LncRNA as a Therapeutic Target for Angiogenesis

Retracted article: Functional analysis of ceRNA network of lncRNA TSIX/miR-34a-5p/RBP2 in acute myocardial infarction based on GEO database

Jiezhong Lin, Jianyi Zhou, Guiting Xie, Xiongwei Xie, Yanfang Luo and Jinguang Liu. Functional analysis of ceRNA network of lncRNA TSIX/miR-34a-5p/RBP2 in acute myocardial infarction based on GEO database. 2021 Oct. doi: 10.1080/21655979.2021.2006865.Since publication, significant concerns have been raised about the compliance with ethical policies for human research and the integrity of the data reported in the article.When approached for an explanation, the authors provided some original data but were not able to provide all the necessary supporting information. As verifying the validity of published work is core to the scholarly record's integrity, we are retracting the article. All authors listed in this publication have been informed.We have been informed in our decision-making by our editorial policies and the COPE guidelines.The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as 'Retracted.'

Clinical significance of LINC02532 in hepatitis B virus-associated hepatocellular carcinoma and its regulatory effect on tumor progression

BACKGROUND AND AIM

Long non-coding RNAs (lncRNAs) play an important role in tumor progression, including in hepatocellular carcinoma (HCC) induced by hepatitis B virus (HBV). Therefore, the aim of this study was to investigate the role of LINC02532 in HCC, mainly for diagnostic prognostic value and cellular function, as well as mechanistic aspects.

METHODS

Initially, GEO and VirBase databases were used to screen for aberrant lncRNAs in HBV-HCC.Then, HBV-HCC persons followed up in our center were retrospectively studied to investigate the diagnostic, prognostic value of LINC02532 in HBV-HCC. Subsequently, the role of LINC02532 in HBV-HCC was measured using cellular function assay methods and possible mechanisms were analyzed in conjunction with bioinformatic predictive science.

RESULTS

LINC02532 was a lncRNA abnormally expressed in HBV-HCC. LINC02532 was significantly up-regulated in the expression level in HBV-HCC tissues compared with normal tissues from patients. Moreover, LINC02532 could distinguish HBV-HCC and predict the prognosis of HBV-HCC. In vitro experiments showed that LINC02532 could regulate miR-455-3p and promote the malignant characterization of HBV-HCC cells. CHEK2 was a target gene of miR-455-3p.

CONCLUSIONS

The prognosis and diagnosis of HBV-HCC can rely on the expression of LINC02532. LINC02532 was important for further progression of HBV-HCC, by moderating miR-455-3p/CHEK2.

Alteration in DNA methylation patterns: Epigenetic signatures in gastrointestinal cancers

Abnormalities in epigenetic modifications can cause malignant transformations in cells, leading to cancers of the gastrointestinal (GI) tract, which accounts for 20% of all cancers worldwide. Among the epigenetic alterations, DNA hypomethylation is associated with genomic instability. In addition, CpG methylation and promoter hypermethylation have been recognized as biomarkers for different malignancies. In GI cancers, epigenetic alterations affect genes responsible for cell cycle control, DNA repair, apoptosis, and tumorigenic-specific signaling pathways. Understanding the pattern of alterations in DNA methylation in GI cancers could help scientists discover new molecular-based pharmaceutical treatments. This study highlights alterations in DNA methylation in GI cancers. Understanding epigenetic differences among GI cancers may improve targeted therapies and lead to the discovery of new diagnostic biomarkers.

Long Noncoding RNA MALAT1: Salt-Sensitive Hypertension

Hypertension stands as the leading global cause of mortality, affecting one billion individuals and serving as a crucial risk indicator for cardiovascular morbidity and mortality. Elevated salt intake triggers inflammation and hypertension by activating antigen-presenting cells (APCs). We found that one of the primary reasons behind this pro-inflammatory response is the epithelial sodium channel (ENaC), responsible for transporting sodium ions into APCs and the activation of NADPH oxidase, leading to increased oxidative stress. Oxidative stress increases lipid peroxidation and the formation of pro-inflammatory isolevuglandins (IsoLG). Long noncoding RNAs (lncRNAs) play a crucial role in regulating gene expression, and MALAT1, broadly expressed across cell types, including blood vessels and inflammatory cells, is also associated with inflammation regulation. In hypertension, the decreased transcriptional activity of nuclear factor erythroid 2-related factor 2 (Nrf2 or Nfe2l2) correlates with heightened oxidative stress in APCs and impaired control of various antioxidant genes. Kelch-like ECH-associated protein 1 (Keap1), an intracellular inhibitor of Nrf2, exhibits elevated levels of hypertension. Sodium, through an increase in Sp1 transcription factor binding at its promoter, upregulates MALAT1 expression. Silencing MALAT1 inhibits sodium-induced Keap1 upregulation, facilitating the nuclear translocation of Nrf2 and subsequent antioxidant gene transcription. Thus, MALAT1, acting via the Keap1-Nrf2 pathway, modulates antioxidant defense in hypertension. This review explores the potential role of the lncRNA MALAT1 in controlling the Keap1-Nrf2-antioxidant defense pathway in salt-induced hypertension. The inhibition of MALAT1 holds therapeutic potential for the progression of salt-induced hypertension and cardiovascular disease (CVD).

Downregulation of lncRNA CDKN2B-AS1 attenuates inflammatory response in mice with allergic rhinitis by regulating miR-98-5p/SOCS1 axis

Long non-coding RNA cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) in various diseases has been verified. However, the underlying mechanism of CDKN2B-AS1 contributes to the development of allergic rhinitis (AR) remains unknown. To evaluate the impact of CDKN2B-AS1 on AR, BALB/c mice were sensitized by intraperitoneal injection of normal saline containing ovalbumin (OVA) and calmogastrin to establish an AR model. Nasal rubbing and sneezing were documented after the final OVA treatment. The concentrations of IgE, IgG1, and inflammatory elements were quantified using ELISA. Hematoxylin and eosin (H&E) staining and immunofluorescence were used to assess histopathological variations and tryptase expression, respectively. StarBase, TargetScan and luciferase reporter assays were applied to predict and confirm the interactions among CDKN2B-AS1, miR-98-5p, and SOCS1. CDKN2B-AS1, miR-98-5p, and SOCS1 levels were assessed by quantitative real-time PCR (qRT-PCR) or western blotting. Our results revealed that CDKN2B-AS1 was obviously over-expressed in the nasal mucosa of AR patients and AR mice. Down-regulation of CDKN2B-AS1 significantly decreased nasal rubbing and sneezing frequencies, IgE and IgG1 concentrations, and cytokine levels. Furthermore, down-regulation of CDKN2B-AS1 also relieved the pathological changes in the nasal mucosa, and the infiltration of eosinophils and mast cells. Importantly, these results were reversed by the miR-98-5p inhibitor, whereas miR-98-5p directly targeted CDKN2B-AS1, and miR-98-5p negatively regulated SOCS1 level. Our findings demonstrate that down-regulation of CDKN2B-AS1 improves allergic inflammation and symptoms in a murine model of AR through the miR-98-5p/SOCS1 axis, which provides new insights into the latent functions of CDKN2B-AS1 in AR treatment.

The role of long noncoding RNA DGCR5 in cancers: Focus on molecular targets

Long noncoding RNAs (lncRNAs) are major components of cellular transcripts that are emerging as important players in various biological pathways. Due to their specific expression and functional diversity in a variety of cancers, lncRNAs have promising applications in cancer diagnosis, prognosis, and therapy. Studies have shown that lncRNA DiGeorge syndrome critical region gene 5 (DGCR5) with high specificity and accuracy has the potential to become biomarkers in cancers. LncRNA DGCR5 can be noninvasively extracted from body fluids, tissues, and cells, and can be used as independent or auxiliary biomarkers to improve the accuracy of diagnosis or prognosis. Now, the underlying mechanisms of lncRNAs such as DGCR5 were explored as therapeutic targets, which have been investigated in clinical trials of several cancers. The DGCR5 lacks an appropriate animal model, which is necessary to gain greater knowledge of their functions. While some studies on the uses of DGCR5 have been carried out, the small sample size makes them unreliable. In this review, we presented a compilation of recent publications addressing the potential of lncRNA DGCR5 that could be considered as biomarkers or therapeutic targets, with the hopes of providing promised implications for future cancer therapy.

