Silence of long intergenic noncoding RNA HOTAIR ameliorates oxidative stress and inflammation response in ox-LDL-treated human macrophages by upregulating miR-330-5p

Emerging roles of HOTAIR lncRNA in the pathogenesis and prognosis of cardiovascular diseases

Highlights HOTAIR, a long noncoding RNA, plays a role in the regulation of proteins involved in the pathogenesis of cardiovascular disease. Furthermore, it has been identified as a biomarker of this type of disease. Several factors and cells contribute to atherosclerosis, a progressive disease. However, the prognosis of HOTAIR in this disease varies depending on the path in which it plays a role. For this condition, there is no single prognosis to consider.

Deciphering the emerging landscape of HOX genes in cardiovascular biology, atherosclerosis and beyond (Review)

Atherosclerosis, a dominant driving force underlying multiple cardiovascular events, is an intertwined and chronic inflammatory disease characterized by lipid deposition in the arterial wall, which leads to diverse cardiovascular problems. Despite unprecedented advances in understanding the pathogenesis of atherosclerosis and the substantial decline in cardiovascular mortality, atherosclerotic cardiovascular disease remains a global public health issue. Understanding the molecular landscape of atherosclerosis is imperative in the field of molecular cardiology. Recently, compelling evidence has shown that an important family of homeobox (HOX) genes endows causality in orchestrating the interplay between various cardiovascular biological processes and atherosclerosis. Despite seemingly scratching the surface, such insight into the realization of biology promises to yield extraordinary breakthroughs in ameliorating atherosclerosis. Primarily recapitulated herein are the contributions of HOX in atherosclerosis, including diverse cardiovascular biology, knowledge gaps, remaining challenges and future directions. A snapshot of other cardiovascular biological processes was also provided, including cardiac/vascular development, cardiomyocyte pyroptosis/apoptosis, cardiac fibroblast proliferation and cardiac hypertrophy, which are responsible for cardiovascular disorders. Further in‑depth investigation of HOX promises to provide a potential yet challenging landscape, albeit largely undetermined to date, for partially pinpointing the molecular mechanisms of atherosclerosis. A plethora of new targeted therapies may ultimately emerge against atherosclerosis, which is rapidly underway. However, translational undertakings are crucially important but increasingly challenging and remain an ongoing and monumental conundrum in the field.

LncRNA/CircRNA-miRNA-mRNA Axis in Atherosclerotic Inflammation: Research Progress

Atherosclerosis is characterized by chronic inflammation of the arterial wall. However, the exact mechanism underlying atherosclerosis-related inflammation has not been fully elucidated. To gain insight into the mechanisms underlying the inflammatory process that leads to atherosclerosis, there is need to identify novel molecular markers. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-protein-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have gained prominence in recent years. LncRNAs/circRNAs act as competing endogenous RNAs (ceRNAs) that bind to miRNAs via microRNA response elements (MREs), thereby inhibiting the silencing of miRNA target mRNAs. Inflammatory mediators and inflammatory signaling pathways are closely regulated by ceRNA regulatory networks in atherosclerosis. In this review, we discuss the role of LncRNA/CircRNA-miRNA-mRNA axis in atherosclerotic inflammation and how it can be targeted for early clinical detection and treatment.

Is the suppression of CD36 a promising way for atherosclerosis therapy?

Atherosclerosis is the main underlying pathology of many cardiovascular diseases and is marked by plaque formation in the artery wall. It has posed a serious threat to the health of people all over the world. CD36 acts as a significant regulator of lipid homeostasis, which is closely associated with the onset and progression of atherosclerosis and may be a new therapeutic target. The abnormal overexpression of CD36 facilitates lipid accumulation, foam cell formation, inflammation, endothelial apoptosis, and thrombosis. Numerous natural products and lipid-lowering agents are found to target the suppression of CD36 or inhibit the upregulation of CD36 to prevent and treat atherosclerosis. Here, the structure, expression regulation and function of CD36 in atherosclerosis and its related pharmacological therapies are reviewed. This review highlights the importance of drugs targeting CD36 suppression in the treatment and prevention of atherosclerosis, in order to develop new therapeutic strategies and potential anti-atherosclerotic drugs both preclinically and clinically.

Relationship between long non-coding RNA MALAT1 and HOTAIR expression with sperm parameters, DNA and malondialdehyde levels in male infertility

BACKGROUND

Sperm quality is a complex index used to evaluate the fertility potential of men. The long non-coding RNA (lncRNA) MALAT1 participate in sperm development and HOTAIR have critical roles in the regulation of oxidative stress responses. This study aimed to evaluate the relationship of lncRNA MALAT1 and HOTAIR expression with sperm parameters, DNA fragmentation and malondialdehyde (MDA)levels in sperm fertility.

METHODS

In this experimental study, semen samples (n = 30 fertile, n = 30 infertile) men were collected and evaluated for sperm parameters by computer-aided sperm analysis(CASA). Sperm DNA integrity quality was assessed by the Acridine orange(AO) test. MDA levels were determined by the Thiobarbituric acid reaction method. The expression of MALAT1 and HOTAIR was detected by RT-PCR.

RESULTS

We observed a decreased level of MALAT1and HOTAIR expression in the infertile men (p < 0.001). The relative expression level of MALAT1and HOTAIR showed a positive correlation with motility and morphology (p < 0.001). Subsequently, we found the DNA damage and MDA levels was negatively correlated with expression level of genes of sperm (p < 0.001).

CONCLUSION

In this study the low expression of MALATI and HOTAIR resulted in the high level of MDA, DNA damage, and reduced motility of sperm. This study suggests the therapeutic opportunities in respect to MALATI and HOTAIR expression in the sperm function.

Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

Background

RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. Despite these advancements, there remains a gap in our understanding of the implications of different RNA-seq library protocols on comprehensive lncRNA expression analysis, particularly in non-mammalian organisms.

Results

In this study, we sought to bridge this knowledge gap by investigating lncRNA expression patterns in Drosophila melanogaster under thermal stress conditions. To achieve this, we conducted a comparative analysis of two RNA-seq library protocols: polyA + RNA capture and rRNA-depletion. Our approach involved the development and application of a Transcriptome Analysis Pipeline (TAP) designed to systematically assess both the technical and functional dimensions of RNA-seq, facilitating a robust comparison of these library protocols. Our findings underscore the efficacy of the polyA + protocol in capturing the majority of expressed lncRNAs within the Drosophila melanogaster transcriptome. In contrast, rRNA-depletion exhibited limited advantages in the context of D. melanogaster studies. Notably, the polyA + protocol demonstrated superior performance in terms of usable read yield and the accurate detection of splice junctions.

Conclusions

Our study introduces a versatile transcriptomic analysis pipeline, TAP, designed to uniformly process RNA-seq data from any organism with a reference genome. It also highlights the significance of selecting an appropriate RNA-seq library protocol tailored to the specific research context.

Background

Advances in next generation sequencing (NGS) technologies enable the comprehensive analysis of genetic sequences of organisms in a relatively cost-effective manner [1, 2]. Among these technologies, RNA-sequencing (RNA-seq) has emerged as a preeminent method to study fundamental biological mechanisms at the level of cells, tissues, and whole organisms. RNA-seq enables the detection and quantification of various RNA populations, including messenger RNA (mRNA) and various species of non-coding RNA, such as long non-coding RNA (lncRNA), as well as an assessment of features including splice junctions in RNA.

NLRP3 inflammasome pathway in atherosclerosis: Focusing on the therapeutic potential of non-coding RNAs

NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome pathway has a critical role in the pathogenesis of atherosclerosis. Activation of this pathway is implicated in the subendothelial inflammation and atherosclerosis progression. The NLRP3 inflammasome are cytoplasmic sensors with the distinct capacity to identify a wide range of inflammation-related signals, which enhance NLRP3 inflammasome assembly and allow it to trigger inflammation. This pathway is triggered by a variety of intrinsic signals which exist in atherosclerotic plaques, like cholesterol crystals and oxidized LDL. Further pharmacological findings indicated that NLRP3 inflammasome enhanced caspase-1-mediated secretion of pro-inflammatory mediators like interleukin (IL)- 1β/18. Newly published cutting-edge studies suggested that non-coding RNAs (ncRNAs) including microRNAs (miRNAs, miRs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) are major modulators of NLRP3 inflammasome in atherosclerosis. Therefore, in this review, we aimed to discuss the NLRP3 inflammasome pathway, biogenesis of ncRNAs as well as the modulatory role of ncRNAs in regulating the various mediators of NLRP3 inflammasome pathway including TLR4, NF-kB, NLRP3, and caspase 1. We also discussed the importance of NLRP3 inflammasome pathway-related ncRNAs as a diagnostic biomarker in atherosclerosis and current therapeutics in the modulation of NLRP3 inflammasome in atherosclerosis. Finally, we speak about the limitations and future prospects of ncRNAs in regulating inflammatory atherosclerosis via the NLRP3 inflammasome pathway.

