IGF2R circular RNA hsa_circ_0131235 expression in the middle temporal cortex is associated with AD pathology

Exploring the complex dimensions of Alzheimer's disease: The promising role of circular RNAs and their potential contributions

Circular RNAs (circRNAs) are multifunctional molecules that regulate gene expression at transcriptional and post-transcriptional levels. They are generated through the back-splicing of mRNA precursors and exhibit tissue-specific expression patterns. CircRNAs highly conserved among various species, exhibit significant abundance and dynamic expression within the nervous system, especially at synaptic sites. Research has shown varied distributions of circRNAs across different organs, including the brain, heart, liver, and lungs, with pronounced enrichment in the nervous system. Neurological disorders lead to alterations in gene expression, transcript profiles, and modifications of non-coding RNAs, including circRNAs. Alzheimer's disease is marked by the accumulation of amyloid-beta (Aβ) plaques and the presence of phosphorylated tau (P-tau) neurofibrillary tangles, both of which are key histological features that contribute to the pathophysiology of the disease. Notably, circRNAs cross the blood-brain barrier (BBB), presenting promising avenues for therapeutic interventions in neurological conditions like Alzheimer's disease (AD) due to their stability and the specificity of their expression in various tissues, circular RNAs are increasingly recognized as promising candidates for therapeutic intervention.

Circular RNA and Neuropsychiatric Practice: A Scoping Review of the Literature and Discussion of Unmet Clinical Needs

Circular RNA (circRNA) is a recently characterized species of RNA that is highly enriched in the human brain, differentially expressed in neuropsychiatric disorders, and readily detectable in the peripheral circulation. These characteristics make circRNA an attractive candidate biomarker for neuropsychiatric illness and suggest it as a potential missing link in the understanding of the specific biological underpinnings of neuropsychiatric illness. In this scoping review, the authors summarize the literature on circRNA in neuropsychiatric disorders and add clinical context. The authors searched PubMed, PsycInfo, Embase, the Cochrane Database of Systematic Reviews, and the Cochrane Central Register of Controlled Trials for articles describing research on circRNA and mental disorders published in or after 2012. The authors included peer-reviewed studies with substantive discussions of circRNA and mental disorders that included human participants or cell lines. Only studies written in English or with English translations were considered. Seventy-eight studies met the authors' inclusion criteria. Common and serious neuropsychiatric illnesses were well represented among these studies, including schizophrenia, major depressive disorder, and major neurocognitive disorder. Many studies identified altered circRNA levels in peripheral blood and specific brain regions that were both sensitive to and specific for neuropsychiatric disorders. Few studies discussed the role that circRNA-based diagnostic tests might play in clinical practice, and research on prognostic, therapeutic, or monitoring biomarkers was limited. Although circRNAs have the potential to change the understanding and treatment of neuropsychiatric disorders, the research field would benefit from more clinician involvement in this area to identify and address urgent clinical needs.

Distinct roles of the circMKNK2/miR-15a Axis in regulating chicken skeletal muscle development and glucose metabolism

Circular RNAs (circRNAs) have emerged as critical regulators of biological processes, but their roles in avian muscle development remain less explored. Here we characterize circMKNK2, a novel circRNA derived from the MKNK2 gene, which is highly expressed in slow-growing Silky chickens compared to fast-growing broilers. Functional studies demonstrate that circMKNK2 acts as a sponge for miR-15a, with overexpression inhibiting myoblast proliferation, differentiation, apoptosis, and glucose metabolism, while miR-15a knockdown produces similar effects except for enhanced glucose uptake. RNA-seq analysis identified 2189 differentially expressed genes regulated by circMKNK2 in chicken primary myoblasts, including key targets of the circMKNK2/miR-15a axis such as PIK3R1 (a core node regulating PI3K-Akt signaling), BHLHE41, KANK1, and ARHGAP20. Pathway analysis revealed modulation of myogenesis through Calcium signaling pathway, ECM-receptor interaction, Neuroactive ligand-receptor interaction and immune-related pathways (Toll-like receptor, cytokine-cytokine receptor interactions). Further analysis highlighted the circMKNK2/miR-15a axis's role in suppressing myogenesis through transcriptional regulation of key factors (e.g., SOX7, MAF) and metabolic reprogramming. Unlike pro-myogenic circRNAs, circMKNK2 uniquely inhibited muscle development and glucose metabolism, suggesting its involvement in breed-specific phenotypic differences. This study provides insights into circRNA-mediated regulation of muscle biology and offers potential targets for improving poultry production through genetic and metabolic modulation.