Mini crRNA-mediated CRISPR/Cas12a system (MCM-CRISPR/Cas12a) and its application in RNA detection

Some non-coding RNAs are abnormally expressed during the occurrence and development of diseases, so it is necessary to develop analytical methods that can specifically and sensitively detect them. In typical CRISPR/Cas12a system, a complete crRNA that can recognize single-stranded or double-stranded DNA is necessary to activate its trans-cleavage activity, which limits its direct application in RNA detection. Here, we prospectively find that slicing the facilitated crRNA in the typical CRISPR/Cas12a system at a fitted site did not affect its trans-cleavage activity, and a mini crRNA-mediated CRISPR/Cas12a system (MCM-CRISPR/Cas12a) was proposed based on this. This system can detect non-coding RNA to pM-level (10 pM for miRNA-21). To expand the application of this system, we combined it with HCR and CHA to establish a detection platform for non-coding RNA. The results show that the proposed method can specifically detect RNA to fM-level (2.5 fM for miRNA-21, 8.98 fM for miR-128-3p, and 81.6 fM for lncRNA PACER). The spiked recovery rates of miRNA-21, miR-128-3p, and lncRNA PACER in normal human serum were in range from 104.7 to 109.4 %, indicating the proposed method owns good applicability. In general, this MCM-CRISPR/Cas12a system further breaks the limitations of the typical CRISPR/Cas12a system that cannot be directly used for non-coding RNA detection. Besides, its combination with HCR and CHA achieves highly sensitive detection of non-coding RNA.

Long Non-Coding RNAs (lncRNAs) in Heart Failure: A Comprehensive Review

Heart failure (HF) is a widespread cardiovascular condition that poses significant risks to a wide spectrum of age groups and leads to terminal illness. Although our understanding of the underlying mechanisms of HF has improved, the available treatments still remain inadequate. Recently, long non-coding RNAs (lncRNAs) have emerged as crucial players in cardiac function, showing possibilities as potential targets for HF therapy. These versatile molecules interact with chromatin, proteins, RNA, and DNA, influencing gene regulation. Notable lncRNAs like Fendrr, Trpm3, and Scarb2 have demonstrated therapeutic potential in HF cases. Additionally, utilizing lncRNAs to forecast survival rates in HF patients and distinguish various cardiac remodeling conditions holds great promise, offering significant benefits in managing cardiovascular disease and addressing its far-reaching societal and economic impacts. This underscores the pivotal role of lncRNAs in the context of HF research and treatment.

Long non-coding RNA signature for predicting gastric cancer survival based on genomic instability

BACKGROUND

Gastric cancer is a prevalent type of tumor with a poor prognosis. Given the high occurrence of genomic instability in gastric cancer, it is essential to investigate the prognostic significance of genes associated with genomic instability in this disease.

METHODS

We identified genomic instability-related lncRNAs (GInLncRNAs) by analyzing somatic mutation and transcriptome profiles. We evaluated co-expression and enrichment using various analyses, including univariate COX analysis and LASSO regression. Based on these findings, we established an lncRNA signature associated with genomic instability, which we subsequently assessed for prognostic value, immune cell and checkpoint analysis, drug sensitivity, and external validation. Finally, PCR assay was used to verify the expression of key lncRNAs.

RESULTS

Our study resulted in the establishment of a seven-lncRNA prognostic signature, including PTENP1-AS, LINC00163, RP11-169F17.1, C8ORF87, RP11-389G6.3, LINCO1210, and RP11-115H13.1. This signature exhibited independent prognostic value and was associated with specific immune cells and checkpoints in gastric cancer. Additionally, the model was correlated with somatic mutation and several chemotherapeutic drugs. We further confirmed the prognostic value of LINC00163, which was included in our model, in an independent dataset. Our model demonstrated superior performance compared to other models. PCR showed that LINC00163 was significantly up-regulated in 4 adjacent normal tissues compared with the GC tissues.

CONCLUSIONS

Our study resulted in the establishment of a seven-lncRNA signature associated with genomic instability, which demonstrated robust prognostic value in predicting the prognosis of gastric cancer. The signature also identified potential chemotherapeutic drugs, making it a valuable tool for clinical decision-making and medication use.

MicroRNAs as the critical regulators of tumor angiogenesis in liver cancer

Liver cancer is one of the most common malignancies in human digestive system. Despite the recent therapeutic methods, there is a high rate of mortality among liver cancer patients. Late diagnosis in the advanced tumor stages can be one of the main reasons for the poor prognosis in these patients. Therefore, investigating the molecular mechanisms of liver cancer can be helpful for the early stage tumor detection and treatment. Vascular expansion in liver tumors can be one of the important reasons for poor prognosis and aggressiveness. Therefore, anti-angiogenic drugs are widely used in liver cancer patients. MicroRNAs (miRNAs) have key roles in the regulation of angiogenesis in liver tumors. Due to the high stability of miRNAs in body fluids, these factors are widely used as the non-invasive diagnostic and prognostic markers in cancer patients. Regarding, the importance of angiogenesis during liver tumor growth and invasion, in the present review, we discussed the role of miRNAs in regulation of angiogenesis in these tumors. It has been reported that miRNAs mainly exert an anti-angiogenic function by regulation of tumor microenvironment, transcription factors, and signaling pathways in liver tumors. This review can be an effective step to suggest the miRNAs for the non-invasive early detection of malignant and invasive liver tumors.

DNA methylation-regulated LINC02587 inhibits ferroptosis and promotes the progression of glioma cells through the CoQ-FSP1 pathway

BACKGROUND

Long noncoding RNAs (lncRNAs) are considered key players in the formation and development of tumors. Herein, Gene Expression Profiling Interactive Analysis (GEPIA) was employed as a bioinformatics technology. LINC02587 is differentially expressed in bladder urothelial cancer, glioblastoma, lung adenocarcinoma, lung SCC, melanoma, and other tumor tissue and cells. However, its impact on the emergence of glioma and its mechanism is remaining elusive.

METHODS

Some of the in vitro assays employed in this study were the CCK-8 / Annexin-V / Transwell assays, colony formation, and wound healing, together with Western blot (WB) evaluation. MSP / BSP assays were employed for assessing the CpG island's methylation status in the LINC02587 promoter. Through transcriptome, ferroptosis-related experiments, and WB evaluation, it was confirmed that LINC02587 is correlated with the regulation of ferroptosis in tumor cells, and CoQ-Fsp1 is one of its regulatory pathways. Moreover, the underlined in-vitro results were further validated by in-vivo studies.

RESULTS

The current study shows that the promoter sequence of LINC02587 is regulated by methylation. The silencing of LINC02587 can inhibit cellular proliferative, migrative, and invasive properties, and induce ferroptosis within gliomas through the CoQ-FSP1 pathway.

CONCLUSIONS

LINC02587 is likely to be a novel drug target in treating glioma.

The Role of Long Non-Coding RNAs in Cardiovascular Diseases

Long non-coding RNAs (lncRNAs) are non-coding RNA molecules longer than 200 nucleotides that regulate gene expression at the transcriptional, post-transcriptional, and translational levels. Abnormal expression of lncRNAs has been identified in many human diseases. Future improvements in diagnostic, prognostic, and therapeutic techniques will be facilitated by a deeper understanding of disease etiology. Cardiovascular diseases (CVDs) are the main cause of death globally. Cardiac development involves lncRNAs, and their abnormalities are linked to many CVDs. This review examines the relationship and function of lncRNA in a variety of CVDs, including atherosclerosis, myocardial infarction, myocardial hypertrophy, and heart failure. Therein, the potential utilization of lncRNAs in clinical diagnostic, prognostic, and therapeutic applications will also be discussed.

Probing the links: Long non-coding RNAs and NF-κB signalling in atherosclerosis

Atherosclerosis is a chronic inflammatory disease that involves the accumulation of lipids and immune cells in the arterial wall. NF-kB signaling is a key regulator of inflammation and is known to play a critical role in atherosclerosis. Recent studies have shown that lncRNAs can regulate NF-kB and contribute to the development and progression of atherosclerosis. Preliminary findings reveal significant alterations in the expression of specific lncRNAs in atherosclerotic lesions compared to healthy arterial tissue. Experimental evidence suggests that these dysregulated lncRNAs can influence the NF-kB pathway. By unravelling the crosstalk between lncRNAs and NF-kB signaling, this review aims to enhance our understanding of the molecular mechanisms underlying atherosclerosis. Identifying novel therapeutic targets and diagnostic markers may lead to developing interventions and management strategies for this prevalent cardiovascular disease. This review summarizes the current knowledge on the role of lncRNAs in NF-kB signaling in atherosclerosis and highlights their potential as therapeutic targets for this disease.