Oxidative Stress Modulation by ncRNAs and Their Emerging Role as Therapeutic Targets in Atherosclerosis and Non-Alcoholic Fatty Liver Disease

Atherosclerosis and non-alcoholic fatty liver disease (NAFLD) are pathologies related to ectopic fat accumulation, both of which are continuously increasing in prevalence. These threats are prompting researchers to develop effective therapies for their clinical management. One of the common pathophysiological alterations that underlies both diseases is oxidative stress (OxS), which appears as a result of lipid deposition in affected tissues. However, the molecular mechanisms that lead to OxS generation are different in each disease. Non-coding RNAs (ncRNAs) are RNA transcripts that do not encode proteins and function by regulating gene expression. In recent years, the involvement of ncRNAs in OxS modulation has become more recognized. This review summarizes the most recent advances regarding ncRNA-mediated regulation of OxS in atherosclerosis and NAFLD. In both diseases, ncRNAs can exert pro-oxidant or antioxidant functions by regulating gene targets and even other ncRNAs, positioning them as potential therapeutic targets. Interestingly, both diseases have common altered ncRNAs, suggesting that the same molecule can be targeted simultaneously when both diseases coexist. Finally, since some ncRNAs have already been used as therapeutic agents, their roles as potential drugs for the clinical management of atherosclerosis and NAFLD are analyzed.

Silencing circ_0074371 inhibits the progression of sepsis-induced acute kidney injury by regulating miR-330-5p/ELK1 axis

BACKGROUND

Sepsis-induced acute kidney injury (AKI) is a common in clinic. Circular RNAs (circRNAs) play significant roles in ameliorating AKI. The purpose of this study was aimed to identify the role of circ_0074371 and the potential action mechanism in sepsis-induced AKI.

METHODS

AKI patients and healthy individual serum samples were collected and the relative expression of circ_0074371 was measured by real-time polymerase chain reaction (RT-PCR). HK2 cells were treated with different dose (0, 2.5, 5 and 10 μg/ml) lipopolysaccharide (LPS) to establish the AKI cell model. The cell viability and apoptosis of HK2 cells were detected using cell counting kit-8 (CCK-8) and flow cytometry, respectively. The contents of malondialdehyde (MDA), and superoxide dismutase (SOD) were evaluated using the relative commercial kits. The IL-1β and TNF-α levels in cell culture supernatants were measured by ELISA. The interaction relationship between miR-330-5p and circ_0074371 or ELK1 was predicted by Targetscan database and further confirmed by the dual-luciferase reporter assay system.

RESULTS

The circ_0074371 expression was up-regulated in sepsis patients and LPS-induced HK2 cells. Silencing circ_0074371 promoted HK2 cells viability and inhibited the HK2 cells apoptosis. miR-330-5p inhibitor weakened circ_0074371 inhibitor-induced cell viability, apoptosis and oxidative stress. Further mechanism analysis showed that circ_0074371 acted as a sponge for miR-330-5p to increase ELK1 expression level. Importantly, miR-330-5p downregulation or ELK1 upregulation reversed the action of circ_0074371 knockdown on LPS-induced HK2 cells.

CONCLUSION

Knockdown of circ_0074371 ameliorated LPS-induced HK2 cells apoptosis, inflammation and oxidative stress via regulating miR-330-5p/ELK1, opening a new window into the pathogenesis AKI.

Foam Cells in Atherosclerosis: Novel Insights Into Its Origins, Consequences, and Molecular Mechanisms

Foam cells play a vital role in the initiation and development of atherosclerosis. This review aims to summarize the novel insights into the origins, consequences, and molecular mechanisms of foam cells in atherosclerotic plaques. Foam cells are originated from monocytes as well as from vascular smooth muscle cells (VSMC), stem/progenitor cells, and endothelium cells. Novel technologies including lineage tracing and single-cell RNA sequencing (scRNA-seq) have revolutionized our understanding of subtypes of monocyte- and VSMC-derived foam cells. By using scRNA-seq, three main clusters including resident-like, inflammatory, and triggering receptor expressed on myeloid cells-2 (Trem2 ^hi ) are identified as the major subtypes of monocyte-derived foam cells in atherosclerotic plaques. Foam cells undergo diverse pathways of programmed cell death including apoptosis, autophagy, necroptosis, and pyroptosis, contributing to the necrotic cores of atherosclerotic plaques. The formation of foam cells is affected by cholesterol uptake, efflux, and esterification. Novel mechanisms including nuclear receptors, non-coding RNAs, and gut microbiota have been discovered and investigated. Although the heterogeneity of monocytes and the complexity of non-coding RNAs make obstacles for targeting foam cells, further in-depth research and therapeutic exploration are needed for the better management of atherosclerosis.

NCP-BiRW: A Hybrid Approach for Predicting Long Noncoding RNA-Disease Associations by Network Consistency Projection and Bi-Random Walk

Long non-coding RNAs (lncRNAs) play significant roles in the disease process. Understanding the pathological mechanisms of lncRNAs during the course of various diseases will help clinicians prevent and treat diseases. With the emergence of high-throughput techniques, many biological experiments have been developed to study lncRNA-disease associations. Because experimental methods are costly, slow, and laborious, a growing number of computational models have emerged. Here, we present a new approach using network consistency projection and bi-random walk (NCP-BiRW) to infer hidden lncRNA-disease associations. First, integrated similarity networks for lncRNAs and diseases were constructed by merging similarity information. Subsequently, network consistency projection was applied to calculate space projection scores for lncRNAs and diseases, which were then introduced into a bi-random walk method for association prediction. To test model performance, we employed 5- and 10-fold cross-validation, with the area under the receiver operating characteristic curve as the evaluation indicator. The computational results showed that our method outperformed the other five advanced algorithms. In addition, the novel method was applied to another dataset in the Mammalian ncRNA-Disease Repository (MNDR) database and showed excellent performance. Finally, case studies were carried out on atherosclerosis and leukemia to confirm the effectiveness of our method in practice. In conclusion, we could infer lncRNA-disease associations using the NCP-BiRW model, which may benefit biomedical studies in the future.

Association of Polymorphisms within HOX Transcript Antisense RNA (HOTAIR) with Type 2 Diabetes Mellitus and Laboratory Characteristics: A Preliminary Case-Control Study

Type 2 diabetes mellitus (T2DM) is a complex heterogeneous disease resulting from the environment and genetic interactions. Lately, genetic association studies have shown that polymorphisms in long noncoding RNAs (lncRNAs) are associated with T2DM susceptibility. This preliminary study is aimed at investigating if HOX transcript antisense RNA (HOTAIR) polymorphisms contribute to T2DM development. Five hundred clinically diagnosed T2DM cases and 500 healthy controls were recruited from the southeast Iranian population. Genomic DNA was isolated from nucleated blood cells and genotyped for MspI (C/T) (rs920778) and AluI (A/G) (rs4759314) polymorphisms using the PCR-RFLP technique. For genotyping rs12826786 C/T and rs1899663 G/T variants, ARMS-PCR method was applied. Our findings indicated that HOTAIR rs920778 C/T, rs12826786 C/T, and rs4759314 A/G polymorphisms have a significant positive association with T2DM, while a negative association was observed between rs1899663 G/T T2DM susceptibility. Significant associations were also observed between rs920778 C/T and HDL-C as well as s4759314 A/G and both FBS and LDL-C in T2DM patients. Haplotype analysis indicated that the CGCG, CTTG, TGTA, and TTTG haplotypes of rs920778/rs1899663/rs12826786/rs4759314 significantly enhanced T2DM risk by 1.47, 1.96, 2.81, and 4.80 folds, respectively. No strong linkage disequilibrium was found between the four HOTAIR SNPs. We firstly reported that HOTAIR rs1899663 G/T, rs12826786 C/T, rs4759314 A/G, and rs920778 C/T polymorphisms might influence T2DM susceptibility by modulating different signaling pathways and could be regarded as potential prognostic markers in T2DM patients.

