Noncoding RNAs in protein clearance pathways: implications in neurodegenerative diseases

Non-coding RNAs in Regulation of Protein Aggregation and Clearance Pathways: Current Perspectives Towards Alzheimer's Research and Therapy

Alzheimer's disease (AD) is the leading cause of dementia, affecting approximately 45.0 million people worldwide and ranking as the fifth leading cause of mortality. AD is identified by neurofibrillary tangles (NFTs), which include abnormally phosphorylated tau-protein and amyloid protein (amyloid plaques). Peptide dysregulation is caused by an imbalance between the production and clearance of the amyloid-beta (Aβ) and NFT. AD begins to develop when these peptides are not cleared from the body. As a result, understanding the processes that control both normal and pathological protein recycling in neuronal cells is critical. Insufficient Aβ and NFT clearance are important factors in the development of AD. Autophagy, lysosomal dysfunction, and ubiquitin-proteasome dysfunction have potential roles in the pathogenesis of many neurodegenerative disorders, particularly in AD. Modulation of these pathways may provide a novel treatment strategy for AD. Non-coding RNAs (ncRNAs) have recently emerged as important biological regulators, with particular relevance to the emergence and development of neurodegenerative disorders such as AD. ncRNAs can be used as potential therapeutic targets and diagnostic biomarkers due to their critical regulatory functions in several biological processes involved in disease development, such as the aggregation and accumulation of Aβ and NFT. It is evident that ncRNAs play a role in the pathophysiology of AD. In this communication, we explored the link between ncRNAs and AD and their regulatory mechanisms that may help in finding new therapeutic targets and AD medications.

Lnc001209 Participates in aluminium-induced apoptosis of PC12 cells by regulating PI3K-AKT-mTOR signalling pathway

Aluminium (Al) is a common environmental neurotoxin, but the molecular mechanism underlying its toxic effects remains unclear. Many studies have shown that aluminium exposure leads to increased neuronal apoptosis. This study aimed to investigate the mechanisms and signalling pathways involved in aluminium exposure-induced neuronal apoptosis. The results showed a decrease in the number of PC12 cells and changes in cell morphology in the aluminium maltol exposure group. The viability of PC12 cells decreased gradually with increasing of exposure doses, and the apoptosis rate increased. The expression of Lnc001209 decreased gradually with an increase in the aluminium exposure dose. After transfection of Lnc001209 siRNA in aluminium-exposed PC12 cells, the protein expression levels of p-Akt Ser473, p-Akt Thr308, p-P85 Tyr467, p-mTOR Ser2448 and CD36 were increased. RNA pull-down MS showed that Lnc001209 interacts with the CD36 protein. Expression of the CD36 protein was increased in PC12 cells exposed to aluminium. The results of the CD36 intervention experiment showed that the protein expression levels of p-Akt Ser473, p-Akt Thr308, p-P85 Tyr467, and p-mTOR Ser2448 likely increased after CD36 overexpression. In addition, the phosphorylation level of AKT had the most significant increase. The enhancement of p-Akt activity promotes neuronal apoptosis.

Integrated analysis of mRNA and microRNA expression profiles in hepatopancreas of Litopenaeus vannamei under acute exposure to MC-LR

Intensive shrimp farming is often threatened by microcystins Hepatopancreas is the primary target organ of MCs in shrimp. To investigate the response of hepatopancreas to acute MC-LR exposure, the expression profiles of RNA-seq and miRNA-seq in the hepatopancreas of L. vannamei were determined, and data integration analysis was performed at 72 h after MC-LR injection. The expression of 5 DEGs and three DEMs were detected by Quantitative PCR (qPCR). The results showed that the cumulative mortality rate of shrimp in MC-LR treatment group was 41.1%. A total of 1229 differentially expressed genes (844 up- and 385 down-regulated) and 86 differentially expressed miRNAs (40 up- and 46 down-regulated) were identified after MC-LR exposure. Functional analysis indicated that DEGs is mainly involved in the oxidative activity process in molecular functional categories, and proteasome was the most enriched KEGG pathway for mRNAs profile. According to the functional annotation of target genes of DEMs, protein binding was the most important term in the GO category, and protein processing in endoplasmic reticulum (ER) was the most enriched KEGG pathway. The regulatory network of miRNAs and DEGs involved in the pathway related to protein degradation in endoplasmic reticulum was constructed, and miR-181-5p regulated many genes in this pathway. The results of qPCR showed that there were significant differences in the expression of five DEGs and three DEMs, which might play an important role in the toxicity and hepatopancreas detoxification of MC-LR in shrimp. The results revealed that MC-LR exposure affected the degradation pathway of misfolded protein in ER of L. vannamei hepatopancreas, and miR-181-5p might play an important role in the effect of MC-LR on the degradation pathway of misfolded protein.