Galectin-1-dependent ceRNA network in HRMECs revealed its association with retinal neovascularization

BACKGROUND

Retinal neovascularization (RNV) is a leading cause of blindness worldwide. Long non-coding RNA (lncRNA) and competing endogenous RNA (ceRNA) regulatory networks play vital roles in angiogenesis. The RNA-binding protein galectin-1 (Gal-1) participates in pathological RNV in oxygen-induced retinopathy mouse models. However, the molecular associations between Gal-1 and lncRNAs remain unclear. Herein, we aimed to explore the potential mechanism of action of Gal-1 as an RNA-binding protein.

RESULTS

A comprehensive network of Gal-1, ceRNAs, and neovascularization-related genes was constructed based on transcriptome chip data and bioinformatics analysis of human retinal microvascular endothelial cells (HRMECs). We also conducted functional enrichment and pathway enrichment analyses. Fourteen lncRNAs, twenty-nine miRNAs, and eleven differentially expressed angiogenic genes were included in the Gal-1/ceRNA network. Additionally, the expression of six lncRNAs and eleven differentially expressed angiogenic genes were validated by qPCR in HRMECs with or without siLGALS1. Several hub genes, such as NRIR, ZFPM2-AS1, LINC0121, apelin, claudin-5, and C-X-C motif chemokine ligand 10, were found to potentially interact with Gal-1 via the ceRNA axis. Furthermore, Gal-1 may be involved in regulating biological processes related to chemotaxis, chemokine-mediated signaling, the immune response, and the inflammatory response.

CONCLUSIONS

The Gal-1/ceRNA axis identified in this study may play a vital role in RNV. This study provides a foundation for the continued exploration of therapeutic targets and biomarkers associated with RNV.

Long non-coding RNA TCL6 induced by SCRT1 promotes proliferation and metastasis of non-small cell lung cancer through PDK1/AKT signaling

Non-small cell lung cancer (NSCLC) ranks the most lethal malignancies around the world, nearly 85 % of lung cancers are NSCLC. Its high prevalence and morbidity pose a considerable burden to human health, identifying promising therapeutic targets for NSCLC is urgently needed. The essential function of long non-coding RNAs (lncRNAs) in multiple cellular progressions and pathophysiological processes are widely understood, thus we investigated the role of lncRNA T-cell leukemia/lymphoma 6 (TCL6) in NSCLC progression. LncRNA TCL6 level is increased in NSCLC samples and downregulation of lncRNA TCL6 inhibited NSCLC tumorigenesis. Moreover, Scratch Family Transcriptional Repressor 1 (SCRT1) can modulate lncRNA TCL6 expression in NSCLC cells, with lncRNA TCL6 promoting NSCLC development through Pyruvate Dehydrogenase Kinase 1 (PDK1)/AKT signaling by interacting with PDK1, thereby providing a novel framework for NSCLC research.

LINC00659 exacerbates endothelial progenitor cell dysfunction in deep vein thrombosis of the lower extremities by activating DNMT3A-mediated FGF1 promoter methylation

It has been shown that long non-coding RNA (lncRNA) LINC00659 was markedly upregulated in the peripheral blood of patients with deep venous thrombosis (DVT). However, the function of LINC00659 in lower extremity DVT (LEDVT) remains to be largely unrevealed. A total of 30 inferior vena cava (IVC) tissue samples and peripheral blood (60 ml per subject) were obtained from LEDVT patients (n = 15) and healthy donors (n = 15), and then LINC00659 expression was detected by RT-qPCR. The results displayed that LINC00659 is upregulated in IVC tissues and isolated endothelial group cells (EPCs) of patients with LEDVT. LINC00659 knock-down promoted the proliferation, migration, and angiogenesis ability of EPCs, while an pcDNA-eukaryotic translation initiation factor 4A3 (EIF4A3), a EIF4A3 overexpression vector, or fibroblast growth factor 1 (FGF1) small interfering RNA (siRNA) combined with LINC00659 siRNA could not enhance this effect. Mechanistically, LINC00659 bound with EIF4A3 promoter to upregulated EIF4A3 expression. Besides, EIF4A3 could facilitate FGF1 methylation and its downregulated expression by recruiting DNA methyltransferases 3A (DNMT3A) to the FGF1 promoter region. Additionally, LINC00659 inhibition could alleviate LEDVT in mice. In summary, the data indicated the roles of LINC00659 in the pathogenesis of LEDVT, and the LINC00659/EIF4A3/FGF1 axis could be a novel therapeutic target for the treatment of LEDVT.

Clinicopathological and prognostic value of lncRNA TPT1-AS1 in cancer: a systematic review study and meta-analysis

INTRODUCTION

Aberrant expression of lncRNAs in cancer cells can impact their key phenotypes. We aimed to summarize available evidence on clinicopathological and prognostic value of lncRNA TPT1-AS1 in cancer.

METHODS

A systematic search was performed on Medline and Embase databases using relevant key terms covering lncRNA TPT1-AS1, cancer, and clinical outcomes. The effect size estimates and their 95 % confidence interval (CI) were pooled using random-effects models. Meta- analyses were conducted using STATA 16.0 software.

RESULTS

Seventeen articles met our eligibility criteria. Tumor tissue compared to normal tissue showed increased level of lncRNA TPT1-AS1 expression (pooled standardized mean difference (95 % CI): 0.65 (0.52-0.79)). Overexpression of this lncRNA was a significant predictor for poor prognosis (Pooled log-rank test P-value < 0.001); in patients with high-level of lncRNA TPT1-AS1, the risk of death at five years was 1.40 times greater than their counterparts. The pooled Odds ratios for association lncRNA TPT1-AS1 with tumor stage, tumor size, and lymph node metastasis were 1.94 (95 % CI: 0.90-4.19, 8 studies, I² = 79.6 %), 2.33 (95 % CI: 1.31-4.14, 5 studies, I² = 40.0 %), and 1.89 (95 % CI: 1.08-3.36, 5 studies, I² = 61.7 %), respectively. Regarding the identified potential mechanisms, lncRNA TPT1-AS1 plays a role in cancer growth mainly by sponging miRNAs and regulating their downstream targets or controlling the expression of key cell cycle regulators.

CONCLUSION

In cancer patients, elevated expression of lncRNA TPT1-AS1 might be associated with a shorter Overall Survival, advanced stages, larger tumor size, and lymph node metastasis.

A review on the roles and molecular mechanisms of MAFG-AS1 in oncogenesis

Long non-coding RNAs (lncRNAs) have more than 200 nucleotides and do not encode proteins. At the same time, they can regulate various biological functions and therefore play an essential role as oncogenes or tumor suppressors in human cancers. MAFG-AS1 is an antisense RNA of MAF BZIP Transcription Factor G (MAFG) located at chromosome 17q25.3 head-to-head with the MAFG encoding gene containing a transcript size of 1895 bp. Accumulating evidence shows that MAFG-AS1 is overexpressed in many cancers, functions as an oncogene, and is significantly associated with poor clinical characteristics and prognosis. In this review, we first discuss the recent literature regarding the role of MAFG-AS1 in different cancers as well as its diagnostic and prognostic values. Then we will provide insights into its biological functions, such as its role in cancer progression, competing endogenous RNA (ceRNA) activity, regulation of EMT, glycolysis, energy metabolism, transcription factors, proteasomal degradation, and signaling pathways.

Upregulation LncRNA MEG3 expression suppresses proliferation and metastasis in melanoma via miR-208/SOX4

Long non-coding RNAs (lncRNAs) regulate gene expression and play a significant role in cancer progression. Previously, downregulation of lncRNA MEG3 was shown to associate with poor clinical outcomes in melanoma patients. The basis for this association has not been described and the aims of this study were to identify a role for lncRNA MEG3 in melanoma and to describe its regulatory mechanism of action. RT-qPCR was used to detect lncRNA MEG3 expression in melanoma cells and tissues. Luciferase reporter assays were used to identify lncRNA MEG3 downstream targets. Melanoma cells were transfected with various expression vectors and these transfected cells were assessed for; migration, colony formation, proliferation, in vivo tumorigenesis, and metastatic potential. Melanoma cell lines were found to be sensitive to lncRNA MEG3 expression levels and overexpression was found to inhibit melanoma cell proliferation and invasion, both in vitro and in vivo. Luciferase reporter assays identified miR-208 and SOX4 as downstream targets of lncRNA MEG3. Overexpression of miR-208 and silencing of SOX4 rescued invasion and proliferation by cells that overexpressed lncRNA MEG3. Moreover, lncRNA MEG3 inhibited cancer stem cell differentiation and suppressed melanoma progression and metastasis through inhibition of miR-208 by SOX4.