Knockdown of circRNA Paralemmin 2 Ameliorates Lipopolysaccharide-induced Murine Lung Epithelial Cell Injury by Sponging miR-330-5p to Reduce ROCK2 Expression

Previous data have reported the high expression of circRNA paralemmin 2 (circPALM2) in mice with acute lung injury (ALI). However, the role of circPALM2 in ALI pathogenesis remains unclear. The study aims to reveal the function of circPALM2 in ALI and the underlying mechanism. C57BL/6 J mice and murine lung epithelial-12 (MLE-12) cells were treated with lipopolysaccharide (LPS) to simulate ALI mouse and ALI cell models, respectively. Lung injury score and lung wet-to-dry ratio assays were used to evaluate the ALI mouse model. Quantitative real-time polymerase chain reaction and Western blot assays were implemented to analyze the expressions of circPALM2, microRNA-330-5p (miR-330-5p), rho-associated coiled-coil containing protein kinase 2 (ROCK2), and apoptosis-related markers. Cell viability, apoptosis, and the production of inflammatory cytokines were investigated by cell counting kit-8, flow cytometry, and enzyme-linked immunosorbent assays. The expressions of circPALM2 and ROCK2 were significantly increased, while miR-330-5p was decreased in ALI mice and LPS-induced MLE-12 cells compared with controls. LPS treatment inhibited cell viability but induced apoptosis, inflammatory cytokine production, and oxidative stress; however, these effects were attenuated after the combination of circPALM2 knockdown and LPS. CircPALM2 regulated LPS-caused MLE-12 cell damage by targeting miR-330-5p. Additionally, ROCK2, a target gene of miR-330-5p, participated in LPS-induced MLE-12 cell injury. Further, circPALM2 activated ROCK2 by associating with miR-330-5p. CircPALM2 modulated LPS-caused murine lung epithelial cell injury by the miR-330-5p/ROCK2 pathway, providing a therapeutic target for ALI.

Hsa_circ_0003204 Knockdown Weakens Ox-LDL-Induced Cell Injury by Regulating miR-188-3p/TRPC6 Axis in Human Carotid Artery Endothelial Cells and THP-1 Cells

Background: Circular RNAs (circRNAs) are involved in atherosclerosis (AS) development. However, the function and mechanism of circRNA hsa_circ_0003204 (circ_0003204) in carotid artery AS remain unclear.

Methods: Oxidized low-density lipoprotein (ox-LDL)-treated human carotid artery endothelial cells (HCtAECs) and THP-1 cells were used as cell models of carotid artery AS. Relative levels of circ_0003204, microRNA-188-3p (miR-188-3p), and transient receptor potential canonical channel 6 (TRPC6) were detected by quantitative reverse transcription–polymerase chain reaction or Western blotting. The targeting relationship between circ_0003204 or TRPC6 and miR-188-3p was assessed via dual-luciferase reporter analysis and RNA immunoprecipitation. Cell proliferation was assessed via 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay and 5-ethynyl-2′-deoxyuridine (EdU) assay. Cell apoptosis was analyzed via assessing cell caspase-3 activity, apoptosis, and apoptosis-related protein. Inflammatory response was analyzed via analysis of interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α). Oxidative stress was assessed via determination of reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD).

Results: Circ_0003204 and TRPC6 levels were elevated, and miR-188-3p expression declined in ox-LDL-treated HCtAECs and THP-1 cells. Circ_0003204 could regulate TRPC6 expression via mediating miR-188-3p. Circ_0003204 silencing weakened ox-LDL-induced viability inhibition and apoptosis in HCtAECs, and inflammatory response and oxidative stress in THP-1 cells via regulating miR-188-3p. MiR-188-3p overexpression attenuated ox-LDL-induced injury in HCtAECs and THP-1 cells by targeting TRPC6.

Conclusion: Circ_0003204 knockdown mitigated ox-LDL-induced injury in HCtAECs and THP-1 cells via regulating the miR-188-3p/TRPC6 axis, indicating that circ_0003204 might play an important role in carotid artery AS.

The Combined Regulation of Long Non-coding RNA and RNA-Binding Proteins in Atherosclerosis

Atherosclerosis is a complex disease closely related to the function of endothelial cells (ECs), monocytes/macrophages, and vascular smooth muscle cells (VSMCs). Despite a good understanding of the pathogenesis of atherosclerosis, the underlying molecular mechanisms are still only poorly understood. Therefore, atherosclerosis continues to be an important clinical issue worthy of further research. Recent evidence has shown that long non-coding RNAs (lncRNAs) and RNA-binding proteins (RBPs) can serve as important regulators of cellular function in atherosclerosis. Besides, several studies have shown that lncRNAs are partly dependent on the specific interaction with RBPs to exert their function. This review summarizes the important contributions of lncRNAs and RBPs in atherosclerosis and provides novel and comprehensible interaction models of lncRNAs and RBPs.

Knockdown of circular RNA hsa_circ_0003204 inhibits oxidative stress and apoptosis through the miR-330-5p/Nod2 axis to ameliorate endothelial cell injury induced by low-density lipoprotein

Introduction

Atherosclerosis (AS) is the leading cause of cardiovascular disease. Circular RNA hsa_circ_0003204 (hsa_circ_0003204) was elevated in oxidized low-density lipoprotein (ox-LDL)-induced human umbilical vein endothelial cells. However, the role and molecular mechanism of hsa_circ_0003204 in the AS process have not been studied.

Material and methods

Human primary aortic endothelial cells (HAECs) were treated with low-density lipoprotein (ox-LDL) to establish the AS model. The viability of ox-LDL-induced HAECs was assessed by counting kit-8 (CCK8) assay. Reactive oxygen species (ROS), malondialdehyde (MDA) and superoxide dismutase (SOD) levels in ox-LDL-induced HAECs supernatant were evaluated with the relevant kits. The apoptosis of ox-LDL-induced HAECs was determined via flow cytometry assay. The expression of hsa_circ_0003204, miR-330-5p, and nucleotide-binding oligomerization domain 2 (Nod2) was analyzed through quantitative real-time polymerase chain reaction (qRT-PCR). The relationship between hsa_circ_0003204 or Nod2 and miR-330-5p was verified by dual-luciferase reporter assay. Protein level of Nod2 was detected using western blot analysis.

Results

Hsa_circ_0003204 and Nod2 were upregulated while miR-330-5p was decreased in ox-LDL-induced HAECs. Hsa_circ_0003204 depletion restrained the oxidative stress and apoptosis of ox-LDL-induced HAECs. Notably, hsa_circ_0003204 regulated Nod2 expression via sponging miR-330-5p in HAECs. Moreover, miR-330-5p inhibition restored the constraint of the oxidative stress and apoptosis of ox-LDL-induced HAECs caused by hsa_circ_0003204 silencing. Additionally, miR-330-5p targeted Nod2 and Nod2 enhancement abolished the repressive effects of miR-330-5p overexpression on the oxidative stress and apoptosis of ox-LDL-induced HAECs.

Conclusions

Hsa_circ_0003204 exhaustion mitigated endothelial cell injury through suppressing the oxidative stress and apoptosis in ox-LDL-induced HAECs via the miR-330-5p/Nod2 axis.

Aberrant Post-Transcriptional Regulation of Protein Expression in the Development of Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is an incurable and prevalent respiratory disorder that is characterized by chronic inflammation and emphysema. COPD is primarily caused by cigarette smoke (CS). CS alters numerous cellular processes, including the post-transcriptional regulation of mRNAs. The identification of RNA-binding proteins (RBPs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) as main factors engaged in the regulation of RNA biology opens the door to understanding their role in coordinating physiological cellular processes. Dysregulation of post-transcriptional regulation by foreign particles in CS may lead to the development of diseases such as COPD. Here we review current knowledge about post-transcriptional events that may be involved in the pathogenesis of COPD.

