circSAMD4A participates in the apoptosis and autophagy of dopaminergic neurons via the miR‑29c‑3p‑mediated AMPK/mTOR pathway in Parkinson's disease

Integrated bioinformatics analysis for exploring potential biomarkers related to Parkinson's disease progression

BACKGROUND

Parkinson's disease (PD) is a progressive neurodegenerative disease with increasing prevalence. Effective diagnostic markers and therapeutic methods are still lacking. Exploring key molecular markers and mechanisms for PD can help with early diagnosis and treatment improvement.

METHODS

Three datasets GSE174052, GSE77668, and GSE168496 were obtained from the GEO database to search differentially expressed circRNA (DECs), miRNAs (DEMis), and mRNAs (DEMs). GO and KEGG enrichment analyses, and protein-protein interaction (PPI) network construction were implemented to explore possible actions of DEMs. Hub genes were selected to establish circRNA-related competing endogenous RNA (ceRNA) networks.

RESULTS

There were 1005 downregulated DECs, 21 upregulated and 21 downregulated DEMis, and 266 upregulated and 234 downregulated DEMs identified. The DEMs were significantly enriched in various PD-associated functions and pathways such as extracellular matrix organization, dopamine synthesis, PI3K-Akt, and calcium signaling pathways. Twenty-one hub genes were screened out, and a PD-related ceRNA regulatory network was constructed containing 31 circRNAs, one miRNA (miR-371a-3p), and one hub gene (KCNJ6).

CONCLUSION

We identified PD-related molecular markers and ceRNA regulatory networks, providing new directions for PD diagnosis and treatment.

Regulatory mechanism of circular RNAs in neurodegenerative diseases

BACKGROUND

Neurodegenerative disease is a collective term for a category of diseases that are caused by neuronal dysfunction, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Circular RNAs (circRNAs) are a class of non-coding RNAs without the 3' cap and 5' poly(A) and are linked by covalent bonds. CircRNAs are highly expressed in brain neurons and can regulate the pathological process of neurodegenerative diseases by affecting the levels of various deposition proteins.

AIMS

This review is aiming to suggest that the majority of circRNAs influence neurodegenerative pathologies mainly by affecting the abnormal deposition of proteins in neurodegenerative diseases.

METHODS

We systematically summarized the pathological features of neurodegenerative diseases and the regulatory mechanisms of circRNAs in various types of neurodegenerative diseases.

RESULTS

Neurodegenerative disease main features include intercellular ubiquitin-proteasome system abnormalities, changes in cytoskeletal proteins, and the continuous deposition of insoluble protein fragments and inclusion bodies in the cytoplasm or nucleus, resulting in impairment of the normal physiological processes of the neuronal system. CircRNAs have multiple mechanisms, such as acting as microRNA sponges, binding to proteins, and regulating transcription. CircRNAs, which are highly stable molecules, are expected to be potential biomarkers for the pathological detection of neurodegenerative diseases such as AD and PD.

CONCLUSIONS

In this review, we describe the regulatory roles and mechanisms of circRNAs in neurodegenerative diseases and aim to employ circRNAs as biomarkers for the diagnosis and treatment of neurodegenerative diseases.

Parkinson's Disease and MicroRNAs: A Duel Between Inhibition and Stimulation of Apoptosis in Neuronal Cells

Parkinson's disease (PD) is one of the most prevalent diseases of central nervous system that is caused by degeneration of the substantia nigra's dopamine-producing neurons through apoptosis. Apoptosis is regulated by initiators' and executioners' caspases both in intrinsic and extrinsic pathways, further resulting in neuronal damage. In that context, targeting apoptosis appears as a promising therapeutic approach for treating neurodegenerative diseases. Non-coding RNAs-more especially, microRNAs, or miRNAs-are a promising target for the therapy of neurodegenerative diseases because they are essential for a number of cellular processes, including signaling, apoptosis, cell proliferation, and gene regulation. It is estimated that a substantial portion of coding genes (more than 60%) are regulated by miRNAs. These small regulatory molecules can have wide-reaching consequences on cellular processes like apoptosis, both in terms of intrinsic and extrinsic pathways. Furthermore, it was recommended that a disruption in miRNA expression levels could also result in perturbation of typical apoptosis pathways, which may be a factor in certain diseases like PD. The latest research on miRNAs and their impact on neural cell injury in PD models by regulating the apoptosis pathway is summarized in this review article. Furthermore, the importance of lncRNA/circRNA-miRNA-mRNA network for regulating apoptosis pathways in PD models and treatment is explored. These results can be utilized for developing new strategies in PD treatment.