Non-Coding RNAs in Cell-to-Cell Communication: Exploiting Physiological Mechanisms as Therapeutic Targets in Cardiovascular Pathologies

Cardiovascular disease, the leading cause of death worldwide, has been characterized at the molecular level by alterations in gene expression that contribute to the etiology of the disease. Such alterations have been shown to play a critical role in the development of atherosclerosis, cardiac remodeling, and age-related heart failure. Although much is now known about the cellular and molecular mechanisms in this context, the role of epigenetics in the onset of cardiovascular disease remains unclear. Epigenetics, a complex network of mechanisms that regulate gene expression independently of changes to the DNA sequence, has been highly implicated in the loss of homeostasis and the aberrant activation of a myriad of cellular pathways. More specifically, non-coding RNAs have been gaining much attention as epigenetic regulators of various pathologies. In this review, we will provide an overview of the ncRNAs involved in cell-to-cell communication in cardiovascular disease, namely atherosclerosis, cardiac remodeling, and cardiac ageing, and the potential use of epigenetic drugs as novel therapeutic targets.

Identification of Alternative Splicing and LncRNA Genes in Brain Tissues of Fetal Mice at Different Developmental Stages

BACKGROUND

Brain development is an extremely complex and precisely regulated process, with about one-third of genes expressed and precisely regulated during brain development.

OBJECTIVE

This study aims to explore the molecular mechanisms involved in brain development.

METHODS

We first established the expression profile of long non-coding RNAs (lncRNAs) and mRNAs in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d through high-throughput sequencing. Second, the associated functions, pathways, and networks of the co-differentially expressed lncRNAs and mRNAs were identified via Gene Ontology (GO), pathway analysis, and PPI network. After bioinformatic analysis and screening, 8 differentially expressed lncRNAs and mRNAs with the same genetic origin were verified by RT-qPCR analysis in brain tissues of fetal mice at different developmental stages.

RESULTS

The data revealed that there were 972 co-differentially expressed lncRNAs and 992 codifferentially expressed mRNAs in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d. And we discovered 125 differentially expressed lncRNAs and mRNAs, which have the same genetic origin, in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d through sequencing results and bioinformatics analysis. Besides, we proved that 8 lncRNAs, which have had the same genetic origin as differentially expressed mRNAs, were prominently downregulated, while their maternal genes were upregulated during brain development in fetal mice.

CONCLUSION

Our results preliminarily illustrated the differentially expressed lncRNAs and mRNAs, both of which were derived from the same parent genes, during brain development in fetal mice, which suggests that alternative splicing of lncRNA exists during brain development. Besides, our study provides a perspective on critical genes for brain development, which might be the underlying therapeutic targets for developmental brain diseases in children.

The role of lncRNA CERS6-AS1 in cancer and its molecular mechanisms: A systematic review and meta-analysis

BACKGROUND

LncRNAs have the potential to play a regulatory role in different processes of cancer development and progression. We conducted a systematic review and meta-analysis of evidence on the clinical significance and prognostic value of lncRNA CERS6-AS1 in cancer.

METHODS

This systematic review was conducted following PRISMA guidelines. Medline and Embase databases were searched using the relevant key terms covering lncRNA CERS6-AS1 and cancer. We pooled the estimated effect sizes and their 95 % confidence interval (CI) using random-effects models in STATA 16.0 (StataCorp, College Station, TX, USA).

RESULTS

Eleven articles on pancreatic, colorectal, gastric, papillary thyroid, breast, and hepatocellular cancers fulfilled our eligibility criteria. Studies consistently found that lncRNA CERS6-AS1 expression is upregulated in all assessed cancers. Based on our meta-analysis, its aberrant expression was directly associated with unfavorable clinical outcomes, including higher stage (pooled Odds ratios (95 % CI): 3.15 (2.01-4.93; I² = 0.0 %), tumor size (1.97 (1.27-3.05; I² = 37.8 %), lymph node metastasis (6.48 (4.01-10.45; I² = 0.40 %), and poor survival (Pooled log-rank test P-value < 0.001) in patients. Regarding potential mechanisms, functional studies revealed that LncRNA CERS6-AS1 is involved in cancer growth mainly by sponging miRNAs and regulating their downstream targets.

CONCLUSION

Available evidence suggests that LncRNA CERS6-AS1 is upregulated in different cancers and has an oncogenic role. LncRNA CERS6-AS1 expression level might predict cancer prognosis, highlighting its potential application as a prognostic biomarker for cancer.

The Mechanism Underlying the Regulation of Long Non-coding RNA MEG3 in Cerebral Ischemic Stroke

Cerebral ischemic stroke is one of the leading causes of morbidity and mortality worldwide, and rapidly increasing annually with no more effective therapeutic measures. Thus, the novel diagnostic and prognostic biomarkers are urgent to be identified for prevention and therapy of ischemic stroke. Recently, long noncoding RNAs (lncRNAs), a major family of noncoding RNAs with more than 200 nucleotides, have been considered as new targets for modulating pathological process of ischemic stroke. In this review, we summarized that the lncRNA-maternally expressed gene 3 (MEG3) played a critical role in promotion of neuronal cell death and inhibition of angiogenesis in response to hypoxia or ischemia condition, and further described the challenge of overcrossing blood-brain barrier (BBB) and determination of optimal carrier for delivering lncRNA' drugs into the specific brain regions. In brief, MEG3 will be a potential diagnostic biomarker and drug target in treatment and therapy of ischemic stroke in the future.

Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer

Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer Genome Atlas database were categorized according to the expression level of NAT10, which drives acetylation of cytidine in RNA to N(4)-acetylcytidine (ac4C) and affects mRNA stability. A total of 703 differentially expressed long non-coding RNAs (lncRNAs) were found between high- and low-expressed NAT10 groups in TNBC. Twenty of these lncRNAs were significantly associated with prognosis. Two breast cancer tissues and their paired normal tissues were sequenced at the whole genome level using acetylated RNA immunoprecipitation sequencing (acRIP-seq) technology to identify acetylation features in TNBC, and 180 genes were significantly differentially ac4c acetylated in patients. We also analyzed the genome-wide lncRNA expression profile and constructed a co-expression network, containing 116 ac4C genes and 1080 lncRNAs. Three of these lncRNAs were prognostic risk lncRNAs affected by NAT10 and contained in the network. The corresponding reciprocal pairs were "LINC01614-COL3A1", "OIP5-AS1-USP8", and "RP5-908M14.9-TRIR". These results indicate that RNA ac4c acetylation involves lncRNAs and affects the tumor process and prognosis of TNBC. This will aid the prediction of drug targets and drug sensitivity.

Renal Carcinoma and Angiogenesis: Therapeutic Target and Biomarkers of Response in Current Therapies

Due to the aberrant hypervascularization and the high immune infiltration of renal tumours, current therapeutic regimens of renal cell carcinoma (RCC) target angiogenic or immunosuppressive pathways or both. Tumour angiogenesis plays an essential role in tumour growth and immunosuppression. Indeed, the aberrant vasculature promotes hypoxia and can also exert immunosuppressive functions. In addition, pro-angiogenic factors, including VEGF-A, have an immunosuppressive action on immune cells. Despite the progress of treatments in RCC, there are still non responders or acquired resistance. Currently, no biomarkers are used in clinical practice to guide the choice between the different available treatments. Considering the role of angiogenesis in RCC, angiogenesis-related markers are interesting candidates. They have been studied in the response to antiangiogenic drugs (AA) and show interest in predicting the response. They have been less studied in immunotherapy alone or combined with AA. In this review, we will discuss the role of angiogenesis in tumour growth and immune escape and the place of angiogenesis-targeted biomarkers to predict response to current therapies in RCC.