Insulin-Like Growth Factor Signaling in Alzheimer's Disease: Pathophysiology and Therapeutic Strategies

Alzheimer's disease (AD) is the leading cause of dementia among the elderly population, posing a significant public health challenge due to limited therapeutic options that merely delay cognitive decline. AD is associated with impaired energy metabolism and reduced neurotrophic signaling. The insulin-like growth factor (IGF) signaling pathway, crucial for central nervous system (CNS) development, metabolism, repair, cognition, and emotion regulation, includes IGF-1, IGF-2, IGF-1R, IGF-2R, insulin receptor (IR), and six insulin-like growth factor binding proteins (IGFBPs). Research has identified abnormalities in IGF signaling in individuals with AD and AD models. Dysregulated expression of IGFs, receptors, IGFBPs, and disruptions in downstream phosphoinositide 3-kinase-protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) pathways collectively increase AD susceptibility. Studies suggest modulating the IGF pathway may ameliorate AD pathology and cognitive decline. This review explores the CNS pathophysiology of IGF signaling in AD progression and assesses the potential of targeting the IGF system as a novel therapeutic strategy. Further research is essential to elucidate how aberrant IGF signaling contributes to AD development, understand underlying molecular mechanisms, and evaluate the safety and efficacy of IGF-based treatments.

Potential mechanisms of non-coding RNA regulation in Alzheimer's disease

Alzheimer's disease, a progressively degenerative neurological disorder, is the most common cause of dementia in the elderly. While its precise etiology remains unclear, researchers have identified diverse pathological characteristics and molecular pathways associated with its progression. Advances in scientific research have increasingly highlighted the crucial role of non-coding RNAs in the progression of Alzheimer's disease. These non-coding RNAs regulate several biological processes critical to the advancement of the disease, offering promising potential as therapeutic targets and diagnostic biomarkers. Therefore, this review aims to investigate the underlying mechanisms of Alzheimer's disease onset, with a particular focus on microRNAs, long non-coding RNAs, and circular RNAs associated with the disease. The review elucidates the potential pathogenic processes of Alzheimer's disease and provides a detailed description of the synthesis mechanisms of the three aforementioned non-coding RNAs. It comprehensively summarizes the various non-coding RNAs that have been identified to play key regulatory roles in Alzheimer's disease, as well as how these non-coding RNAs influence the disease's progression by regulating gene expression and protein functions. For example, miR-9 targets the UBE4B gene, promoting autophagy-mediated degradation of Tau protein, thereby reducing Tau accumulation and delaying Alzheimer's disease progression. Conversely, the long non-coding RNA BACE1-AS stabilizes BACE1 mRNA, promoting the generation of amyloid-² and accelerating Alzheimer's disease development. Additionally, circular RNAs play significant roles in regulating neuroinflammatory responses. By integrating insights from these regulatory mechanisms, there is potential to discover new therapeutic targets and potential biomarkers for early detection and management of Alzheimer's disease. This review aims to enhance the understanding of the relationship between Alzheimer's disease and non-coding RNAs, potentially paving the way for early detection and novel treatment strategies.

Noncoding RNAs in Alzheimer's Disease: Overview of Functional and Therapeutic Significance

Alzheimer's disease (AD) is a multifactorial disorder resulting from the complex interaction between genetic, epigenetic, and environmental factors. It represents an impending epidemic and lacks effective pharmacological interventions. The emergence of high throughput sequencing techniques and comprehensive genome evaluation has uncovered a diverse spectrum of noncoding RNA (ncRNA) families. ncRNAs are the critical modulators of an eclectic array of biological processes and are now transpiring as imperative players in diagnosing and treating various diseases, including neurodegenerative disorders. Several ncRNAs are explicitly augmented in the brain, wherein they potentially regulate cognitive abilities and other functions of the central nervous system. Growing evidence suggests the substantial role of ncRNAs as modulators of tau phosphorylation, Aβ production, neuroinflammation, and neuronal survival. It indicates their therapeutic relevance as a biomarker and druggable targets against AD. The current review summarizes the existing literature on the functional significance of ncRNAs in AD pathogenesis and its imminent implications in clinics.