LINC00667 regulates MPP + ‐induced neuronal injury in Parkinson’s disease

Objective

Parkinson’s disease (PD), also known as paralysis tremor, is a chronic disease of the central nervous system. It has been reported that hepatocyte nuclear factor 4 alpha (HNF4A) is upregulated in PD, but its specific function has not been well explored.

Methods

We established an in vitro PD model in SH‐SY5Y cells stimulated with 1‐methyl‐4‐phenylpyridinium (MPP⁺). Meanwhile, the effect of HNF4A on MPP⁺‐treated SH‐SY5Y cell behavior was monitored by functional assays. Mechanism assays were conducted to verify the relationship among LINC00667/miR‐34c‐5p/HNF4A. Rescue experiments validated the regulatory mechanism in PD model.

Results

The results revealed that depletion of HNF4A suppressed cell cytotoxicity and apoptosis caused by MPP⁺. Knockdown of HNF4A recovered MPP⁺‐stimulated oxidative stress and neuroinflammation. Mechanically, HNF4A was targeted and inhibited by miR‐34c‐5p. Furthermore, we found that LINC00667 positively modulated HNF4A expression via sequestering miR‐34c‐5p in MPP⁺‐stimulated SH‐SY5Y cells. Interestingly, the data indicated that HNF4A could transcriptionally activate LINC00667 expression. Rescue experiments presented that miR‐34c‐5p interference or HNF4A overexpression could mitigate the effects of LINC00667 knockdown on cell viability, cytotoxicity, cell apoptosis, oxidative stress, and neuroinflammation in MPP⁺‐treated SH‐SY5Y cells.

Conclusion

Our study first proved LINC00667, miR‐34c‐5p, and HNF4A constructed a positive feedback loop in MPP⁺‐treated SH‐SY5Y cells, enriching our understanding of PD.

Human Satellite III long non-coding RNA imparts survival benefits to cancer cells

Long non-coding RNAs (lncRNAs) are heterogeneous group of transcripts that lack coding potential and have essential roles in gene regulations. Recent days have seen an increasing association of non-coding RNAs with human diseases, especially cancers. One interesting group of non-coding RNAs strongly linked to cancers are heterochromatic repetitive Satellite RNAs. Satellite RNAs are transcribed from pericentromeric heterochromatic region of the human chromosomes. Satellite II RNA, most extensively studied, is upregulated in wide variety of epithelial cancer. Similarly, alpha satellite is over expressed in BRCA1- deficient tumors. Though much is known about alpha satellites and SatII repeats, little is known about Satellite III (SatIII) lncRNAs in human cancers. SatIII repeats, though transcriptionally silent in normal conditions is actively transcribed under condition of stress, mainly heat shock. In the present study, we show that colon and breast cancer cells aberrantly transcribes SatIII, in a Heat shock factor I (HSF1)-independent manner. Our study also reveals that, overexpression of SatIII RNA favours cancer cell survival by overriding chemo drug-induced cell death. Interestingly, knockdown of SatIII sensitizes cells towards chemotherapeutic drugs. This sensitization is possibly mediated by restoration of p53 protein expression that facilitates cell death. Heat shock however helps SatIII to continue with its pro-cell survival function. Our results, therefore suggest SatIII to be an important regulator of human cancers. Induction of SatIII is not only a response to the oncogenic stress but also facilitates cancer progression by a distinct pathway that is different from heat stress pathway. This article is protected by copyright. All rights reserved.