Long Non-coding RNA Therapeutics: Recent Advances and Challenges

The discovery of the roles of RNA other than just as a messenger, such as a ribozyme, and regulatory RNAs, such as microRNA and long noncoding RNAs, is fascinating. RNA is now recognized as an important regulator involved in practically every biological process. Research in the field of non-coding RNAs, specifically microRNAs (miRNAs) and long non-coding RNAs (LncRNAs) have developed immensely over the years. Recent studies identified diverse RNAs, including non-coding RNAs such as LncRNA and their various modes of action in the cells. These RNAs are anticipated to be key targets for the treatment of various diseases since they control a broad array of biological pathways. LncRNA-targeted drug platform delivers the pharmaceutical industry a myriad of opportunities and has the potential to modulate diseases at the genetic level while also overcoming the limitations of inconsistent proteins. This article focuses on the recent advancement as well as the major challenges in the field and describes the various RNA-based therapeutics that alter the quality of healthcare for many diseases and bring personalized medicines to fruition. The article also summarizes RNA-based therapeutics that are undergoing testing in clinical trials or have been granted FDA approval.

Targeting the lncMST-EPRS/HSP90AB1 complex as novel therapeutic strategy for T-2 toxin-induced growth retardation

Growth retardation is a global public health problem that is highly prevalent especially in low-and middle-income countries, which is closely related to the consumption of grains contaminated with T-2 toxin, a risk for human and animal health. However, the possible targets that can relieve T-2 toxin-induced growth retardation still need to be explored. In the present study, T-2 toxin was used as an environmental exposure factor to induce growth retardation and further explore the regulatory role of lncRNA in growth retardation. The present study systematically characterised the expression profiles of lncRNAs and identified a lncRNA lncMST that is related to growth retardation in T-2 toxin-administered rats. Functionally, lncMST could alleviate cell cycle arrest and apoptosis in T-2 toxin-treated GH3 cells. Mechanistically, lncMST, serve as an inducible chaperone RNA, involved in the paradigm "Chemical-induced stress related growth retardation", through recruiting the EPRS/HSP90AB1 complex to increase HDAC6 expression, thus further alleviating T-2 toxin-induced growth retardation. These findings for the first time demonstrate that the probable therapeutic relationship between lncMST and growth retardation, providing an explanation and therapeutic targets for the pathogenesis of growth retardation.

Expression of long noncoding RNAs in the ovarian granulosa cells of women with diminished ovarian reserve using high-throughput sequencing

Background

Infertility is a global reproductive-health problem, and diminished ovarian reserve (DOR) is one of the common causes of female infertility. Long noncoding RNAs (lncRNAs) are crucial regulators of numerous physiological and pathological processes in humans. However, whether lncRNAs are involved in the development of DOR remains to be elucidated.

Methods

Ovarian granulosa cells (OGCs) extracted from infertile women with DOR and from women with normal ovarian reserve (NOR) were subjected to high-throughput sequencing. Comprehensive bioinformatics analysis was conducted to identify the differential expression of messenger RNAs (mRNAs) and lncRNAs. Sequencing results were validated by the selection of lncRNAs and mRNAs using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

Results

Compared with the NOR group, a total of 244 lncRNAs were upregulated (53 known and 191 novel), and 222 lncRNAs were downregulated (36 known and 186 novel) in the DOR group. Similarly, 457 mRNAs had differential expression between the two groups. Of these, 169 were upregulated and 288 were downregulated. Bioinformatics analysis revealed that the differentially expressed genes of mRNA and lncRNAs were considerably enriched in “cell adhesion and apoptosis”, “steroid biosynthesis”, and “immune system”. A co-expression network comprising lncRNAs and their predicted target genes revealed the possible involvement of the “thyroid hormone signaling pathway” and “protein binding, digestion and absorption” in DOR pathogenesis. The expression of SLC16A10 was positively regulated by multiple lncRNAs. After RT-qPCR validation of seven differentially expressed lncRNAs and mRNAs, respectively, the expression of lncRNA NEAT1, GNG12, ZEB2-AS1, and mRNA FN1, HAS3, RGS4, SUOX were in accordance with RNA-sequencing.

Conclusions

We presented the first data showing that the expression profiles of lncRNA and mRNA in OGCs between NOR and DOR patients using RNA sequencing. The lncRNAs and mRNAs that we identified may serve as novel diagnostic biomarkers for patients with DOR.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13048-022-01053-6.

Prediction of prognosis, immune infiltration and immunotherapy response with N6-methyladenosine-related lncRNA clustering patterns in cervical cancer

LncRNAs and tumor microenvironment (TME) exert an important effect in antitumor immunity. Nonetheless, the role of m⁶A-related lncRNA clustering patterns in prognosis, TME and immunotherapy of cervical cancer (CC) remains unknown. Here, based on 7 m⁶A-related prognostic lncRNAs obtained from TCGA-CC dataset, two m⁶AlncRNA clustering patterns were determined. m⁶AlncRNA clusterA was characterized by immune cell infiltrates and immune activation. m⁶AlncRNA clusterB was characterized by enrichment of immune evasion and tumorigenic activation pathways as well as survival and clinical stage disadvantage. Then, principal component analysis algorithms were used to construct m⁶AlncRNAscore based on prognostic differentially expressed genes between two m⁶AlncRNA clusters to quantify m⁶AlncRNA clustering patterns. m⁶AlncRNAscore was an independent prognostic protective factor. Higher Th2 and Treg cells and enrichment of immunosuppressive pathways were observed in the low-m⁶AlncRNAscore group, with poorer survival. High-m⁶AlncRNAscore was characterized by increased infiltration of activated CD8 T cell, enrichment of immune activation pathways, lower IL-10 and TGF-beta1 levels, and higher immunophenscore values, indicating inflamed TME and better anti-tumor immunotherapy efficacy. Quantitative Real-Time Polymerase Chain Reaction was used for detection of m⁶A-related prognostic lncRNAs. Collectively, we identified two m⁶AlncRNA clustering patterns which play a nonnegligible role in the prognosis, TME heterogeneity and immunotherapy of CC patients.

Identification of Hypothalamic Long Noncoding RNAs Associated with Hypertension and the Behavior/Neurological Phenotype of Hypertensive ISIAH Rats

Long noncoding RNAs (lncRNAs) play an important role in the control of many physiological and pathophysiological processes, including the development of hypertension and other cardiovascular diseases. Nonetheless, the understanding of the regulatory function of many lncRNAs is still incomplete. This work is a continuation of our earlier study on the sequencing of hypothalamic transcriptomes of hypertensive ISIAH rats and control normotensive WAG rats. It aims to identify lncRNAs that may be involved in the formation of the hypertensive state and the associated behavioral features of ISIAH rats. Interstrain differences in the expression of seven lncRNAs were validated by quantitative PCR. Differential hypothalamic expression of lncRNAs LOC100910237 and RGD1562890 between hypertensive and normotensive rats was shown for the first time. Expression of four lncRNAs (Snhg4, LOC100910237, RGD1562890, and Tnxa-ps1) correlated with transcription levels of many hypothalamic genes differentially expressed between ISIAH and WAG rats (DEGs), including genes associated with the behavior/neurological phenotype and hypertension. After functional annotation of these DEGs, it was concluded that lncRNAs Snhg4, LOC100910237, RGD1562890, and Tnxa-ps1 may be involved in the hypothalamic processes related to immune-system functioning and in the response to various exogenous and endogenous factors, including hormonal stimuli. Based on the functional enrichment analysis of the networks, an association of lncRNAs LOC100910237 and Tnxa-ps1 with retinol metabolism and an association of lncRNAs RGD1562890 and Tnxa-ps1 with type 1 diabetes mellitus are proposed for the first time. Based on a discussion, it is hypothesized that previously functionally uncharacterized lncRNA LOC100910237 is implicated in the regulation of hypothalamic processes associated with dopaminergic synaptic signaling, which may contribute to the formation of the behavioral/neurological phenotype and hypertensive state of ISIAH rats.

Potential epigenetic molecular regulatory networks in ocular neovascularization

Neovascularization is one of the many manifestations of ocular diseases, including corneal injury and vascular diseases of the retina and choroid. Although anti-VEGF drugs have been used to effectively treat neovascularization, long-term use of anti-angiogenic factors can cause a variety of neurological and developmental side effects. As a result, better drugs to treat ocular neovascularization are urgently required. There is mounting evidence that epigenetic regulation is important in ocular neovascularization. DNA methylation and histone modification, non-coding RNA, and mRNA modification are all examples of epigenetic mechanisms. In order to shed new light on epigenetic therapeutics in ocular neovascularization, this review focuses on recent advances in the epigenetic control of ocular neovascularization as well as discusses these new mechanisms.

Characterization of differentially expressed and lipid metabolism-related lncRNA-mRNA interaction networks during the growth of liver tissue through rabbit models

Background

Characterization the long non-coding RNAs (lncRNAs) and their regulated mRNAs involved in lipid metabolism during liver growth and development is of great value for discovering new genomic biomarkers and therapeutic targets for fatty liver and metabolic syndrome.