Circular RNA ciRS-7 signature as a potential biomarker for the early detection of diabetes with Alzheimer's disease: a hypothesis

In the 1970s, Circular RNAs (CircRNAs) were first discovered in RNA viruses as viroids and were initially assumed to be RNA splicing defects. The roles and topologies of these circular RNA loops were later revealed using computer analysis and RNA-sequencing. They were found to demonstrate various functions, including protein scaffolding, parental gene regulation, microRNA sponges, and RNA-protein interactions. CircRNAs play a crucial role in controlling gene expression and are essential for biological development and illness detection, as demonstrated by their roles as miRNA sponges, endogenous RNAs, and potential biomarkers. Insulin resistance is caused by damage to β-cells in the pancreatic islets, which reduces the body's response to the hormone insulin. This reduction in insulin response hinders glucose from entering cells and providing energy for critical processes. As a result, insulin-resistant cells elevate blood sugar levels, leading to diabetes. Diabetes, in turn, increases the risk of heart disease and stroke, which can damage the heart and arteries. Additionally, an excess of insulin can impact the brain's chemical balance, contributing to the development of Alzheimer's disease. Furthermore, oxidative stress created by damaged pancreatic cells during high blood sugar conditions may lead to the destruction of brain cells and the onset of Alzheimer's disease. The hypothesis of this review is to provide an overview of the most dominant ciRS-7 circRNA identified in pancreatic islet cell dysfunction and neurologic disorders, such as Alzheimer's disease. By considering ciRS-7 circRNA as a potential biomarker for diabetes, early detection and treatment of diabetes may be facilitated, potentially reducing the risk of Alzheimer's disease onset in the future.

Alzheimer's disease pathogenetic progression is associated with changes in regulated retained introns and editing of circular RNAs

Introduction

The molecular changes leading to Alzheimer's disease (AD) progression are poorly understood. A decisive factor in the disease occurs when neurofibrillary tangles (NFT) composed of microtubule associated protein tau (MAPT) form in the entorhinal cortex and then spread throughout the brain.

Methods

We therefore determined mRNA and circular RNA changes during AD progression, comparing Braak NFT stages I-VI. Total RNA was isolated from human brain (entorhinal and frontotemporal cortex). Poly(A)+ RNA was subjected to Nanopore sequencing, and total RNA was analyzed by standard Illumina sequencing. Circular RNAs were sequenced from RNase R treated and rRNA depleted total RNA. The sequences were analyzed using different bioinformatic tools, and expression constructs for circRNAs were analyzed in transfection experiments.

Results

We detected 11,873 circRNAs of which 276 correlated with Braak NFT stages. Adenosine to inosine RNA editing increased about threefold in circRNAs during AD progression. Importantly, this correlation cannot be detected with mRNAs. CircMAN2A1 expression correlated with AD progression and transfection experiments indicated that RNA editing promoted its translation using start codons out of frame with linear mRNAs, which generates novel proteins.

Discussion

Thus, we identified novel regulated retained introns that correlate with NFT Braak stages and provide evidence for a role of translated circRNAs in AD development.

Brain-protective mechanisms of autophagy associated circRNAs: Kick starting self-cleaning mode in brain cells via circRNAs as a potential therapeutic approach for neurodegenerative diseases

Altered autophagy is a hallmark of neurodegeneration but how autophagy is regulated in the brain and dysfunctional autophagy leads to neuronal death has remained cryptic. Being a key cellular waste-recycling and housekeeping system, autophagy is implicated in a range of brain disorders and altering autophagy flux could be an effective therapeutic strategy and has the potential for clinical applications down the road. Tight regulation of proteins and organelles in order to meet the needs of complex neuronal physiology suggests that there is distinct regulatory pattern of neuronal autophagy as compared to non-neuronal cells and nervous system might have its own separate regulator of autophagy. Evidence has shown that circRNAs participates in the biological processes of autophagosome assembly. The regulatory networks between circRNAs, autophagy, and neurodegeneration remains unknown and warrants further investigation. Understanding the interplay between autophagy, circRNAs and neurodegeneration requires a knowledge of the multiple steps and regulatory interactions involved in the autophagy pathway which might provide a valuable resource for the diagnosis and therapy of neurodegenerative diseases. In this review, we aimed to summarize the latest studies on the role of brain-protective mechanisms of autophagy associated circRNAs in neurodegenerative diseases (including Alzheimer's disease, Parkinson's disease, Huntington's disease, Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, and Friedreich's ataxia) and how this knowledge can be leveraged for the development of novel therapeutics against them. Autophagy stimulation might be potential one-size-fits-all therapy for neurodegenerative disease as per considerable body of evidence, therefore future research on brain-protective mechanisms of autophagy associated circRNAs will illuminate an important feature of nervous system biology and will open the door to new approaches for treating neurodegenerative diseases.