Long noncoding RNAs in the regulation of p53-mediated apoptosis in human cancers

Long noncoding RNAs (lncRNAs) are widely known for their regulatory function in transcriptional and posttranscriptional processes. The involvement of such non-protein-coding RNAs in nuclear organization and chromatin remodeling is often associated with an increased risk of human malignancies. In cancer, lncRNAs either promote cell survival or may act as a growth suppressor, thus conferring a key regulatory function other than their established role in fundamental cellular processes. Interestingly, lncRNAs interfere with the stages of apoptosis and related pathways involving p53. Many of these molecules either regulate or are regulated by p53 while mounting oncogenic events. Consequently, they may confer both prosurvival or proapoptotic functions depending upon the tissue type. Since the mechanism of cell death is bypassed in many human cancers, it has emerged that the lncRNAs are either overexpressed or knocked down to sensitize cells to apoptotic stimuli. Nonetheless, the abundant expression of lncRNAs in tumor cells renders them suitable targets for anticancer therapies. Although the role of lncRNAs in the p53 network and apoptosis has been independently defined, their interplay in activating p53-target genes during cell cycle arrest remains unexplored. Thus, we have specifically reviewed the possible involvement of lncRNAs in the p53-mediated apoptosis of human cancer cells. In particular, we summarize the growing evidence from individual studies and analyze whether lncRNAs are essential to facilitate apoptosis in a p53-dependent manner. This may lead to the identification of p53-associated lncRNAs that are suitable therapeutic targets or diagnostic/prognostic markers.

LncRNA-mRNA Expression Profiles and Functional Networks Associated with Cognitive Impairment in Folate-deficient Mice

BACKGROUND

Cognitive impairment is a common neurocognitive disorder that affects millions of worldwide people's health,related tofolate deficiency.

OBJECTIVE

The present study aimed to investigate the lncRNA-mRNA functional networks associated with cognitive impairment in folate-deficient mice and elucidate their possible molecular mechanisms.

METHODS

We downloaded the gene expression profile (GSE148126) of lncRNAs and mRNAs from NCBI Gene Expression Omnibus (GEO) database. Four groups of mouse hippocampi were analyzed, including 4 months (4mo) and 18 months (18mo) of folic acid (FA) deficiency/supplementation. The differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified using gplots and heatmap packages. The functions of the DEmRNAs were evaluated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The hub genes wereidentified by CytoHubba plugins of Cytoscape, and protein-protein interaction (PPI) network of deregulated mRNAs was performed using STRING database. Finally, lncRNA-mRNA co-expression and competitive endogenous RNA (ceRNA) network analyses were constructed.

RESULTS

In total, we screened 67 lncRNAs with 211 mRNAs, and 89 lncRNAs with 229 mRNAs were differentially expressed in 4mo_FAand 18mo_FA deficient mice, respectively. GO analyses indicated that DEmRNAs were highly related to terms involved in binding and biological regulation. KEGG pathway analyses demonstrated that these genes were significantly enriched for Renin secretion, Pancreatic secretion and AMPK signaling pathways in 18mo_FA deficiency group. Subsequently, the top 5 hub genes werescreened from the PPI network, which may be key genes with the progression of folate deficiency. Upon the lncRNA-mRNA co-expression network analysis, we identified the top 10 lncRNAs having the maximum number of connections with related mRNAs. Finally, a ceRNA network was constructed for DE lncRNAs and DEmRNAs, and several pivotal miRNAs were predicted.

CONCLUSIONS

This study identified the lncRNA-mRNA expression profiles and functional networks associated with cognitive impairment in folate-deficient mice, which provided support for the possible mechanisms and therapy for this disease.

SOX21-AS1 modulates neuronal injury of MMP+-treated SH-SY5Y cells via targeting miR-7-5p and inhibiting IRS2

Parkinson's disease (PD), caused by the decreased number of dopaminergic neurons in the substantia nigra, is identified as the second most familiar age-dependent neurodegenerative disease to the public. Long non-coding RNAs (lncRNAs) have been reported to participate in the development of PD. In our research, the expression of lncRNA SRY-box transcription factor 21 antisense divergent transcript 1 (SOX21-AS1) was up-regulated in 1-methyl-4-phenylpyridinium (MMP⁺)-treated SH-SY5Y cells. In addition, SOX21-AS1 depletion weakened the cell injury induced by MMP⁺. Moreover, SOX21-AS1 knockdown decreased Reactive Oxygen Species (ROS) generation and levels of TNF-α, IL-1β and IL-6, but increased SOD activity. However, SOX21-AS1 up-regulation led to opposite results. Further, SOX21-AS1 could bind with miR-7-5p, whose overexpression relieved MMP⁺-induced cell injury. Additionally, insulin receptor substrate 2 (IRS2) served as the target gene of miR-7-5p, and its expression was positively modulated by SOX21-AS1. Similarly, IRS2 knockdown also had alleviative effects on cell injury stimulated by MMP⁺ treatment. In sum up, our study demonstrated a new regulatory network consisted of SOX21-AS1, miR-7-5p and IRS2 in SH-SY5Y cells, supplying with a better comprehension about the pathogenic mechanism of PD.