Materials and methods

Liver samples from sixteen rabbit models during the four growth stages (birth, weaning, sexual maturity, and somatic maturity) were used for RNA-seq and subsequent bioinformatics analyses. Differentially expressed (DE) lncRNAs and mRNAs were screened, and the cis/trans-regulation target mRNAs of DE lncRNAs were predicted. Then the function enrichment analyses of target mRNAs were performed through Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. The target protein interaction (PPI) and lncRNA-mRNA co-expression networks were constructed using string version 11.0 platform and R Stats. Finally, six lncRNAs and six mRNAs were verified taking RT-qPCR.

Results

Liver Oil Red O detection found that the liver showed time-dependent accumulation of lipid droplets. 41,095 lncRNAs, 30,744 mRNAs, and amount to 3,384 DE lncRNAs and 2980 DE mRNAs were identified from 16 cDNA sequencing libraries during the growth of liver. 689 out of all DE lncRNAs corresponded to 440 DE mRNAs by cis-regulation and all DE mRNAs could be regulated by DE lncRNAs by trans-regulation. GO enrichment analysis showed significant enrichment of 892 GO terms, such as protein binding, cytosol, extracellular exsome, nucleoplasm, and oxidation-reduction process. Besides, 52 KEGG pathways were significantly enriched, including 11 pathways of lipid metabolism were found, like Arachidonic acid metabolism, PPAR signaling pathway and Biosynthesis of unsaturated fatty acids. After the low expression DE mRNAs and lncRNAs were excluded, we further obtained the 54 mRNAs were regulated by 249 lncRNAs. 351 interaction pairs were produced among 38 mRNAs and 215 lncRNAs through the co-expression analysis. The PPI network analysis found that 10 mRNAs such as 3β-Hydroxysteroid-Δ24 Reductase (DHCR24), lathosterol 5-desaturase (SC5D), and acetyl-CoA synthetase 2 (ACSS2) were highly interconnected hub protein-coding genes. Except for MSTRG.43041.1, the expression levels of the 11 genes by RT-qPCR were the similar trends to the RNA-seq results.

Conclusion

The study revealed lncRNA-mRNA interation networks that regulate lipid metabolism during liver growth, providing potential research targets for the prophylaxis and treatment of related diseases caused by liver lipid metabolism disorders.

The clinical significance, immune infiltration, and tumor mutational burden of angiogenesis-associated lncRNAs in kidney renal clear cell carcinoma

Background

Poor prognosis of kidney renal clear cell carcinoma (KIRC) is often related to angiogenesis. The lncRNAs that regulate angiogenesis could also affect the prognosis of KIRC. It is meaningful for us to use lncRNAs related to angiogenesis to construct a generic, individualized prognostic signature for patients with KIRC.

Methods

We identified eight angiogenesis-associated genes (AAGs) by differential expression analysis and univariate Cox regression from The Cancer Genome Atlas dataset, including 537 KIRC samples and 72 normal samples. In total, 23 prognostic lncRNAs were screened out after Pearson correlation analysis and univariate Cox regression analysis. Then, we performed least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression to establish a four-AAG-related lncRNA prognostic signature.

Results

The risk score was calculated for each KIRC patients by using a four-AAG-related lncRNA prognostic signature. We divided the KIRC patients into high- and low-risk groups by the median of the risk score. It was confirmed that the AAG-related lncRNA prognostic signature has good prognostic value for KIRC patients by time-dependent receiver operating characteristic and Kaplan–Meier survival analysis. We identified 3,399 differentially expressed genes between the high- and low-risk groups and performed their functional enrichment analyses. The AAG-related lncRNA prognostic signature was an independent prognostic predictor for KIRC patients and was used to perform a combined nomogram. We reevaluated them in terms of survival, clinic characteristics, tumor-infiltrating immune cells and tumor mutation burden.

Conclusion

Our research indicates that the AAG-related lncRNA prognostic signature is a promising and potential independent prognostic indicator for KIRC patients. Then, it could offer new insights into the prognosis assessment and potential treatment strategies of KIRC patients.

A Novel Necroptosis-Associated IncRNAs Signature for Prognosis of Head and Neck Squamous Cell Carcinoma

Purpose: The prognosis of head and neck squamous cell carcinoma (HNSCC) is poor. Necroptosis is a novel programmed form of necrotic cell death. The prognostic value of necroptosis-associated lncRNAs expression in HNSCC has not been explored. Methods: We downloaded mRNA expression data of HNSCC patients from TCGA databases. Prognostic lncRNAs were identified by univariate Cox regression. LASSO was used to establish a model with necroptosis-related lncRNAs. Kaplan-Meier analysis and ROC were applied to verify the model. Finally, functional studies including gene set enrichment analyses, immune microenvironment analysis, and anti-tumor compound IC50 prediction were performed. Results: We identified 1,117 necroptosis-related lncRNAs. The Cox regression showed 55 lncRNAs were associated with patient survival (p < 0.05). The risk model of 24- lncRNAs signature categorized patients into high and low risk groups. The patients in the low-risk group survived longer than the high-risk group (p < 0.001). Validation assays including ROC curve, nomogram and correction curves confirmed the prediction capability of the 24-lncRNA risk mode. Functional studies showed the two patient groups had distinct immunity conditions and IC50. Conclusion: The 24-lncRNA model has potential to guide treatment of HNSCC. Future clinical studies are needed to verify the model.

Long Non-coding RNA HOTAIR in Central Nervous System Disorders: New Insights in Pathogenesis, Diagnosis, and Therapeutic Potential

Central nervous system (CNS) disorders, such as ischemic stroke, neurodegenerative diseases, multiple sclerosis, traumatic brain injury, and corresponding neuropathological changes, often lead to death or long-term disability. Long non-coding RNA (lncRNA) is a class of non-coding RNA with a transcription length over 200 nt and transcriptional regulation. lncRNA is extensively involved in physiological and pathological processes through epigenetic, transcription, and post-transcriptional regulation. Further, dysregulated lncRNA is closely related to the occurrence and development of human diseases, including CNS disorders. HOX Transcript antisense RNA (HOTAIR) is the first discovered lncRNA with trans-transcriptional regulation. Recent studies have shown that HOTAIR may participate in the regulation of the occurrence and development of CNS disorders. In addition, HOTAIR has the potential to become a new biomarker for the diagnosis and prognosis assessment of CNS disorders and even provide a new therapeutic target for CNS disorders. Here, we reviewed the research results of HOTAIR in CNS disorders to provide new insights into the pathogenesis, diagnostic value, and therapeutic target potential of HOTAIR in human CNS disorders.

Identifying a novel KLF2/lncRNA SNHG12/miR-494-3p/RAD23B axis in Spare Nerve Injury-induced neuropathic pain

Spinal cord injury (SCI) is a devastating condition for patients, affecting nearly 2.5 million people globally. Multiple side effects of SCI have resulted in a terrible life experience for SCI patients, of which neuropathic pain has attracted the most scientific interest. Even though many efforts have been made to attenuate or eliminate neuropathic pain induced by SCI, the outcomes for patients are still poor. Therefore, identifying novel diagnosis or therapeutic targets of SCI-induced neuropathic pain is urgently needed. Recently, multiple functions of long non-coding RNA (lncRNA) have been elucidated, including those in SCI-induced neuropathic pain. In this study, lncRNA small nucleolar RNA host gene 12 (SNHG12) was found to be upregulated in the dorsal root ganglion (DRGs) of rats with spare nerve injury (SNI). By constructing SCI rat models, we found that lncRNA SNHG12 expression was increased in the DRGs, and mainly distributed in the cytoplasm of PC12 cells. Paw withdrawal threshold (PWT), paw withdrawal latency (PWL), and enzyme linked immunosorbent assay (ELISA) results indicated that lncRNA SNHG12 knockdown attenuated SNI-induced neuropathic pain, and decreased the expression levels of interleukin (IL)−1β, IL-6, and tumour necrosis factor α (TNF-α) in the DRGs. Bioinformatics analysis, RNA pull-down, chromatin immunoprecipitation (ChIP), and luciferase reporter gene assays showed that lncRNA SNHG12 regulates the RAD23 homologue B, nucleotide excision repair protein (RAD23B) expression, through targeting micro RNA (miR)−494-3p. Furthermore, the study indicated that Kruppel-Like Factor 2 (KLF2) could regulate lncRNA SNHG12 expression in PC12 cells. This study identified a novel KLF2/lncRNA SNHG12/miR-494-3p/RAD23B axis in SNI-induced neuropathic pain, which might provide a new insight for developing novel diagnosis, or therapeutic targets of SCI-induced neuropathic pain in the future.