Circular RNAs: emerging players in brain aging and neurodegenerative diseases

Brain aging is closely related to neurodegenerative diseases. Circular RNAs (circRNAs) are a type of conserved RNAs with covalently closed continuous loops. Emerging evidence has shown that circRNAs are implicated in the biology of brain aging and the pathology of age-related neurodegenerative diseases. Here, we summarize current studies on circRNAs associated with brain aging and neurodegenerative diseases by discussing their expression features, pathophysiological roles, and mechanisms of action. We also discuss the potential challenges of circRNA-based therapy against brain aging and neurodegenerative diseases, as well as their potential as diagnostic biomarkers of neurodegenerative diseases. The review provides insights into current progress in the functions of circRNAs in the process of brain aging and neurodegenerative diseases. © 2022 The Pathological Society of Great Britain and Ireland.

Circular RNAs in Alzheimer's Disease: A New Perspective of Diagnostic and Therapeutic Targets

BACKGROUND

Circular RNAs (circRNAs), as covalently closed single-stranded noncoding RNA molecules, have been recently identified to involve in several biological processes, principally through targeting microRNAs. Among various neurodegenerative diseases (NDs), accumulating evidence has proposed key roles for circRNAs in the pathogenesis of Alzheimer's disease (AD); although the exact relationship between these RNA molecules and AD progression is not clear, they have been believed to mostly act as miRNA sponges or gene transcription modulators through correlating with multiple proteins, involved in the accumulation of Amyloid β (Aβ) peptides, as well as tau protein, as AD's pathological hallmark. More interestingly, circRNAs have also been reported to play diagnostic and therapeutic roles during AD progression.

OBJECTIVE

Literature review indicated that circRNAs could essentially contribute to the onset and development of AD. Thus, in the current review, the circRNAs' biogenesis and functions are addressed at first, and then the interplay between particular circRNAs and AD is comprehensively discussed. Eventually, the diagnostic and therapeutic significance of these noncoding RNAs is highlighted in brief.

RESULTS

A large number of circRNAs are expressed in the brain. Thereby, these RNA molecules are noticed as potential regulators of neural functions in healthy circumstances, as well as neurological disorders. Moreover, circRNAs have also been reported to have potential diagnostic and therapeutic capacities in relation to AD, the most prevalent ND.

CONCLUSION

CircRNAs have been shown to act as sponges for miRNAs, thereby regulating the function of related miRNAs, including oxidative stress, reduction of neuroinflammation, and the formation and metabolism of Aβ, all of which developed in AD. CircRNAs have also been proposed as biomarkers that have potential diagnostic capacities in AD. Despite these characteristics, the use of circRNAs as therapeutic targets and promising diagnostic biomarkers will require further investigation and characterization of the function of these RNA molecules in AD.

CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning

Background

Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can create a circular shape via the back splicing process and convert into a new type called circular RNA (circRNA). circRNAs are among the essential non-coding RNAs in the cell that involve multiple disorders. One of the critical functions of circRNAs is to regulate the expression of other genes through sponging micro RNAs (miRNAs) in diseases. This mechanism, known as the competing endogenous RNA (ceRNA) hypothesis, and additional information obtained from biological datasets can be used by computational approaches to predict novel associations between disease and circRNAs.

Results

We applied multiple classifiers to validate the extracted features from the heterogeneous network and selected the most appropriate one based on some evaluation criteria. Then, the XGBoost is utilized in our pipeline to generate a novel approach, called CircWalk, to predict CircRNA-Disease associations. Our results demonstrate that CircWalk has reasonable accuracy and AUC compared with other state-of-the-art algorithms. We also use CircWalk to predict novel circRNAs associated with lung, gastric, and colorectal cancers as a case study. The results show that our approach can accurately detect novel circRNAs related to these diseases.

Conclusions

Considering the ceRNA hypothesis, we integrate multiple resources to construct a heterogeneous network from circRNAs, mRNAs, miRNAs, and diseases. Next, the DeepWalk algorithm is applied to the network to extract feature vectors for circRNAs and diseases. The extracted features are used to learn a classifier and generate a model to predict novel CircRNA-Disease associations. Our approach uses the concept of the ceRNA hypothesis and the miRNA sponge effect of circRNAs to predict their associations with diseases. Our results show that this outlook could help identify CircRNA-Disease associations more accurately.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04883-9.

