mechanism	Trial Phase	Outcomes	References
Mivelsiran	APP mRNA	siRNA reduces APP production	Phase 1 (NCT05231785)	50 mg/75 mg doses reduced CSF Aβ40/42 and soluble APP; well-tolerated	Sharon Cohen et al., n.d.
Tau-targeting siRNA	MAPT mRNA	siRNA silences tau protein expression	Phase 1/2	> 50% reduction in CSF tau levels; no serious side effects reported	Genomics Education Programme 2024

Natural products, rich in antioxidants, can target ncRNAs to mediate their biological effects on oxidative stress and inflammation-associated disorders. Baicalein, Tanshinone IIA, Geniposide, Carvacrol/Thymol, Triptolide, Oleacein, Curcumin, Resveratrol, Solarmargine, Allicin, aqueous extract or pulp of Açai, Quercetin, and Genistein, which have been reported to target ncRNAs as mediators of their biological effects on oxidative stress and several inflammation-associated disorders (Ngum et al. 2023). These natural compounds confer neuroprotection, at least in part, through modulation of specific miRNAs and lncRNAs, thereby regulating key pathological pathways associated with AD, including Aβ deposition, tau hyperphosphorylation, oxidative stress, and neuroinflammatory responses. For instance, curcumin has been demonstrated to upregulate miR-15b, which subsequently suppresses BACE1, a critical enzyme in Aβ generation, resulting in reduced Aβ accumulation in AD models (Liu et al. 2017). Resveratrol enhances the expression of miR-132, which targets GSK-3β, leading to diminished tau phosphorylation and improved synaptic integrity (Li et al. 2024; Xu et al. 2021).

Likewise, baicalein downregulates miR-155, thereby attenuating microglial activation and decreasing the production of pro-inflammatory cytokines (Li et al. 2022). Tanshinone IIA, a bioactive diterpene from Salvia miltiorrhiza, has been shown to suppress lncRNA MALAT1 expression, resulting in decreased oxidative stress and neuronal apoptosis (Yang et al. 2024). Collectively, these mechanistic findings highlight the potential of phytochemicals to modulate non-coding RNAs as a strategic approach to ameliorate AD pathology and advance therapeutic development.

Translational applications of ncRNA in AD

Recent studies have focused on the potential of circulating ncRNAs as biomarkers for early diagnosis and prognosis of AD. Specific miRNAs such as miR-181c and miR-146a have been identified in cerebrospinal fluid (CSF) and blood, showing differential expression patterns between AD patients and healthy controls. RN7SK LncRNA expression may function as a biomarker with 50% sensitivity and specificity of 80% for distinguishing AD patients from controls, suggests that circRNAs expression in body fluids of patients with various progression of disease to determine their diagnostic and prognostic value as noninvasive biomarkers (Kazemi et al. 2024; Canoy et al. 2024). It indicates that while ncRNAs may not be definitive biomarkers, they can remarkably contribute to diagnostic panels when combined with other clinical assessments. The recent development of omics technologies is expected to improve the identification of novel ncRNA biomarkers, refining their diagnostic utility in clinical research (Kazemi et al. 2024; Garofalo et al. 2021).

Targeting ncRNAs presents a promising therapeutic approach for mitigating the pathology of AD. Recent research focused on modulating specific ncRNAs that are involved in crucial pathological processes such as Aβ aggregation and tau phosphorylation. The interventions targeted at downregulating pro-inflammatory lncRNAs have shown potential in reducing neuroinflammation associated with AD. This approach addresses the symptoms and targets the underlying mechanisms that contributes to disease progression, indicating a shift towards more personalized therapeutic treatement (Liu et al. 2022; Pierouli et al. 2022).

Challenges such as delivery methods, off-target effects, and RNA molecules stability in vivo, pose significant hurdles. Advancements in the system of delivery, such as lipid nanoparticles and conjugated oligonucleotides, are explored to improve the efficacy of these therapies. The increasing understanding of ncRNA functions in AD opens up new opportunities for developing targeted interventions that could complement existing treatment modalities, potentially leading to more effective management of the disease (Canoy et al. 2024; Black et al. 2024).