An update on the functional roles of long non‑coding RNAs in ischemic injury (Review)

Ischemic injuries result from ischemia and hypoxia in cells. Tissues and organs receive an insufficient supply of nutrients and accumulate metabolic waste, which leads to the development of inflammation, fibrosis and a series of other issues. Ischemic injuries in the brain, heart, kidneys, lungs and other organs can cause severe adverse effects. Acute renal ischemia induces acute renal failure, heart ischemia induces myocardial infarction and cerebral ischemia induces cerebrovascular accidents, leading to loss of movement, consciousness and possibly, life-threatening disabilities. Existing evidence suggests that long non-coding RNAs (lncRNAs) are regulatory sequences involved in transcription, post-transcription, epigenetic regulation and multiple physiological processes. lncRNAs have been shown to be differentially expressed following ischemic injury, with the severity of the ischemic injury being affected by the upregulation or downregulation of certain types of lncRNA. The present review article provides an extensive summary of the functional roles of lncRNAs in ischemic injury, with a focus on the brain, heart, kidneys and lungs. The present review mainly summarizes the functional roles of lncRNA MALAT1, lncRNA MEG3, lncRNA H19, lncRNA TUG1, lncRNA NEAT1, lncRNA AK139328 and lncRNA CAREL, among which lncRNA MALAT1, in particular, plays a crucial role in ischemic injury and is currently a hot research topic.

DMDRMR promotes angiogenesis via antagonizing DAB2IP in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) patients are highly angiogenic and treated by targeted therapies against VEGFA/VEGFR signaling pathway. However, tumors with such targeted therapies remain a significant clinic challenge. Understanding the underlying mechanism against angiogenesis is highly desired. Here, we demonstrated that the lncRNA DMDRMR serves as a sponge of miR-378a-5p to increase EZH2 and SMURF1 expression, thus promoting EZH2-mediated transcriptional repression of DAB2IP and SMURF1-mediated degradation of DAB2IP. Consequently, this axis activates VEGFA/VEGFR2 signaling pathway, resulting in angiogenesis and resistance of tumor cells to sunitinib in ccRCC. Moreover, the competing endogenous RNA regulatory axis of DMDRMR is clinically relevant to ccRCC pathogenesis and prognosis of patients with ccRCC. Our results support that the DMDRMR/miR-378a-5p/DAB2IP axis may serve as a novel target for combination diagnosis or therapy of ccRCC patients. Our findings may have highly clinical relevance for future translation to develop the targeted therapies for patients with ccRCC.

Role of lncRNA TUG1 in Adenomyosis and its Regulatory Mechanism in Endometrial Epithelial Cell Functions

OBJECTIVE

Adenomyosis (AM) is a common gynecological disorder that can cause pelvic pain. The regulatory role of long noncoding RNAs (lncRNAs) in AM progression has been widely reported. This study investigated the effect and mechanism of lncRNA taurine-upregulated gene 1 (TUG1) on endometrial epithelial cells (EECs) in AM.

METHODS

Endometrial tissues of AM patients and controls were collected. A murine model of AM was established by tamoxifen induction. TUG1 expression in endometrial tissues of AM patients and mice was determined. In vivo, the effect of TUG1 on AM mice was measured through H&E staining, Masson's staining, uterine weight, and estradiol concentration. EECs isolated from AM patients were transfected with sh-TUG1. In vitro, the effect of TUG1 on the proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), and angiogenesis of EECs was evaluated by CCK8, colony formation, immunofluorescence, wound healing, and Transwell assays. The binding relationship among TUG1, E2F4, and KLF5 was confirmed using RNA immunoprecipitation and RNA pull-down assays. A function rescue experiment was designed to verify the effect of KLF5 on EECs.

RESULTS

TUG1 expression was elevated in AM mice and patients. Downregulation of TUG1 promoted the recovery of AM mice. Downregulation of TUG1 suppressed proliferation, migration, invasion, EMT, and angiogenesis of EECs. Mechanically, TUG1 suppressed KLF5 transcription by binding to E2F4. Downregulation of KLF5 reversed the inhibitory effect of TUG1 silencing on the functions of EECs.

CONCLUSION

TUG1 expression was elevated in AM, and TUG1 facilitated proliferation, migration, invasion, EMT, and angiogenesis of EECs via E2F4/KLF5, thereby aggravating AM.

Dexmedetomidine promotes cell proliferation and inhibits cell apoptosis by regulating LINC00982 and activating the phosphoinositide-3-kinase (PI3K)/protein kinase B (AKT) signaling in hypoxia/reoxygenation-induced H9c2 cells

Previous studies showed dexmedetomidine (DEX) could alleviate myocardial ischemia/reperfusion injury (MIRI). Nevertheless, the mechanisms by which DEX alleviated MIRI remain to be determined. Our results demonstrated that DEX reversed hypoxia/reoxygenation (H/R)-induced decreased proliferation, and enhanced LINC00982 level, apoptosis, and inflammation in H9c2 cells. Moreover, LINC00982 overexpression attenuated the DEX-mediated protective effect of H9c2 cells under H/R. In addition, DEX upregulated p-phosphoinositide-3-kinase (p-PI3K) and p-protein kinase B (p-AKT) levels, and the silencing of LINC00982 further enhanced this effect in H/R-induced H9c2 cells. Furthermore, LINC00982 deletion enhanced the protective effect of DEX on H9c2 cells under H/R condition, while PI3K inhibitor, LY294002, obviously reversed this phenomenon. In sum, our work determined that DEX could suppress cell apoptosis and inflammation in H/R-triggered H9c2 through downregulating LINC00982 and activating PI3K/AKT signaling.

A novel risk score model based on five angiogenesis-related long non-coding RNAs for bladder urothelial carcinoma

Background

Tumour angiogenesis is an independent risk factor for bladder urothelial carcinoma (BUC) progression, but viable and promising antiangiogenic targets are understudied. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play prominent role in the tumour microenvironment and tumour angiogenesis.

Methods

The clinical data of BUC patients were obtained from TCGA database and clinical specimens of 138 BUC patients. Univariate and multivariate COX regression analyses were used to identify survival-related ARLNRs (sARLNRs) from The Molecular Signatures Database v4.0. Fisher’s exact probability method was used to detect the correlations between sARLNRs levels and clinicopathological characteristics. A chain of experiments including FACS, qPCR, immunohistochemistry, tube formation, migration and invasion assays, combining with co-culture models, were utilized to validate the clinical significance and angiogenetic correlation of sARLNRs.

Results

Five sARLNRs were employed to establish an angiogenesis-related risk score model, by which patients in the low-risk group obtained better overall survival than those in the high-risk group. The expression of AC005625.1 and AC008760.1 was significantly related to ECs percentage, tumour size and muscle invasion status. Besides, AC005625.1 and AC008760.1 expressed lower in BUC cell lines and tumour tissues than that in normal urothelial cells and adjacent normal tissues, with much lower levels in more advanced T stages. A prominently higher proportion of ECs was detected in tumour tissues with lower expression of AC005625.1 and AC008760.1. In the co-culture models, we found that knockdown of AC005625.1 and AC008760.1 in BUC cells increased the tube formation, migration and invasion abilities of HUVEC. The expression levels of CD31, VEGF-A, VIMENTIN and N-CADHERIN were also enhanced in HUVEC cells co-cultured with siR-AC005625.1 and siR-AC008760.1-treated T24 cells.

Conclusion

In the study, we identify five sARLNRs and validate their clinical significance, angiogenesis correlation and prognosis-predictive values in BUC. These findings may provide a new perspective and some promising antiangiogenic targets for clinical diagnosis and treatment strategies of BUC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-022-02575-1.