Circular RNAs: Emblematic Players of Neurogenesis and Neurodegeneration

In the fascinating landscape of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) are peeping out as a new promising and appreciated class of molecules with great potential as diagnostic and prognostic biomarkers. They come from circularization of single-stranded RNA molecules covalently closed and generated through alternative mRNA splicing. Dismissed for many years, similar to aberrant splicing by-products, nowadays, their role has been regained. They are able to regulate the expression of linear mRNA transcripts at different levels acting as miRNA sponges, interacting with ribonucleoproteins or exerting a control on gene expression. On the other hand, being extremely conserved across phyla and stable, cell and tissue specific, mostly abundant than the linear RNAs, it is not surprising that they should have critical biological functions. Curiously, circRNAs are particularly expressed in brain and they build up during aging and age-related diseases. These extraordinary peculiarities make circRNAs potentially suitable as promising molecular biomarkers, especially of aging and neurodegenerative diseases. This review aims to explore new evidence on circRNAs, emphasizing their role in aging and pathogenesis of major neurodegenerative disorders, Alzheimer's disease, frontotemporal dementia, and Parkinson's diseases with a look toward their potential usefulness in biomarker searching.

Emerging roles of circular RNAs in neuropathic pain

Neuropathic pain is a major type of chronic pain caused by the disease or injury of the somatosensory nervous system. It afflicts about 10% of the general population with a significant proportion of patients’ refractory to conventional medical treatment. This highlights the importance of a better understanding of the molecular pathogenesis of neuropathic pain so as to drive the development of novel mechanism‐driven therapy. Circular RNAs (circRNAs) are a type of non‐coding, regulatory RNAs that exhibit tissue‐ and disease‐specific expression. An increasing number of studies reported that circRNAs may play pivotal roles in the development of neuropathic pain. In this review, we first summarize circRNA expression profiling studies on neuropathic pain. We also highlight the molecular mechanisms of specific circRNAs (circHIPK3, circAnks1a, ciRS‐7, cZRANB1, circZNF609 and circ_0005075) that play key functional roles in the pathogenesis of neuropathic pain and discuss their potential diagnostic, prognostic, and therapeutic utilization in the clinical management of neuropathic pain.

The Emerging Role of Circular RNAs in Alzheimer's Disease and Parkinson's Disease

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are two neurodegenerative diseases (NDDs) commonly found in elderly patients that are difficult to diagnose and lack effective treatment. Currently, the available diagnostic methods for these two NDDs do not meet clinical diagnostic expectations. Circular RNAs (circRNAs) are a diverse group of endogenous non-coding RNAs (ncRNAs) found in eukaryotic cells. Emerging studies suggest that altered expression of circRNAs is involved in the pathological processes of NDDs. CircRNAs could also prove to be promising biomarkers for the early diagnosis of NDDs such as AD and PD. Growing evidence has improved our knowledge of the roles of circRNAs in NDDs, which may lead to new therapeutic approaches that target transcription for preventing neurodegeneration. In this review, we describe the formation mechanisms and functions of circRNAs as well as methods of validation. We also discuss the emerging role of circRNAs in the pathophysiology of AD and PD and their potential value as biomarkers and therapeutic targets for AD and PD in the future.

IGF2R circular RNA hsa_circ_0131235 expression in the middle temporal cortex is associated with AD pathology

OBJECTIVE

To identify circular RNAs as candidates for differential expression in the middle temporal (MT) cortex in a well-characterized cohort with contrasting Alzheimer disease (AD) pathology and cognition. Top screen candidates were assessed for proof of circularity and then quantified by qPCR in a larger number of samples.

METHODS

An initial RNA sequencing screen was performed on n = 20 frozen human tissue samples. Filters were applied to select candidate circular RNAs for further investigation. Frozen human tissue samples were selected for global AD pathology burden and global cognition scores (n = 100). Linear and divergent primers were used to assess circularity using RNaseR digestion. RT-qPCR was performed to quantify relative hsa_circ_0131235 abundance.

RESULTS

Eleven circular RNAs were selected for further investigation. Four candidates produced circular RNA primers with appropriate efficiencies for qPCR. RNaseR treatment and analysis by both basic PCR and qPCR confirmed hsa_circ_0131235 circularity. There was a significant main effect of AD pathology on hsa_circ_0131235 expression.

CONCLUSIONS

Elevated hsa_circ_0131235 expression in the MT cortex was significantly associated with AD pathology.