Neuronal dysfunction and gene modulation by non-coding RNA in Parkinson's disease and synucleinopathies

Over the last few decades, emerging evidence suggests that non-coding RNAs (ncRNAs) including long-non-coding RNA (lncRNA), microRNA (miRNA) and circular-RNA (circRNA) contribute to the molecular events underlying progressive neuronal degeneration, and a plethora of ncRNAs have been identified significantly misregulated in many neurodegenerative diseases, including Parkinson's disease and synucleinopathy. Although a direct link between neuropathology and causative candidates has not been clearly established in many cases, the contribution of ncRNAs to the molecular processes leading to cellular dysfunction observed in neurodegenerative diseases has been addressed, suggesting that they may play a role in the pathophysiology of these diseases. Aim of the present Review is to overview and discuss recent literature focused on the role of RNA-based mechanisms involved in different aspects of neuronal pathology in Parkinson's disease and synucleinopathy models.

Non-Coding RNAs and Neurodegenerative Diseases: Information of their Roles in Apoptosis

Apoptosis can be known as a key factor in the pathogenesis of neurodegenerative disorders. In disease conditions, the rate of apoptosis expands and tissue damage may become apparent. Recently, the scientific studies of the non-coding RNAs (ncRNAs) has provided new information of the molecular mechanisms that contribute to neurodegenerative disorders. Numerous reports have documented that ncRNAs have important contributions to several biological processes associated with the increase of neurodegenerative disorders. In addition, microRNAs (miRNAs), circular RNAs (circRNAs), as well as, long ncRNAs (lncRNAs) represent ncRNAs subtypes with the usual dysregulation in neurodegenerative disorders. Dysregulating ncRNAs has been associated with inhibiting or stimulating apoptosis in neurodegenerative disorders. Therefore, this review highlighted several ncRNAs linked to apoptosis in neurodegenerative disorders. CircRNAs, lncRNAs, and miRNAs were also illustrated completely regarding the respective signaling pathways of apoptosis.

Hsa_circ_0054220 Upregulates HMGA1 by the Competitive RNA Pattern to Promote Neural Impairment in MPTP Model of Parkinson's Disease

Parkinson's disease (PD) is a common neurodegenerative disease. Circular RNAs (circRNAs) have been confirmed to regulate neurodegenerative diseases. This study was aimed to explore hsa_circ_0054220 functions in PD. MPP-stimulated SH-SY5Y cells were established as the PD cell model. PD mouse model was established by MPTP. Gene expression in cells and tissues was tested by RT-qPCR. Cell viability and apoptosis were evaluated through CCK-8 and TUNEL assays. The interactions of RNAs were determined by RNA pull-down assay, RIP assay, and luciferase reporter assay. Circ_0054220 expressed at a high level in MPP-treated SH-SY5Y cells. Circ_0054220 inhibition promoted viability and suppressed apoptosis in MPP-stimulated cells. Furthermore, we found that circ_0054220 can competitively bind to miR-145 and miR-625 to upregulate high mobility group A1 (HMGA1) expression. HMGA1 was positively regulated by circ_0054220 and overexpressed in MPP-treated cells as well as the striatum (STR), substantia nigra pars compacta (SNpc), and serum of MPTP-induced mouse model of PD. HMGA1 overexpression counteracted the function of circ_0054220 silencing on cell apoptosis. Furthermore, HMGA1 inhibition notably alleviated motor dysfunction and increased the quantity of neurons in mice resembling PD. Circ_0054220 upregulates HMGA1 by the competitive endogenous RNAs (ceRNA) pattern to promote neural impairment in PD.