Knockdown of long non-coding RNA AL049437 mitigates MPP+ -induced neuronal injury in SH-SY5Y cells via the microRNA-205-5p/MAPK1 axis

BACKGROUND

Long noncoding RNAs (lncRNAs) have been defined as critical regulators of various human diseases. However, the functions of lncRNAs in Parkinson's disease (PD) have not yet been elucidated. In this study, we investigated the role of lncRNA AL049437 in PD and its underlying mechanism.

METHODS

An in vivo model of PD was established using 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), while an in vitro model was created using N-methyl-4-phenylpyridinium (MPP+). Gene expression was evaluated using quantitative reverse transcriptase polymerase chain reaction and western blotting. The effects and mechanism of AL049437 in PD were explored using Cell Counting Kit-8 assay, flow cytometry, enzyme-linked immunosorbent assay, and 2',7'-dichlorodihydrofluorescein diacetate fluorescence assay. The interaction between AL049437, miR-205-5p, and mitogen-activated protein kinase 1 (MAPK1) was evaluated using luciferase reporter and RNA pull-down assays.

RESULTS

The expression of AL049437 was upregulated, while that of miR-205-5p was downregulated in MPTP-induced PD mouse model and MPP+-treated SH-SY5Y cells. Silencing of AL049437 mitigated MPP+-induced neurotoxicity in SH-SY5Y cells, as demonstrated by increased cell viability and reduced cell apoptosis. Furthermore, silencing of AL049437 alleviated MPP+-induced neuroinflammation and oxidative stress, as indicated by the reduction in tumor necrosis factor-α and interleukin-6 levels and reactive oxygen species production. In addition, AL049437 was predominantly localized in the cytoplasm of SH-SY5Y cells and functioned as an miR-205-5p sponge. Moreover, MAPK1 was identified as a downstream target of miR-205-5p. Remarkably, the impact of AL049437 silencing on MPP+-induced neuronal damage could be blocked by miR-205-5p inhibition or MAPK1 overexpression.

CONCLUSION

Knockdown of lncRNA AL049437 mitigates MPP+ -induced neuronal injury in SH-SY5Y cells by regulating the miR-205-5p/MAPK1 axis. Our research reveals a novel regulatory mechanism of AL049437 in PD progression.

Online Databases and Non-coding RNAs in Cardiovascular Diseases

Cardiovascular disease is characterized by its highest morbidity and mortality. One of the main pathological basis of this disease is the dysregulation of gene expression. Non-coding RNA (ncRNA) is a kind of functional RNA, which is transcript from DNA but not translated into proteins. More and more studies have established the important roles of ncRNAs, including transcription, RNA maturation, translation, protein degradation, and their involvement in the pathogenesis of diseases such as cancer and cardiovascular diseases. This chapter will focus on the biological functions of ncRNAs and their advances in cardiovascular disease. With the development of sequencing and computer technology, more and more databases can be easily obtained on the internet. In another part of this chapter, we will summarize some commonly used non-coding RNA databases, which can be easily and quickly used for relevant research.

Long non-coding RNA-p21 regulates MPP+-induced neuronal injury by targeting miR-625 and derepressing TRPM2 in SH-SY5Y cells

Parkinson's disease (PD), the second most prevalent age-related neurodegenerative disease, occurs as a result of the loss of dopaminergic neurons in the substantia nigra. Long non-coding RNA-p21 (lnc-p21) has been demonstrated to be upregulated in PD. However, its role in PD is unknown. Here, the results showed that lnc-p21 was highly expressed in human neuroblastoma SH-SY5Y cells treated with MPP⁺. Knockdown of lnc-p21 attenuated the cytotoxicity and cell apoptosis induced by MPP⁺ as shown by enhanced cell viability, decreased LDH release and cell apoptosis rate, accompanying with reduction of caspase-3 activity and Bax expression, and enhancement of Bcl-2 expression. Furthermore, knockdown of lnc-p21 mitigated MPP⁺-induced oxidative stress and neuroinflammation, as evidenced by the decrease in ROS generation, increase in SOD activity and decline in TNF-α, IL-1β and IL-6 levels. Conversely, overexpression of lnc-p21 resulted in the opposite effect. miR-625 was identified as a target of lnc-p21. lnc-p21 overturned the inhibitory effect of miR-625 on MPP⁺-induced neuronal injury in SH-SY5Y cells. Additionally, lnc-p21 positively regulated TRPM2 expression by targeting miR-625, and knockdown of TRPM2 inhibited MPP⁺-induced neuronal injury. Overall, our study identified a new lnc-p21-miR-625-TRPM2 regulatory network that lnc-p21 regulated MPP + -induced neuronal injury by sponging miR-625 and upregulating TRPM2 in SH-SY5Y cells, which provide a better understanding for the pathogenesis of PD.