LncRNA growth arrest specific transcript 5 inhibits the growth of pituitary neuroendocrine tumors via miR-27a-5p/cylindromatosis axis

The long noncoding RNA growth arrest-specific transcript 5 (GAS5) has been reported to function as a suppressor in many cancers. However, the role and mechanism of lncRNA GAS5 in pituitary neuroendocrine tumors (PitNETs) remain unclear. Here, we found that lncRNA GAS5 and cylindromatosis (CYLD) expression was downregulated in invasive PitNET tissues and was negatively correlated with miR-27a-5p expression. LncRNA GAS5 overexpression inhibited proliferation of PitNETs cell line MMQ and GH3 cells and induced cell apoptosis, simultaneously, inhibited miR-27a-5p expression and increased CYLD expression. Moreover, miR-27a-5p mimic significantly decreased the luciferase activities of lncRNA GAS5 and CYLD luciferase reporter vector and downregulated CYLD expression, while miR-27a-5p inhibitor increased the expression of CYLD in MMQ and GH3 cells. Furthermore, RNA-immunoprecipitation assay revealed the direct binding between lncRNA GAS5 and miR-27a-5p. Additionally, miR-27a-5p mimic or silenced CYLD attenuated the effect of lncRNA GAS5 on MMQ and GH3 cell proliferation. In vivo lncRNA GAS5 overexpression inhibited GH3 cell tumor growth, while miR-27a-5p mimic or silenced CYLD attenuated the effect of lncRNA GAS5 on GH3 cell tumor growth. These results suggest that lncRNA GAS5 acts as an endogenous sponge by binding miR-27a-5p to increase the expression of its target gene CYLD, thereby inhibits PitNETs cell proliferation and tumor growth.

LINC01578 affects the radiation resistance of lung cancer cells through regulating microRNA-216b-5p/TBL1XR1 axis

Radiation resistance largely limits the survival of patients with non-small-cell lung cancer (NSCLC). To understand the mechanism underlying radiation resistance, we explored the influence of LINC01578 in radiation-resistant NSCLC cells. LINC01578, miR-216b-5p and Transducin (beta)-like 1 X-linked receptor 1 (TBL1XR1) expression was evaluated in patients with NSCLC, and their correlation with patients' prognosis was examined. Radiation-resistant NSCLC cell line (A549-RR) was induced and treated with oligonucleotide or plasmid transfection, and cell biological functions were captured. The interplay between LINC01578, miR-216b-5p and TBL1XR1 was clarified. NSCLC patients showed high LINC01578 and TBL1XR1 expression, and low miR-216b-5p expression, which was correlated to shorter patients' prognosis, respectively. LINC01578 or TBL1XR1 deficiency or miR-216b-5p elevation suppressed the functional activities of A549-RR cells. LINC01578 suppression elevated miR-216b-5p expression, consequently leading to the down-regulation of TBL1XR1. miR-216b-5p silencing or TBL1XR1 overexpression compromised LINC01578 knockdown's effects on radiation resistance of A549-RR cells. In brief, LINC01578 suppresses miR-216b-5p and enhances TBL1XR1 expression, thus to promote biological functions of radiation-resistant NSCLC cells.

Identification of an Iron Metabolism-Related lncRNA Signature for Predicting Osteosarcoma Survival and Immune Landscape

Background: Long noncoding RNAs (lncRNAs) act as epigenetic regulators in the process of ferroptosis and iron metabolism. This study aimed to identify an iron metabolism-related lncRNA signature to predict osteosarcoma (OS) survival and the immune landscape.

Methods: RNA-sequencing data and clinical information were obtained from the TARGET dataset. Univariate Cox regression and LASSO Cox analysis were used to develop an iron metabolism-related lncRNA signature. Consensus clustering analysis was applied to identify subtype-based prognosis-related lncRNAs. CIBERSORT was used to analyze the difference in immune infiltration and the immune microenvironment in the two clusters.

Results: We identified 302 iron metabolism-related lncRNAs based on 515 iron metabolism-related genes. The results of consensus clustering showed the differences in immune infiltration and the immune microenvironment in the two clusters. Through univariate Cox regression and LASSO Cox regression analysis, we constructed an iron metabolism-related lncRNA signature that included seven iron metabolism-related lncRNAs. The signature was verified to have good performance in predicting the overall survival, immune-related functions, and immunotherapy response of OS patients between the high- and low-risk groups.

Conclusion: We identified an iron metabolism-related lncRNA signature that had good performance in predicting survival outcomes and showing the immune landscape for OS patients. Furthermore, our study will provide valuable information to further develop immunotherapies of OS.

A Prognostic Model of Bladder Cancer Based on Metabolism-Related Long Non-Coding RNAs

Background

Some studies have revealed a close relationship between metabolism-related genes and the prognosis of bladder cancer. However, the relationship between metabolism-related long non-coding RNAs (lncRNA) regulating the expression of genetic material and bladder cancer is still blank. From this, we developed and validated a prognostic model based on metabolism-associated lncRNA to analyze the prognosis of bladder cancer.

Methods

Gene expression, lncRNA sequencing data, and related clinical information were extracted from The Cancer Genome Atlas (TCGA). And we downloaded metabolism-related gene sets from the human metabolism database. Differential expression analysis is used to screen differentially expressed metabolism-related genes and lncRNAs between tumors and paracancer tissues. We then obtained metabolism-related lncRNAs associated with prognosis by correlational analyses, univariate Cox analysis, and logistic least absolute shrinkage and selection operator (LASSO) regression. A risk scoring model is constructed based on the regression coefficient corresponding to lncRNA calculated by multivariate Cox analysis. According to the median risk score, patients were divided into a high-risk group and a low-risk group. Then, we developed and evaluated a nomogram including risk scores and Clinical baseline data to predict the prognosis. Furthermore, we performed gene-set enrichment analysis (GSEA) to explore the role of these metabolism-related lncRNAs in the prognosis of bladder cancer.

Results

By analyzing the extracted data, our research screened out 12 metabolism-related lncRNAs. There are significant differences in survival between high and low-risk groups divided by the median risk scoring model, and the low-risk group has a more favorable prognosis than the high-risk group. Univariate and multivariate Cox regression analysis showed that the risk score was closely related to the prognosis of bladder cancer. Then we established a nomogram based on multivariate analysis. After evaluation, the modified model has good predictive efficiency and clinical application value. Furthermore, the GSEA showed that these lncRNAs affected bladder cancer prognosis through multiple links.

Conclusions

A predictive model was established and validated based on 12 metabolism-related lncRNAs and clinical information, and we found these lncRNA affected bladder cancer prognosis through multiple links.

Recent advances of NEAT1-miRNA interactions in cancer

With high incidence rate, cancer is the main cause of death in humans. Non-coding RNAs, as novel master regulators, especially long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), play important roles in the regulation of tumorigenesis. lncRNA NEAT1 has recently gained much attention, as it is dysregulated in a broad spectrum of cancers, where it acts as either an oncogene or a tumor suppressor gene. Accumulating evidence shows that NEAT1 is correlated with the process of carcinogenesis, including proliferation, invasion, survival, drug resistance, and metastasis. NEAT1 is considered to be a biomarker and a novel therapeutic target for the diagnosis and prognosis of different cancer types. The mechanisms by which NEAT1 plays a critical role in cancers are mainly via interactions with miRNAs. NEAT1-miRNA regulatory networks play significant roles in tumorigenesis, which has attracted much attention from researchers around the world. In this review, we summarize the interaction of NEAT1 with miRNAs in the regulation of protein-coding genes in cancer. A better understanding of the NEAT1-miRNA interactions in cancer will help develop new diagnostic biomarkers and therapeutic approaches.

Novel long non-coding RNA lncAMPC downregulates PTEN via miR-214 to promote nasopharyngeal carcinoma progression

Long non-coding RNAs (lncRNAs) are a type of non-coding RNAs with transcript lengths exceeding 200 nt. lncRNAs suppress or promote cancer mainly by regulating gene expression. The aim of this study was to explore the role of lncRNAs activated in metastatic PCa (lncAMPC) in nasopharyngeal carcinoma (NPC). Total RNAs were isolated from NPC and adjacent non-tumor tissues from 60 NPC patients and subjected to RT-qPCR to analyze differential expression of lncAMPC and miR-214. The roles of lncAMPC and miR-214 in regulating PTEN expression were analyzed using RT-qPCR and Western blot. Cell proliferation was analyzed using the BrdU assay. The results showed that lncAMPC was overexpressed in NPC tissues and was localized in both nuclei and cytoplasms of NPC cells. MiR-214 was positively correlated with lncAMPC. LncAMPC overexpression upregulated miR-214 and indirectly downregulated PTEN via miR-214. BrdU incorporation assay showed that lncAMPC and miR-214 overexpression increased cell proliferation. PTEN overexpression completely reversed the promoting effects of lncAMPC and miR-214 overexpression on cell proliferation. Therefore, lncAMPC might downregulate PTEN via miR-214 to increase NPC cell proliferation.