Overexpressed miRNA-nov-1 promotes manganese-induced apoptosis in N27 cells by regulating Dhrs3 to activate mTOR signaling pathway

Environmental and occupational chronic manganese exposure can cause neurotoxicity and apoptosis. Moreover, microRNAs (miRNAs) are extensively involved in the process of neuronal apoptosis. Therefore, it is crucial to study the mechanism of miRNA in manganese-induced neuronal apoptosis and to find potential targets. In the present study, we found that the expression of miRNA-nov-1 was increased after N27 cells were exposed to MnCl₂. Then, seven different cell groups were constructed by lentiviral infection of cells, and the overexpression of miRNA-nov-1 promoted the apoptosis process of N27 cells. Further studies showed a negative regulatory relationship between miRNA-nov-1 and dehydrogenase/reductase 3 (Dhrs3). The up-regulation of miRNA-nov-1 reduced the protein level of Dhrs3 in N27 cells exposed to manganese, increased the expression of a caspase-3 protein, activated the rapamycin (mTOR) signaling pathway, and increased cell apoptosis. Furthermore, we found that the expression of the Caspase-3 protein was decreased after the low expression of miRNA-nov-1, the mTOR signaling pathway was inhibited, and reduced cell apoptosis. However, these effects were reversed by the knockdown of Dhrs3. Taken together, these results suggested that overexpression of miRNA-nov-1 can promote manganese-induced apoptosis in N27 cells by activating the mTOR signaling pathway and negatively regulating Dhrs3.

RNA binding protein SAMD4: current knowledge and future perspectives

SAMD4 protein family is a class of novel RNA-binding proteins that can mediate post-transcriptional regulation and translation repression in eukaryotes, which are highly conserved from yeast to humans during evolution. In mammalian cells, SAMD4 protein family consists of two members including SAMD4A/Smaug1 and SAMD4B/Smaug2, both of which contain common SAM domain that can specifically bind to different target mRNAs through stem-loop structures, also known as Smaug recognition elements (SREs), and regulate the mRNA stability, degradation and translation. In addition, SAMD4 can form the cytoplasmic mRNA silencing foci and regulate the translation of SRE-containing mRNAs in neurons. SAMD4 also can form the cytosolic membrane-less organelles (MLOs), termed as Smaug1 bodies, and regulate mitochondrial function. Importantly, many studies have identified that SAMD4 family members are involved in various pathological processes including myopathy, bone development, neural development, and cancer occurrence and progression. In this review, we mainly summarize the structural characteristics, biological functions and molecular regulatory mechanisms of SAMD4 protein family members, which will provide a basis for further research and clinical application of SAMD4 protein family.

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.

The emerging role of circular RNAs in Parkinson's disease

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease and the most common movement disorder. It involves a gradual loss of dopaminergic neurons in the substantia nigra. Although many studies have been conducted, the underlying molecular pathways of PD remain largely unknown. Circular RNAs (circRNAs), a novel class of non-coding RNAs with a covalently closed loop structure, are common in the brain. They are stable, conserved molecules that are widely expressed in eukaryotes in tissue-, cell-, and development-specific patterns. Many circRNAs have recently been identified in nervous system diseases, and some circRNA expression profiles have been linked to PD. Given that recent research has indicated the essential roles of various circRNAs in the development and progression of neurodegenerative diseases, the identification of individual circRNAs may be a promising strategy for finding new treatment targets for PD. Moreover, the search for circRNAs with high specificity and sensitivity will open up new avenues for the early diagnosis and treatment of PD. Herein, we address the biogenesis, properties, and roles of circRNAs and review their potential utility as biomarkers and therapeutic targets in PD.

A crosstalk between circular RNA, microRNA, and messenger RNA in the development of various brain cognitive disorders

Patients with Alzheimer's disease (AD), Parkinson's disease (PD), traumatic brain injury (TBI), stroke, and postoperative neurocognitive disorder (POND) are commonly faced with neurocognitive disorders with limited therapeutic options. Some non-coding ribonucleic acids (ncRNAs) are involved in the development of various brain cognitive disorders. Circular RNAs (circRNAs), a typical group of ncRNAs, can function as competitive endogenous RNAs (ceRNAs) to dysregulate shared microRNAs (miRNAs) at post-transcription level, inhibiting regulation of miRNAs on their targeted messenger RNAs (mRNAs). circRNAs are abundant in central nervous system (CNS) diseases and cause brain disorders, but the exact roles of circRNAs are unclear. The crosstalk between circRNA, miRNA, and mRNA plays an important role in the pathogenesis of these neurocognitive dysfunction diseases and abnormal conditions including AD, PD, stroke, TBI, and POND. In this review, we summarized the participation of circRNA in neuroglial damage and inflammation. Finally, we aimed to highlight the regulatory mechanisms of circRNA–miRNA–mRNA networks in the development of various brain cognitive disorders and provide new insights into the therapeutics of these diseases.