Challenges and future perspectives

There are several challenges facing ncRNA-based therapies for AD, including delivery, stability, specificity, and regulatory hurdles. However, advances in nanotechnology, chemical modifications, and personalized medicine are making breakthroughs possible. One of the significant challenges in ncRNA study is the variability and reproducibility of findings across studies. This issue arises from differences in sample preparation, sequencing technologies, and bioinformatics analyses, which can lead to inconsistent results. A review highlighted that while high-throughput sequencing has generated vast amounts of data, the lack of standardized protocols often hampers the ability to replicate findings, limiting the reliability of ncRNAs as biomarkers for AD (Pleić et al. 2022). Addressing these inconsistencies through standardized methodologies and rigorous validation processes is essential for advancing ncRNA research.

Despite considerable progress in understanding the roles of ncRNAs in AD, many mechanistic questions remain unresolved. Recent studies indicate that while specific ncRNAs are associated with key pathological markers of AD-like Aβ accumulation and tau phosphorylation, their precise mechanisms of action are still poorly understood (Canoy et al. 2024). For instance, the upstream regulatory networks governing ncRNA expression and their interactions with target mRNAs need further elucidation. This gap in knowledge hinders the development of targeted treatment aimed at modulating ncRNA functions to combat AD pathology effectively.

The integration of multi-omics data with artificial intelligence (AI) presents exciting opportunities for advancing ncRNA research in AD. Using multiomics approaches involves the recognition and the study of genes, genomic, transcriptomic, proteomic, epigenomic, metabolomic and lipidomic profiles to identify disease subtypes and progression (Pierouli et al. 2022). This approach can enhance our understanding of how ncRNAs interact within broader biological networks and contribute to disease mechanisms. Additionally, AI-driven models can facilitate the identification of new biomarkers and treatment agents by integrating genomic, transcriptomic, and clinical data, paving the way for precision medicine approaches in AD management.

Conclusion

ncRNAs have emerged as pivotal players in the pathogenesis of AD, affecting various biological cycles such as apoptosis and neuroinflammation. Recent studies have demonstrated that different classes of ncRNAs, including miRNAs, circRNAs, lncRNAs, and piRNAs are involved in the molecular mechanisms underlying AD. ncRNAs regulate key signaling pathways that are associated with Aβ aggregation and tau phosphorylation, contributing to neuronal loss and cognitive depreciation. As such, they represent critical components in understanding the complex etiology of AD and highlight the need for further exploration of their functions in disease progression. The translational potential of ncRNA research in AD is significant, as these molecules serve as biomarkers for early diagnosis and also represent novel therapeutic targets. The ability to modulate ncRNA expression could lead to innovative treatment strategies aimed at altering disease pathways and mitigating neurodegeneration. Furthermore, the identification of ncRNA profiles in patient samples could facilitate personalized medicine approaches, allowing for tailored therapies based on individual molecular signatures. This potential underscore the importance of advancing ncRNA research into clinical applications. Given the complexities surrounding ncRNA functions and their roles in AD, there is a pressing need for further studies to elucidate their mechanisms of action. Collaborative efforts among researchers across various disciplines—such as molecular biology, bioinformatics, and clinical neuroscience—are essential to advance our understanding of ncRNAs in AD. Multi-omics approaches integrating genomic, transcriptomic, and proteomic data will be crucial for uncovering the intricate networks involving ncRNAs. Such collaborations can accelerate the translation of findings from bench to bedside, ultimately improving diagnostic tools and therapeutic options for individuals affected by AD.

Author contribution

Sami I. Alzarea: Conceptualization, Methodology, Funding Acquisition, writing—original draft preparation —review and editing.

Funding

This work was funded by the Deanship of Graduate Studies and Scientific Research at Jouf University under grant No. (DGSSR-2024–01-01074).

Data availability

All data available to this manuscript presented in manuscript.

Declarations

Competing interests

None.

Ethics declaration

This article does not contain any studies with human participants or animals performed by the author.