Comprehensive Bioinformatics Analysis of Lipopolysaccharide-Induced Altered Autophagy in Acute Lung Injury and Construction of Underlying Competing Endogenous RNA Regulatory Mechanism

Background

Acute lung injury (ALI) is a fatal syndrome frequently induced by lipopolysaccharide (LPS) released from the bacterial cell wall. LPS could also trigger autophagy of lung bronchial epithelial cell to relieve the inflammation, while the overwhelming LPS would impair the balance of autophagy consequently inducing serious lung injury.

Methods

We observed the autophagy variation of 16HBE, human bronchial epithelial cell, under exposure to different concentrations of LPS through western blot, immunofluorescence staining, and electron microscopy. Eight strands of 16HBE were divided into two groups upon 1000 ng/ml LPS stimulation or not, which were sent to be sequenced at whole transcriptome. Subsequently, we analyzed the sequencing data in functional enrichment, pathway analysis, and candidate gene selection and constructed a hsa-miR-663b-related competing endogenous RNA (ceRNA) network.

Results

We set a series of concentrations of LPS to stimulate 16HBE and observed the variation of autophagy in related protein expression and autophagosome count. We found that the effective concentration of LPS was 1000 ng/ml at 12 hours of exposure and sequenced the 1000 ng/ml LPS-stimulated 16HBE. As a result, a total of 750 differentially expressed genes (DEGs), 449 differentially expressed lncRNAs (DElncRNAs), 76 differentially expressed circRNAs (DEcircRNAs), and 127 differentially expressed miRNAs (DEmiRNAs) were identified. We constructed the protein-protein interaction (PPI) network to visualize the interaction between DEGs and located 36 genes to comprehend the core discrepancy between LPS-stimulated 16HBE and the negative control group. In combined analysis of differentially expressed RNAs (DERNAs), we analyzed all the targeted relationships of ceRNA in DERNAs and figured hsa-miR-663b as a central mediator in the ceRNA network to play when LPS induced the variation of autophagy in 16HBE.

Conclusion

Our research indicated that the hsa-miR-663b-related ceRNA network may contribute to the key regulatory mechanism in LPS-induced changes of autophagy and ALI.

Silencing lncRNA HOTAIR improves the recovery of neurological function in ischemic stroke via the miR-148a-3p/KLF6 axis

Ischemic stroke (IS), caused by a permanent or transient local reduction in blood supply to the brain, is one of the most widespread causes of public health problems in modern society. Long non-coding RNA (LncRNA) has been reported to be related to angiogenesis following IS. In this study, we explored the effect and potential molecular mechanism of lncRNA homeobox antisense non-coding RNA (HOTAIR) in IS. Permanent middle cerebral artery occlusion (pMCAO) model and oxygen and glucose deprivation (OGD) model were established. HOTAIR was increased in vivo and in vitro models post-ischemic. HOTAIR knockdown promoted neurological function recovery, manifesting in decreased modified neurological severity score, cerebral infarcted area, apoptosis and inflammation, and improved balance ability, spatial learning and memory ability. Silencing HOTAIR also improved the viability of OGD-induced N2a cells, and attenuated apoptosis and inflammation. HOTAIR can compete with KLF6 to bind to miR-148a-3p. miR-148a-3p knockdown or KLF6 overexpression partially reversed the effect of sh-HOTAIR on OGD-induced N2a cells. HOTAIR suppressed the activation of STAT3 pathway via the miR-148a-3p/KLF6 axis. To summarize, this study demonstrated that lncRNA HOTAIR absorbed miR-148a-3p and up-regulated KLF6 expression through ceRNA mechanism, and inhibited STAT3 pathway, promoted apoptosis and inflammation, and aggravated neurological injury post-IS.

MiRNAs Correlate with HLA Expression in Uveal Melanoma: Both Up- and Downregulation Are Related to Monosomy 3

Simple Summary

Uveal melanoma (UM) is a rare ocular malignancy that often gives rise to metastases. Tumours with an inflammatory phenotype have an especially bad prognosis. As an increased HLA expression and the presence of tumour-infiltrating lymphocytes and macrophages may be regulated by miRNAs, we set out to investigate whether any miRNAs are associated with inflammatory parameters in this malignancy. Some miRNAs were increased in UM with a high HLA expression and high T cell numbers, while others were decreased, showing two opposing patterns; however, both patterns were related to the tumour’s chromosome 3/BAP1 status. We conclude that specific miRNAs are related to the inflammatory phenotype and that these are differentially expressed between disomy 3/BAP1-positive versus monosomy 3/BAP1-negative UM.

Abstract

MicroRNAs are known to play a role in the regulation of inflammation. As a high HLA Class I expression is associated with a bad prognosis in UM, we set out to determine whether any miRNAs were related to a high HLA Class I expression and inflammation. We also determined whether such miRNAs were related to the UM’s genetic status. The expression of 125 miRNAs was determined in 64 primary UM from Leiden. Similarly, the mRNA expression of HLA-A, HLA-B, TAP1, BAP1, and immune cell markers was obtained. Expression levels of 24 of the 125 miRNAs correlated with expression of at least three out of four HLA Class I probes. Four miRNAs showed a positive correlation with HLA expression and infiltration with leukocytes, 20 a negative pattern. In the first group, high miRNA levels correlated with chromosome 3 loss/reduced BAP1 mRNA expression, in the second group low miRNA levels. The positive associations between miRNA-22 and miRNA-155 with HLA Class I were confirmed in the TCGA study and Rotterdam cohort, and with TAP1 in the Rotterdam data set; the negative associations between miRNA-125b2 and miRNA-211 and HLA-A, TAP1, and CD4 were confirmed in the Rotterdam set. We demonstrate two patterns: miRNAs can either be related to a high or a low HLA Class I/TAP1 expression and the presence of infiltrating lymphocytes and macrophages. However, both patterns were associated with chromosome 3/BAP1 status, which suggests a role for BAP1 loss in the regulation of HLA expression and inflammation in UM through miRNAs.

Long Noncoding RNA MALAT1 Regulates the Progression of Atherosclerosis by miR-330-5p/NF-κB Signal Pathway

ABSTRACT

Long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) was reported to be related to atherosclerosis (AS) progression. However, the underlying mechanism of MALAT1 in AS remains unknown. Quantitative real-time polymerase chain reaction was performed to detect the expression of MALAT1 and miR-330-5p. Western blot was applied to assess the protein levels of cluster of differentiation 36, interleukin-1β, interleukin-6 and tumor necrosis factor-α, phosphorylation of nuclear factor kappa-B inhibitor alpha and phosphorylation of p65. Flow cytometry assay, cell counting kit 8 assay, triglyceride, and total cholesterol detection assays were used to detect the apoptosis, viability, and lipid indexes of THP-1 macrophages-derived foam cells. Online database starbasev2.0 was used to predict the binding sequences between MALAT1 and miR-330-5p and it was verified by dual-luciferase reporter system and RNA immunoprecipitation assay. Besides, an AS mice model was used to evaluate the effect of MALAT1 in vivo. As a result, MALAT1 was overexpressed, whereas miR-330-5p was downregulated in THP-1 macrophages-derived foam cells. MiR-330-5p was a target of MALAT1. MALAT1 depletion inhibited cell formation, apoptosis, and inflammation in THP-1 macrophages-derived foam cells. Besides, MALAT1 overexpression promoted the inflammation in AS mice model, which promoted the pathogenesis of AS. Furthermore, miR-330-5p regulated the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway in THP-1 macrophages-derived foam cells. Moreover, MALAT1 regulated NF-κB signal pathway to mediate the pathogenesis of AS by sponging miR-330-5p. MALAT1 sponges miR-330-5p to activate NF-κB signal pathway in THP-1 macrophages-derived foam cells. This finding may provide a novel biomarker for AS diagnosis.

Plasma miRNAs improve the prediction of coronary atherosclerosis in patients with rheumatoid arthritis

OBJECTIVE

MicroRNAs (miRNAs) regulate gene expression and are disease biomarkers. Rheumatoid arthritis (RA) patients have accelerated atherosclerosis leading to excess cardiovascular morbidity and mortality, but traditional risk factors for cardiovascular risk stratification are inadequate. In the general population, miRNAs improve cardiovascular risk estimation beyond traditional risk factors. Our objective was to develop a miRNA panel that predicts coronary atherosclerosis in RA patients.