LncRNA Riken-201 and Riken-203 modulates neural development by regulating the Sox6 through sequestering miRNAs

Objectives

Long non‐coding RNAs (LncRNAs) play important roles in epigenetic regulatory function during the development processes. In this study, we found that through alternative splicing, LncRNA C130071C03Riken variants Riken‐201 (Riken‐201) and Riken‐203 (Riken‐203) are both expressed highly in brain, and increase gradually during neural differentiation. However, the function of Rik‐201 and Rik‐203 is unknown.

Materials and methods

Embryonic stem cells (ESCs); RNA sequencing; gene expression of mRNAs, LncRNAs and miRNAs; over‐expression and RNA interference of genes; flow cytometry; real‐time quantity PCR; and Western blot were used in the studies. RNA pull‐down assay and PCR were employed to detect any miRNA that attached to Rik‐201 and Rik‐203. The binding of miRNA with mRNA of Sox6 was presented by the luciferase assay.

Results

Repression of Rik‐201 and Rik‐203 inhibited neural differentiation from mouse embryonic stem cells. Moreover, Rik‐201 and Rik‐203 functioned as the competing endogenous RNA (ceRNA) to repress the function of miR‐96 and miR‐467a‐3p, respectively, and modulate the expression of Sox6 to further regulate neural differentiation. Knockout of the Rik‐203 and Rik‐201 induced high ratio of brain developmental retardation. Further we found that C/EBPβ might potentially activated the transcription of Rik‐201 and Rik‐203.

Conclusions

These findings identify the functional role of Rik‐201 and Rik‐203 in facilitating neural differentiation and further brain development, and elucidate the underlying miRNAs‐Sox6‐associated molecular mechanisms.

Upregulated lncRNA small nucleolar RNA host gene 1 promotes 1-methyl-4-phenylpyridinium ion-induced cytotoxicity and reactive oxygen species production through miR-15b-5p/GSK3β axis in human dopaminergic SH-SY5Y cells

Long noncoding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) has been demonstrated to be upregulated and play a crucial role in the pathology of Parkinson's disease (PD). However, the exact role of SNHG1 and its underlying mechanisms in PD remains elusive. In this study, we found that SNHG1 and glycogen synthase kinase 3 beta (GSK3β) were upregulated, but miR-15b-5p was downregulated in 1-methyl-4-phenylpyridinium ion (MPP⁺ )-treated SH-SY5Y cells. The upregulation of SNHG1 enhanced MPP⁺ -induced cellular toxicity in SH-SY5Y cells, as shown by decreased cell viability, increased ROS production, and increased number of TdT-mediated dUTP Nick-End labeling-positive cells, accompanied with the upregulation of cleaved caspase 3 and elevation of cytochrome C release. Meanwhile, SNHG1 knockdown presented the converse effects. SNHG1 was demonstrated to interact with miR-15b-5p. Moreover, SNHG1 could attenuate the inhibitory effects of miR-15b-5p on MPP⁺ -induced cytotoxicity and production of ROS. Besides, GSK3β was identified as a direct target of miR-15b-5p. The inhibitory effects of SNHG1 knockdown or miR-15b-5p overexpression on MPP⁺ -induced cytotoxicity and reactive oxygen species (ROS) production were abrogated by upregulation of GSK3β. Taken together, these results demonstrate that upregulated lncRNA SNHG1 promotes MPP⁺ -induced cytotoxicity and ROS production through the miR-15b-5p/GSK3β axis in human dopaminergic SH-SY5Y cells, suggesting that SNHG1 may act as a potential therapeutic target for PD treatment in the future.