Crosstalk between regulatory non-coding RNAs and oxidative stress in Parkinson’s disease

Parkinson’s disease is the second most common neurodegenerative disease after Alzheimer’s disease, which imposes an ever-increasing burden on society. Many studies have indicated that oxidative stress may play an important role in Parkinson’s disease through multiple processes related to dysfunction or loss of neurons. Besides, several subtypes of non-coding RNAs are found to be involved in this neurodegenerative disorder. However, the interplay between oxidative stress and regulatory non-coding RNAs in Parkinson’s disease remains to be clarified. In this article, we comprehensively survey and overview the role of regulatory ncRNAs in combination with oxidative stress in Parkinson’s disease. The interaction between them is also summarized. We aim to provide readers with a relatively novel insight into the pathogenesis of Parkinson’s disease, which would contribute to the development of pre-clinical diagnosis and treatment.

The Role of Non-Coding RNAs in the Pathogenesis of Parkinson’s Disease: Recent Advancement

Parkinson’s disease (PD) is a prevalent neurodegenerative aging disorder that manifests as motor and non-motor symptoms, and its etiopathogenesis is influenced by non-coding RNAs (ncRNAs). Signal pathway and gene sequence studies have proposed that alteration of ncRNAs is relevant to the occurrence and development of PD. Furthermore, many studies on brain tissues and body fluids from patients with PD indicate that variations in ncRNAs and their target genes could trigger or exacerbate neurodegenerative pathogenesis and serve as potential non-invasive biomarkers of PD. Numerous ncRNAs have been considered regulators of apoptosis, α-syn misfolding and aggregation, mitochondrial dysfunction, autophagy, and neuroinflammation in PD etiology, and evidence is mounting for the determination of the role of competing endogenous RNA (ceRNA) mechanisms in disease development. In this review, we discuss the current knowledge regarding the regulation and function of ncRNAs as well as ceRNA networks in PD pathogenesis, focusing on microRNAs, long ncRNAs, and circular RNAs to increase the understanding of the disease and propose potential target identification and treatment in the early stages of PD.

Circular RNA hsa_circ_0004381 Promotes Neuronal Injury in Parkinson's Disease Cell Model by miR-185-5p/RAC1 Axis

The study aims to explore the molecular mechanism involved in Parkinson's disease (PD). Hsa_circ_0004381, microRNA-185-5p (miR-185-5p), and Rac family small GTPase 1 (RAC1) level were measured by real-time quantitative polymerase chain reaction (RT-qPCR). Furthermore, cell viability and apoptosis rate were assessed by Cell Counting Kit-8 (CCK-8) and flow cytometry assays, respectively. Protein levels of B cell lymphoma-2 (Bcl-2), Bcl-2-related X protein (Bax), cleaved-caspase 3 (c-caspase 3), and RAC1 were determined by western blot assay. The levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and IL-6 were detected by enzyme-linked immunosorbent assay (ELISA). The ROS generation and LDH and SOD activity were detected by the corresponding kits. The binding relationship between miR-185-5p and hsa_circ_0004381 or RAC1 was predicted by Starbase and then verified by a dual-luciferase reporter and RNA Immunoprecipitation (RIP) assays. Hsa_circ_0004381 and RAC1 were increased, and miR-185-5p was decreased in MPP⁺-triggered SK-N-SH cells. Moreover, hsa_circ_0004381 silencing promoted cell viability, and repressed apoptosis, inflammatory response, and oxidative stress in MPP⁺-treated SK-N-SH cells. The mechanical analysis suggested that hsa_circ_0004381 served as a sponge of miR-185-5p to affect RAC1 expression. Hsa_circ_0004381 could contribute to MPP⁺-triggered neuron injury by targeting the miR-185-5p/RAC1 axis, which provided a novel insight into the pathogenesis and treatment of PD.