METHODS

Plasma small RNA next-generation sequencing (NGS) was performed on 161 RA patients whose Agatston scores for coronary artery calcium were previously measured. Random forest analysis of plasma NGS miRNA expression was used to determine which miRNAs best differentiated between those patients with and without coronary artery calcium. Top predictive miRNAs were assayed by quantitative PCR (qPCR). Elastic net regression was used to develop the most parsimonious models with qPCR-measured miRNA concentrations and clinical variables (age, sex, ACC/AHA 10-year risk score, DAS28 score, and diabetes) separately to predict the presence of coronary artery calcium and high coronary artery calcium. C-statistics were used to assess performance model performance.

RESULTS

The top miRNAs which differentiated those with and without coronary atherosclerosis based on random forest analysis included let-7c-5p, miR-30e-5p, miR-30c-5p, miR-4446-3p, miR-126-5p, miR-3168, miR-425-5p, miR-126-3p, miR-30a-5p, and miR-125a-5p. For coronary artery calcium prediction, addition of all miRNAs except miR-126-3p to clinical factors improved the c-statistic modestly from 0.86 to 0.87. For high coronary artery calcium prediction, addition of all miRNAs except miR-30c-5p to clinical factors improved the c-statistic from 0.75 to 0.80.

CONCLUSION

A plasma miRNA panel improved the prediction of high coronary artery calcium beyond traditional risk factors and RA disease activity. Further evaluation of the miRNA panel for prediction of coronary events in RA is necessary. Key Point • A plasma microRNA panel including let-7c-5p, miR-30a-5p, miR-30e-5p, miR-125a-5p, miR-126-3p, miR-126-5p, miR-425-5p, miR-3168, and miR-4446-3p improved the prediction of high coronary artery calcium beyond clinical factors in patients with rheumatoid arthritis.

LncRNA OIP5-AS1 accelerates ox-LDL-treated HUVECs injury by NF-κB pathway via miR-30c-5p

BACKGROUND

Oxidized low-density lipoprotein (ox-LDL) could induce endothelial injury and played a vital role in the progression and development of atherosclerosis. This study aimed to investigate the role of Opa-interacting protein 5 antisense RNA 1 (OIP5-AS1) in ox-LDL-induced human umbilical vascular endothelial cells (HUVECs) injury and the potential mechanisms.

METHODS

Cell proliferation and apoptosis were evaluated by Cell Counting Kit-8 (CCK-8) assay and flow cytometry assay, respectively. The levels of lactate dehydrogenase (LDH), reactive oxygen species (ROS), malondialdehyde (MDA), superoxide dismutase (SOD) and nitric oxide (NO) were detected by corresponding detection kits, respectively. Quantitative real-time PCR (qRT-PCR) was conducted to measure the expression of OIP5-AS1 or microRNA-30c-5p (miR-30c-5p) in HUVECs. Binding between OIP5-AS1 and miR-30c-5p was predicted through bioinformatics analysis and confirmed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP). Western blot was used to analyze p-IκB, IκB, p-p65 and p65 levels.

RESULTS

In HUVECs, exposure to ox-LDL led to a decrease in cell viability and an increase in LDH release and apoptosis with concomitant enhancement of oxidative stress, as evidenced by increased ROS and MDA generation, as well as decreased SOD activity and NO levels, while OIP5-AS1 knockdown or miR-30c-5p upregulation could rescue these effects above. Mechanically, OIP5-AS1 functioned as a sponge of miR-30c-5p. OIP5-AS1-induced injury and apoptosis, oxidative stress and activation of NF-κB pathway were reversed by miR-30c-5p in ox-LDL-treated HUVECs.

CONCLUSION

OIP5-AS1 contributed to ox-LDL-treated HUVECs injury by activation of NF-κB pathway via miR-30c-5p.

Knockdown of circ_0003204 alleviates oxidative low-density lipoprotein-induced human umbilical vein endothelial cells injury: Circulating RNAs could explain atherosclerosis disease progression

Atherosclerosis (AS) is a serious cardiovascular disease. Circular RNAs (circRNAs) play an important role in the progression of many diseases, including AS. However, the role of circ_0003204 in AS is not clear. Oxidized low-density lipoprotein (ox-LDL)-induced human umbilical vein endothelial cells (HUVECs) were used to construct an AS cell model in vitro. Cell viability was assessed using cell counting kit 8 (CCK8) assay. Flow cytometry and caspase-3 activity were used to measure cell apoptosis. The contents of inflammatory cytokines were measured using enzyme-linked immunosorbent assay (ELISA). Oxidative stress marker expression and cell injury marker activity were detected by their corresponding Assay Kits. Besides, the expression levels of circ_0003204, miR-330-5p, and toll-like receptor 4 (TLR4) were tested by real-time polymerase chain reaction (qPCR). The interaction between miR-330-5p and circ_0003204 or TLR4 was examined by dual-luciferase reporter assay and RNA pull-down assay. Western blot (WB) analysis was used to determine the levels of TLR4 protein and nuclear factor-kappa B (NF-κB) signaling pathway-related protein. Our data suggested that ox-LDL could suppress viability and promote apoptosis, inflammatory response, and oxidative stress in HUVECs. circ_0003204 was highly expressed in ox-LDL-induced HUVECs, and its silencing could inhibit ox-LDL-induced HUVECs injury. miR-330-5p could be sponged by circ_0003204, and its inhibitor could reverse the inhibition effect of silenced circ_0003204 on ox-LDL-induced HUVECs injury. Further, TLR4 could be targeted by miR-330-5p, and its overexpression could invert the suppression effect of miR-330-5p on ox-LDL-induced HUVECs injury. The activity of the NF-κB signaling pathway was regulated by the circ_0003204/miR-330-5p/TLR4 axis. Our results indicated that circ_0003204 silencing could alleviate ox-LDL-induced HUVECs injury, suggesting that circ_0003204 might be a novel target for AS treatment.

Emerging roles of non-coding RNAs in the metabolic reprogramming of tumor-associated macrophages

Macrophages are the most common immune cells in the tumor microenvironment, and tumor-associated macrophages play an important role in cancer development. Metabolic reprogramming is important for the functional plasticity of macrophages. Studies investigating the relevance of non-coding RNAs (ncRNAs) in human cancer found that ncRNAs can regulate the metabolism of cancer cells and tumor-associated macrophages. NcRNAs include short ncRNAs, long ncRNAs (lncRNAs), and circular RNAs (circRNAs). The most common short ncRNAs are microRNAs, which regulate glucose, lipid, and amino acid metabolism in macrophages by acting on metabolism-related pathways and targeting metabolism-related enzymes and proteins, and are therefore involved in cancer progression. The role of lncRNAs and circRNAs in the metabolism of tumor-associated macrophages remains unclear. LncRNAs affect the glucose metabolism of macrophages, whereas their role in lipid and amino acid metabolism is not clear. CircRNAs regulate amino acid metabolism in macrophages. The roles of ncRNAs in energy metabolism and the underlying mechanisms need to be investigated further. Here, we summarize recent findings on the involvement of ncRNAs in metabolic reprogramming in tumor-associated macrophages, which affect the tumor microenvironment and play important roles in the development of cancer. Improving our understanding of the effects of ncRNAs on metabolic reprogramming of tumor-associated macrophages may facilitate the development of effective clinical therapies.

miR-330 alleviates dextran sodium sulfate-induced ulcerative colitis through targeting IRAK1 in rats

Ulcerative colitis (UC) is a chronic multifactorial inflammatory bowel disease that severely impairs patients' life quality. microRNAs (miRNAs) have been reported to exhibit potential therapeutic effects in the management of UC. With the aim to investigate the regulatory effects of miR-330 on UC-related colon tissue damage and inflammation, a rat model of experimental colitis was established by oral administration of dextran sodium sulfate (DSS). DSS-treated rats showed mucosal damage, colonic inflammation, and elevated myeloperoxidase activity compared with the healthy controls. Dual-luciferase reporter assay confirmed the binding of interleukin-1 receptor-associated kinase 1 (IRAK1) and miR-330. Subsequently, rats were intracolonically injected with miR-330 argomir with/without administration of IRAK1 during DSS treatment. The miR-330 overexpression reduced DSS-induced colonic injury and the production of proinflammatory cytokines. The level of IRAK1 was negatively regulated by the expression of miR-330. IRAK1 overexpression abolished the protective effect of miR-330 on DSS-induced colonic inflammation and mucosal injury in rats. In conclusion, we clarify the role of miR-330 in pathogenesis of UC, suggesting miR-330 alleviated DSS-induced colitis by downregulating IRAK1, shedding lights on miR-330 as a therapeutic candidate for UC treatment.

Long Noncoding RNAs in the Progression of Atherosclerosis: An Integrated Analysis Based on Competing Endogenous RNA Theory

Long noncoding RNAs (lncRNAs) have been increasingly accepted to function importantly in human diseases by serving as competing endogenous RNAs (ceRNAs). To date, the ceRNA mechanisms of lncRNAs in the progression of atherosclerosis (AS) remain largely unclear. On the basis of ceRNA theory, we implemented a multistep computational analysis to construct an lncRNA-mRNA network for AS progression (ASpLMN). The probe reannotation method and microRNA-target interactions from databases were systematically integrated. Three lncRNAs (GS1-358P8.4, OIP5-AS1, and TUG1) with central topological features in the ASpLMN were firstly identified. By using subnetwork analysis, we then obtained two highly clustered modules and one dysregulated module from the ASpLMN network. These modules, sharing three lncRNAs (GS1-358P8.4, OIP5-AS1, and RP11-690D19.3), were significantly enriched in biological pathways such as regulation of actin cytoskeleton, tryptophan metabolism, lysosome, and arginine and proline metabolism. In addition, random walking in the ASpLMN network indicated that lncRNA RP1-39G22.7 and MBNL1-AS1 may also play an essential role in the pathology of AS progression. The identified six lncRNAs from the aforementioned steps could distinguish advanced- from early-staged AS, with a strong diagnostic power for AS occurrence. In conclusion, the results of this study will improve our understanding about the ceRNA-mediated regulatory mechanisms in AS progression, and provide novel lncRNAs as biomarkers or therapeutic targets for acute cardiovascular events.

LINC01140 Alleviates the Oxidized Low-Density Lipoprotein-Induced Inflammatory Response in Macrophages via Suppressing miR-23b

Our previous study has demonstrated that miR-23b enhances oxidized low-density lipoprotein (oxLDL)-induced inflammatory response of macrophages through the A20/NF-κB signaling pathway, thus contributing to atherosclerosis. This study aims to further investigate the upstream regulators of miR-23b in mediating oxLDL-induced inflammatory response. Human monocyte cell line THP1 was induced to differentiate into macrophages followed by the oxLDL stimulation of inflammatory response. The expression of miR-23b, LINC01140, and p53 mRNA was detected by quantitative PCR. The combination of miR-23b and LINC01140 was confirmed by luciferase reporter assay and RNA immunoprecipitation. The binding of p53 and LINC01140 promoter was determined by luciferase reporter assay. The level of inflammatory cytokines, including MCP-1, TNF-α, and IL-1β, was assessed by enzyme-linked immunosorbent assay. LINC01140 was downregulated, while p53 and miR-23b were upregulated in oxLDL-induced inflammatory response of macrophages. Overexpression of LINC01140 reduced NF-κB activity by reducing miR-23b and increasing A20. The transcription of LINC01140 was inhibited by binding of p53 and the LINC01140 promoter region. Knockdown of p53 significantly reduced NF-κB activity and level of inflammatory cytokines by promoting LINC01140 expression. Our findings demonstrated that LINC01140 acts as an anti-inflammatory factor through negatively regulating miR-23/A20 axis. In addition, p53 is identified as a transcriptional repressor of LINC01140.

miR-330-5p inhibits NLRP3 inflammasome-mediated myocardial ischaemia-reperfusion injury by targeting TIM3

BACKGROUND/AIMS

The Nod-like receptor protein-3 (NLRP3) inflammasome signalling pathway is involved in the inflammatory reaction of myocardial ischaemia-reperfusion (I/R) injury. Our previous study showed that miR-330-5p was differentially expressed in both cerebral and myocardial I/R injury, and thus might be a biomarker for I/R injury-related diseases. Another study also indicated that miR-330-5p could promote NLRP3 inflammasome activation in renal IRI. However, the role of miR-330-5p in myocardial I/R injury-induced inflammatory responses is unknown. This study aimed to investigate the role of miR-330-5p in NLRP3 inflammasome-mediated myocardial I/R injury.

METHODS

Myocardial I/R injury was induced in mice by occlusion of the left anterior descending coronary artery for 45 min followed by reperfusion. For NLRP3 inflammasome stimulation in vitro, cardiomyocytes were treated with 2 h of oxygen and glucose deprivation (OGD) or LPS (100 ng/ml). Myocardial miR-330-5p expression was examined by PCR at different treatment times. A miR-330-5p antagomir and an agomir were used to regulate miR-330-5p expression. To evaluate the role of miR-330-5p in myocardial I/R injury, 2,3,5-triphenyltetrazolium chloride (TTC) staining, echocardiography, and immunoblotting were used to assess infarct volume, cardiac function, and NLRP3 inflammasome activation respectively. A luciferase binding assay was used to examine whether miR-330-5p could directly bind to the T cell immunoglobulin domain and mucin domain-containing molecule-3 (TIM3). Finally, the role of the miR-330-5p/TIM3 axis in regulating apoptosis and NLRP3 inflammasome formation was evaluated with flow cytometry assays and immunofluorescence staining.

RESULTS

Compared to that in the model group, the inhibition of miR-330-5p significantly aggravated myocardial I/R injury, resulting in increased infarct volume and more severe cardiac dysfunction. Moreover, inhibition of miR-330-5p significantly increased the levels of NLRP3 inflammasome-related proteins, including caspase-1, IL-1β, IL-18 and TNF-α, in both in-vivo and in-vitro models. Furthermore, TIM3 was confirmed as a potential target of miR-330-5p. As predicted, suppression of TIM3 by siRNA ameliorated the anti-miR-330-5p-mediated activation of the NLRP3 inflammasome induced by OGD and LPS, thus decreasing cardiomyocyte apoptosis.

CONCLUSIONS

Our study indicated that the miR-330-5p/TIM3 axis was involved in the regulatory mechanism of NLRP3 inflammasome-mediated myocardial inflammation.

Downregulating lncRNA PRNCR1 ameliorates LPS-induced pulmonary vascular endothelial cell injury by modulating miR-330-5p/TLR4 axis

Pulmonary vascular endothelial cell (PVEC) injury following acute lung injury or acute respiratory distress syndrome seriously affects disease development. Recently, accumulating evidence has suggested that long noncoding RNA (lncRNA) exerts significant effects in vascular endothelial cell injury. However, PRNCR1, a novel lncRNA, remains scarcely understood in terms of its functions in PVEC injury. Both in vivo and in vitro models of PVEC injury were constructed by lipopolysaccharide (LPS) administration. The relative expressions of PRNCR1, miR-330-5p, and TLR4 were detected by quantitative reverse transcription-polymerase chain reaction, Western blot, and immunohistochemistry. Besides, gain and loss assays of PRNCR1/miR-330-5p were conducted to verify their effects on LPS-induced PVEC injury. Cell Counting Kit-8 assay used to measure cell viability and flow cytometry was used to detect apoptosis. Besides, the protein levels of caspase 3, nuclear factor-κB (NF-κB), and inflammatory cytokines (including tumor necrosis factor-α, interleukin-1β [IL-1β], and IL-6) were evaluated via Western blot and enzyme-linked immunosorbent assay. Moreover, a dual-luciferase activity experiment and RNA immunoprecipitation were applied to confirm the targeting relationship between PRNCR1 and miR-330-5p, miR-330-5p, and TLR4. PRNCR1 and TLR4 levels were significantly upregulated in LPS-treated PVEC, both in vivo and in vitro, while miR-330-5p were downregulated. Inhibiting PRNCR1 or overexpressing miR-330-5p markedly attenuated LPS-induced PVEC injury, expressions of TLR4, NF-κB, and inflammatory cytokines. Mechanistically, PRNCR1 functioned as a competitive endogenous RNA by sponging miR-330-5p and then promoting TLR4 expression. PRNCR1 was upregulated in LPS-induced PVEC and aggravated its injury via modulating the miR-330-5p/TLR4 axis.

Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease

Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their function in these contexts. Long non-coding RNAs (lncRNAs) have emerged as significant regulators of macrophage function; as such, there is rising interest in understanding how these nucleic acids influence macrophage signaling, cell fate decisions, and activity in health and disease. In this review, we summarize current knowledge regarding lncRNAs in directing various aspects of macrophage function in CVD. These include foam cell formation, Toll-like receptor (TLR) and NF-kβ signaling, and macrophage phenotype switching. This review will provide a comprehensive understanding concerning previous, ongoing, and future studies of lncRNAs in macrophage functions and their importance in CVD.

The Long Non-Coding RNA Landscape of Atherosclerotic Plaques

Currently, cardiovascular diseases continue to be the leading cause of death worldwide; therefore, atherosclerosis remains one of the most crucial public health problems. This chronic and complex disease is considered to be a result of aberrant lipid homeostasis and inflammation of the inner wall of arteries that leads to plaque development. In recent years, a specific class of non-coding RNAs that are characterised by transcript lengths longer than 200 nucleotides, called long non-coding RNAs (lncRNAs), has emerged. Moreover, a growing body of evidence indicates that deregulation of lncRNA expression may contribute to the development of many diseases. Despite continuous efforts in deciphering the molecular basis of atherosclerotic plaque (AP) formation, many aspects of this process remain elusive. Therefore, continuing efforts in this area should remain the highest priority in the coming years. Establishment of a standardised experimental pipeline and validation of lncRNAs as possible relevant biomarkers for cardiovascular disease would enable the translation of gathered findings into clinical practice.

Modulators of MicroRNA Function in the Immune System

MicroRNAs (miRNAs) play a key role in fine-tuning host immune homeostasis and responses through the negative regulation of mRNA stability and translation. The pathways regulated by miRNAs are well characterized, but the precise mechanisms that control the miRNA-mediated regulation of gene expression during immune cell-development and immune responses to invading pathogens are incompletely understood. Context-specific interactions of miRNAs with other RNA species or proteins may modulate the function of a given miRNA. Dysregulation of miRNA function is associated with various human diseases, such as cardiovascular diseases and cancers. Here, we review the potential modulators of miRNA function in the immune system, including the transcription regulators of miRNA genes, miRNA-processing enzymes, factors affecting miRNA targeting, and intercellular communication.

Long Non-Coding RNAs Link Oxidized Low-Density Lipoprotein With the Inflammatory Response of Macrophages in Atherogenesis

Atherosclerosis is characterized as a chronic inflammatory response to cholesterol deposition in arteries. Low-density lipoprotein (LDL), especially the oxidized form (ox-LDL), plays a crucial role in the occurrence and development of atherosclerosis by inducing endothelial cell (EC) dysfunction, attracting monocyte-derived macrophages, and promoting chronic inflammation. However, the mechanisms linking cholesterol accumulation with inflammation in macrophage foam cells are poorly understood. Long non-coding RNAs (lncRNAs) are a group of non-protein-coding RNAs longer than 200 nucleotides and are found to regulate the progress of atherosclerosis. Recently, many lncRNAs interfering with cholesterol deposition or inflammation were identified, which might help elucidate their underlying molecular mechanism or be used as novel therapeutic targets. In this review, we summarize and highlight the role of lncRNAs linking cholesterol (mainly ox-LDL) accumulation with inflammation in macrophages during the process of atherosclerosis.

Targeting of IL-6-Relevant Long Noncoding RNA Profiles in Inflammatory and Tumorous Disease

Interleukin-6 (IL-6) is a critical cytokine with a diverse repertoire of physiological functions. Dysregulation of IL-6 signaling is associated with inflammatory disorders as well as cancers. However, blockade of IL-6 activity via antibodies directed against the IL-6 signaling pathway may compromise the efficacy of the immune system; therefore, patients may not have a uniformly satisfactory response to treatment. Long noncoding RNAs (lncRNAs) have been discovered to be evolutionary conserved transcripts of noncoding DNA sequences and have emerged as biomarkers with great predictive and prognostic value, further employed as a targeted anticancer therapy. LncRNAs have been recently implicated in the regulation of IL-6-related signaling and function; they are tightly linked to the development of a range of IL-6 dysregulated diseases. Here, we will highlight those lncRNAs involved in IL-6 signaling, with an emphasis on the mechanisms of lncRNAs that interact with IL-6. Targeting of such lncRNAs related to IL-6 regulation could be, in the near future, a promising therapeutic strategy in the treatment of inflammatory- and tumor-related diseases.

lncRNA-Triggered Macrophage Inflammaging Deteriorates Age-Related Diseases

Aging and age-related diseases (ARDs) share basic mechanisms largely involving inflammation. A chronic, low-grade, subclinical inflammation called inflammaging occurs during aging. Autophagy defects, oxidative stresses, senescence-associated secretory phenotypes (SASPs), and DNA damage generally contribute to inflammaging and are largely regulated by numerous lncRNA through two-level vicious cycles disrupting cellular homeostasis: (1) inflammaging and the cellular senescence cascade and (2) autophagy defects, oxidative stress, and the SASP cascade. SASPs and inflammasomes simultaneously cause inflammaging. This review discusses the involvement of macrophage inflammaging in various ARDs and its regulation via lncRNA. Among macrophages, this phenomenon potentially impairs its immunosurveillance and phagocytosis mechanisms, leading to decreased recognition and clearance of malignant and senescent cells. Moreover, SASPs extracellularly manifest to induce paracrine senescence. Macrophage senescence escalates to organ level malfunction, and the organism is more prone to ARDs. By targeting genes and proteins or functioning as competing endogenous RNA (ceRNA), lncRNA regulates different phenomena including inflammaging and ARDs. The detailed mechanism warrants further elucidation to obtain pathological evidence of ARDs and potential treatment approaches.

The interplay of signaling pathway in endothelial cells-matrix stiffness dependency with targeted-therapeutic drugs

Cardiovascular diseases (CVDs) have been one of the major causes of human deaths in the world. The study of CVDs has focused on cell chemotaxis for decades. With the advances in mechanobiology, accumulating evidence has demonstrated the influence of mechanical stimuli on arterial pathophysiology and endothelial dysfunction that is a hallmark of atherosclerosis development. An increasing number of drugs have been exploited to decrease the stiffness of vascular tissue for CVDs therapy. However, the underlying mechanisms have yet to be explored. This review aims to summarize how matrix stiffness mediates atherogenesis through various important signaling pathways in endothelial cells and cellular mechanophenotype, including RhoA/Rho-associated protein kinase (ROCK), mitogen-activated protein kinase (MAPK), and Hippo pathways. We also highlight the roles of putative mechanosensitive non-coding RNAs in matrix stiffness-mediated atherogenesis. Finally, we describe the usage of tunable hydrogel and its future strategy to improve our knowledge underlying matrix stiffness-mediated CVDs mechanism.

Targeting Foam Cell Formation in Atherosclerosis: Therapeutic Potential of Natural Products

Foam cell formation and further accumulation in the subendothelial space of the vascular wall is a hallmark of atherosclerotic lesions. Targeting foam cell formation in the atherosclerotic lesions can be a promising approach to treat and prevent atherosclerosis. The formation of foam cells is determined by the balanced effects of three major interrelated biologic processes, including lipid uptake, cholesterol esterification, and cholesterol efflux. Natural products are a promising source for new lead structures. Multiple natural products and pharmaceutical agents can inhibit foam cell formation and thus exhibit antiatherosclerotic capacity by suppressing lipid uptake, cholesterol esterification, and/or promoting cholesterol ester hydrolysis and cholesterol efflux. This review summarizes recent findings on these three biologic processes and natural products with demonstrated potential to target such processes. Discussed also are potential future directions for studying the mechanisms of foam cell formation and the development of foam cell-targeted therapeutic strategies.