Novel insights into the role of circular RNAs in Parkinson disease: An emerging renaissance in the management of neurodegenerative diseases

Parkinson's disease (PD), as a debilitating neurodegenerative disease, particularly affects the elderly population, and is clinically identified by resting tremor, rigidity, and bradykinesia. Pathophysiologically, PD is characterized by an early loss of dopaminergic neurons in the Substantia nigra pars compacta, accompanied by the extensive aggregation of alpha-synuclein (α-Syn) in the form of Lewy bodies. The onset of PD has been reported to be influenced by multiple biological molecules. In this context, circular RNAs (circRNAs), as tissue-specific noncoding RNAs with closed structures, have been recently demonstrated to involve in a set of PD's pathogenic processes. These RNA molecules can either up- or downregulate the expression of α-Syn, as well as moderating its accumulation through different regulatory mechanisms, in which targeting microRNAs (miRNAs) is considered the most common pathway. Since circRNAs have prominent structural and biological characteristics, they could also be considered as promising candidates for PD diagnosis and treatment. Unfortunately, PD has become a global health concern, and a large number of its pathogenic processes are still unclear; thus, it is crucial to elucidate the ambiguous aspects of PD pathophysiology to improve the efficiency of diagnostic and therapeutic strategies. In line with this fact, the current review aims to highlight the interplay between circRNAs and PD pathogenesis, and then discusses the diagnostic and therapeutic potential of circRNAs in PD progression. This study will thus be the first of its kind reviewing the relationship between circRNAs and PD.

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.

Circ_0003611 acts as a miR-885-5p sponge to aggravate the amyloid-β-induced neuronal injury in Alzheimer's disease

Alzheimer's disease (AD) is a chronic degenerative disease in the central nervous system and circular RNAs (circRNAs) are identified as essential regulators in AD. The current research was designed for exploration of circ_0003611 in AD. Circ_0003611 was overexpressed in AD patients and Aβ-treated SK-N-SH cells. Aβ-induced apoptotic, inflammatory and oxidative damages were relieved after knockdown of circ_0003611. MiR-885-5p was validated as a miRNA target of circ_0003611. The protective function of circ_0003611 downregulation was achieved by releasing miR-885-5p in Aβ-treated SK-N-SH cells. KREMEN1 was a downstream gene of miR-885-5p. Overexpression of miR-885-5p attenuated the Aβ-triggered cell injury by reducing the KREMEN1 expression. KREMEN1 was regulated by circ_0003611 via sponging miR-885-5p in Aβ-treated SK-N-SH cells. These experimental data demonstrated that circ_0003611 enhanced the Aβ-induced neuronal cell injury in AD by serving as the miR-885-5p sponge to regulate the level of KREMEN1.

Baicalein Induces Mitochondrial Autophagy to Prevent Parkinson's Disease in Rats via miR-30b and the SIRT1/AMPK/mTOR Pathway

Parkinson's disease (PD) is a prevailing neurodegenerative disorder. Baicalein has neuroprotective effects on PD animals, but its mechanism is not clarified. We explored baicalein effects on PD rats. PD rat models were established by injecting 6-hydroxydopamine into the striatum of substantia nigra on the left side of the rat brain and treated with baicalein. Dopamine (DA) content, neuronal apoptosis, neuronal injury, neuronal mitochondria, and autophagy were assessed. Baicalein-treated PD rats were treated with autophagy inhibitor 3-methyladenine to identify the role of autophagy in PD. PD rats were injected with AgomiR-30b-5p or sh-SIRT1 plasmids and treated with baicalein. PD rats elicited decreased neurological score and DA secretion of the striatum, increased neuronal apoptosis, and injury, and reduced number of mitochondria and autophagy, whereas baicalein alleviated neuronal injury and partly recovered mitochondrial dysfunction, 3-methyladenine inhibited the protection of baicalein. miR-30b-5p was elevated and SIRT1 was diminished in PD rats and inhibited by baicalein. miR-30b-5p targeted SIRT1. miR-30b-5p overexpression or SIRT1 silencing annulled the protection of baicalein. The phosphorylation level of AMPK in the substantia nigra of PD rats was decreased and mTOR was increased, whereas baicalein annulled these trends. Briefly, baicalein activated mitochondrial autophagy via miR-30b-5p and the SIRT1/AMPK/mTOR pathway, thus protecting PD rats.