The role of cigarette smoke-induced epigenetic alterations in inflammation

Background

Exposure to cigarette smoke (CS) is a major threat to human health worldwide. It is well established that smoking increases the risk of respiratory diseases, cardiovascular diseases and different forms of cancer, including lung, liver, and colon. CS-triggered inflammation is considered to play a central role in various pathologies by a mechanism that stimulates the release of pro-inflammatory cytokines. During this process, epigenetic alterations are known to play important roles in the specificity and duration of gene transcription.

Main text

Epigenetic alterations include three major modifications: DNA modifications via methylation; various posttranslational modifications of histones, namely, methylation, acetylation, phosphorylation, and ubiquitination; and non-coding RNA sequences. These modifications work in concert to regulate gene transcription in a heritable fashion. The enzymes that regulate these epigenetic modifications can be activated by smoking, which further mediates the expression of multiple inflammatory genes. In this review, we summarize the current knowledge on the epigenetic alterations triggered by CS and assess how such alterations may affect smoking-mediated inflammatory responses.

Conclusion

The recognition of the molecular mechanisms of the epigenetic changes in abnormal inflammation is expected to contribute to the understanding of the pathophysiology of CS-related diseases such that novel epigenetic therapies may be identified in the near future.

Silencing lncRNA HOTAIR declines synovial inflammation and synoviocyte proliferation and promotes synoviocyte apoptosis in osteoarthritis rats by inhibiting Wnt/β-catenin signaling pathway

Osteoarthritis (OA) is a degenerative injury of the articular cartilage and reactive hyperplasia of the articular rim and subchondral bone. Due to its poor prognosis, this study is to research the influences of lncRNA HOTAIR on synovial inflammation and synoviocyte apoptosis and proliferation in OA rats by regulating the Wnt/β-catenin pathway. Rat OA model was constructed by means of cruciate ligament resection, and the successfully modeled rats were injected with sh-HOTAIR, or Wnt/β-catenin pathway activator (LiCl), and synoviocytes were transfected with sh-HOTAIR or LiCl for investigation of the influences of HOTAIR and Wnt/β-catenin pathway on synoviocytes proliferation and apoptosis. ELISA and RT-qPCR were used to detect the levels of IL-1β, IL-6 and TNF-α in serum, synovial tissue and synoviocytes in rats, respectively. The protein levels of bax, bcl-2, wnt1 and β-catenin in synovial tissue and synoviocytes were tested by Western blot analysis. Highly expressed HOTAIR existed in synovial tissue and synoviocytes of rats. There were declining arthritis index, inflammation, synoviocytes proliferation, cycle progression and promoted synoviocytes apoptosis by silencing HOTAIR and inhibited Wnt/β-catenin pathway. Down-regulation of HOTAIR could reverse the effect of LiCl on progression of OA rats. There was strained activation of Wnt/β-catenin pathway via declining HOTAIR. This study suggests that silencing lncRNA HOTAIR and inhibited Wnt/β-catenin pathway decline synovial inflammation and synoviocyte proliferation and promote apoptosis in OA rats.

Silencing Long Non-coding RNA LINC01224 Inhibits Hepatocellular Carcinoma Progression via MicroRNA-330-5p-Induced Inhibition of CHEK1

Hepatocellular carcinoma (HCC) accounts for approximately 85%–90% of primary liver cancers. Based on in silico analysis, differentially expressed long non-coding RNA (lncRNA) LINC01224 in HCC, the downstream microRNA (miRNA) miR-330-5p, and its target gene checkpoint kinase 1 (CHEK1) were selected as research subjects. Herein, this study was designed to evaluate their interaction effects on the malignant phenotypes of HCC cells. LINC01224 and CHEK1 were upregulated and miR-330-5p was downregulated in HCC cells. miR-330-5p shared negative correlations with LINC01224 and CHEK1, and LINC01224 shared a positive correlation with CHEK1. Notably, LINC01224 could specifically bind to miR-330-5p, and CHEK1 was identified as a target gene of miR-330-5p. When LINC01224 was silenced or miR-330-5p was elevated, the sphere and colony formation abilities and proliferative, migrative, and invasive potentials of HCC cells were diminished, while cell cycle arrest and apoptosis were enhanced. Moreover, LINC01224 induced HCC progression in vitro and accelerated tumor formation in nude mice by increasing CHEK1 expression. The key findings of the present study demonstrated that silencing LINC01224 could downregulate the expression of CHEK1 by competitively binding to miR-330-5p, thus inhibiting HCC progression. This result highlights the LINC01224/miR-330-5p/CHEK1 axis as a novel molecular mechanism involved in the pathology of HCC.

Long non-coding RNA expressed in macrophage co-varies with the inflammatory phenotype during macrophage development and polarization

Advances in microarray, RNA‐seq and omics techniques, thousands of long non‐coding RNAs (lncRNAs) with unknown functions have been discovered. LncRNAs have presented a diverse perspective on gene regulation in diverse biological processes, especially in human immune response. Macrophages participate in the whole phase of immune inflammatory response. They are able to shape their phenotype and arouse extensive functional activation after receiving physiological and pathological stimuli. Emerging studies indicated that lncRNAs participated in the gene regulatory network during complex biological processes of macrophage, including macrophage‐induced inflammatory responses. Here, we reviewed the existing knowledges of lncRNAs in the processes of macrophage development and polarization, and their roles in several different inflammatory diseases. Specifically, we focused on how lncRNAs function in macrophage, which might help to discover some potential therapeutic targets and diagnostic biomarkers.

A secret that underlies Parkinson's disease: The damaging cycle

Parkinson's disease (PD) is a movement disorder, and its common characteristics include the loss of dopaminergic neurons and the accumulation of a special type of cytoplasmic inclusions called Lewy bodies in the substantia nigra pars compacta, which are more prevalent in the elderly. However, the pathophysiology of PD is still elusive. In this review, we summarized five common factors involved in PD, namely, (i) oxidative stress, (ii) mitochondrial dysfunction, (iii) inflammation, (iv) abnormal α-synuclein, and (v) endogenous neurotoxins, and proposed a hypothesis involving a damaging cycle. Oxidative stress-triggered aldehydes react with biogenic amines to produce endogenous neurotoxins. They cause mitochondrial dysfunction and the formation of inflammasomes, which induce the activation of neuroglial cells and the infiltration of T lymphocytes. The synergistic effect of these processes fosters chronic inflammation and α-synuclein aggregation and further exacerbates the impact of oxidative stress to establish a damaging cycle that eventually results in the degeneration of dopaminergic neurons. This damaging cycle provides an explanation of progressive neuronal death during the pathogenesis of PD and provides new potential targets beneficial for developing new drugs and approaches for clinical neuroprotection.

Long Non-Coding RNA in Vascular Disease and Aging

Cardiovascular diseases are the most prominent cause of death in Western society, especially in the elderly. With the increasing life expectancy, the number of patients with cardiovascular diseases will rise in the near future, leading to an increased healthcare burden. There is a need for new therapies to treat this growing number of patients. The discovery of long non-coding RNAs has led to a novel group of molecules that could be considered for their potential as therapeutic targets. This review presents an overview of long non-coding RNAs that are regulated in vascular disease and aging and which might therefore give insight into new pathways that could be targeted to diagnose, prevent, and/or treat vascular diseases.

Cardiovascular inflammation: RNA takes the lead

Inflammation has recently gained tremendous attention as a key contributor in several chronic diseases. While physiological inflammation is essential to counter a wide variety of damaging stimuli and to improve wound healing, dysregulated inflammation such as in the myocardium and vasculature can promote cardiovascular diseases. Given the high severity, prevalence, and economic burden of these diseases, understanding the factors involved in the regulation of physiological inflammation is essential. Like other complex biological phenomena, RNA-based processes are emerging as major regulators of inflammatory responses. Among such processes are cis-regulatory elements in the mRNA of inflammatory genes, noncoding RNAs directing the production or localization of inflammatory cytokines/chemokines, or pathogenic RNA driving inflammatory responses. In this review, we describe several specific RNA-based molecular mechanisms by which physiological inflammation pertaining to cardiovascular diseases is regulated. These include the role of AU-rich element-containing mRNAs, long non-coding RNAs, microRNAs, and viral RNAs.

Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis

Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.