LNCcation: lncRNA localization and function

Long Non-Coding RNA GAS5 Promotes BAX Expression by Competing with microRNA-128-3p in Response to 5-Fluorouracil

The acquisition of drug resistance is a major hurdle for effective cancer treatment. Although several efforts have been made to overcome drug resistance, the underlying mechanisms have not been fully elucidated. This study investigated the role of long non-coding RNA (lncRNA) growth arrest-specific 5 (GAS5) in drug resistance. GAS5 was found to be downregulated in colon cancer cell lines that are resistant to 5-fluorouracil (5-FU). Downregulation of GAS5 decreased the viability of HCT116 cells and the level of the pro-apoptotic BAX protein, while GAS5 overexpression promoted cell death in response to 5-FU. The interaction between GAS5 and BAX mRNA was investigated using MS2-tagged RNA affinity purification (MS2-trap) followed by RT-qPCR, and the results showed that GAS5 bound to the 3'-untranslated region of BAX mRNA and enhanced its expression by interfering with the inhibitory effect of microRNA-128-3p, a negative regulator of BAX. In addition, ectopic expression of GAS5 increased the sensitivity of resistant cells in response to anti-cancer drugs. These results suggest that GAS5 promoted cell death by interfering with miR-128-3p-mediated BAX downregulation. Therefore, GAS5 overexpression in chemo-resistant cancer cells may be a potential strategy to improve the anti-cancer efficacy of drugs.

Construction of a Necroptosis-Related lncRNA Signature for Predicting Prognosis and Immune Response in Kidney Renal Clear Cell Carcinoma

Necroptosis is a new type of programmed cell death and involves the occurrence and development of various cancers. Moreover, the aberrantly expressed lncRNA can also affect tumorigenesis, migration, and invasion. However, there are few types of research on the necroptosis-related lncRNA (NRL), especially in kidney renal clear cell carcinoma (KIRC). In this study, we analyzed the sequencing data obtained from the TGCA-KIRC dataset, then applied the LASSO and COX analysis to identify 6 NRLs (AC124854.1, AL117336.1, DLGAP1-AS2, EPB41L4A-DT, HOXA-AS2, and LINC02100) to construct a risk model. Patients suffering from KIRC were divided into high- and low-risk groups according to the risk score, and the patients in the low-risk group had a longer OS. This signature can be used as an indicator to predict the prognosis of KIRC independent of other clinicopathological features. In addition, the gene set enrichment analysis showed that some tumor and immune-associated pathways were more enriched in a high-risk group. We also found significant differences between the high and low-risk groups in the infiltrating immune cells, immune functions, and expression of immune checkpoint molecules. Finally, we use the "pRRophetic" package to complete the drug sensitivity prediction, and the risk score could reflect patients' response to 8 small molecule compounds. In general, NRLs divided KIRC into two subtypes with different risk scores. Furthermore, this signature based on the 6 NRLs could provide a promising method to predict the prognosis and immune response of KIRC patients. To some extent, our findings helped give a reference for further research between NRLs and KIRC and find more effective therapeutic drugs for KIRC.

Mitochondria-localized lncRNA HITT inhibits fusion by attenuating formation of mitofusin-2 homotypic or heterotypic complexes

Long noncoding RNAs (lncRNAs) are emerging as essential players in multiple biological processes. Mitochondrial dynamics, comprising the continuous cycle of fission and fusion, are required for healthy mitochondria that function properly. Despite long-term recognition of its significance in cell-fate control, the mechanism underlying mitochondrial fusion is not completely understood, particularly regarding the involvement of lncRNAs. Here, we show that the lncRNA HITT (HIF-1α inhibitor at translation level) can specifically localize in mitochondria. Cells expressing higher levels of HITT contain fragmented mitochondria. Conversely, we show that HITT knockdown cells have more tubular mitochondria than is present in control cells. Mechanistically, we demonstrate HITT directly binds mitofusin-2 (MFN2), a core component that mediates mitochondrial outer membrane fusion, by the in vitro RNA pull-down and UV-cross-linking RNA-IP assays. In doing so, we found HITT disturbs MFN2 homotypic or heterotypic complex formation, attenuating mitochondrial fusion. Under stress conditions, such as ultraviolet radiation, we in addition show HITT stability increases as a consequence of MiR-205 downregulation, inhibiting MFN2-mediated fusion and leading to apoptosis. Overall, our data provide significant insights into the roles of organelle (mitochondria)-specific resident lncRNAs in regulating mitochondrial fusion and also reveal how such a mechanism controls cellular sensitivity to UV radiation-induced apoptosis.

Long Noncoding RNAs in the Pathogenesis of Insulin Resistance

Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.

Context-Dependent Function of Long Noncoding RNA PURPL in Transcriptome Regulation during p53 Activation

PURPL is a p53-induced lncRNA that suppresses basal p53 levels. Here, we investigated PURPL upon p53 activation in liver cancer cells, where it is expressed at significantly higher levels than other cell types. Using isoform sequencing, we discovered novel PURPL transcripts that have a retained intron and/or previously unannotated exons. To determine PURPL function upon p53 activation, we performed transcriptome sequencing (RNA-Seq) after depleting PURPL using CRISPR interference (CRISPRi), followed by Nutlin treatment to induce p53. Strikingly, although loss of PURPL in untreated cells altered the expression of only 7 genes, loss of PURPL resulted in altered expression of ~800 genes upon p53 activation, revealing a context-dependent function of PURPL. Pathway analysis suggested that PURPL is important for fine-tuning the expression of specific genes required for mitosis. Consistent with these results, we observed a significant decrease in the percentage of mitotic cells upon PURPL depletion. Collectively, these data identify novel transcripts from the PURPL locus and suggest that PURPL delicately moderates the expression of mitotic genes in the context of p53 activation to control cell cycle arrest.

LncRNA Taurine Up-Regulated 1 plays a proapoptotic role by regulating nuclear-cytoplasmic shuttle of HuR under the condition of neuronal ischemia

The study aimed to identify TUG1 as an essential regulator of apoptosis in HT22 (mouse hippocampal neuronal cells) by direct interaction with the RNA-binding protein HuR. In order to study the role of TUG1 in the context of ischemia, we used mouse hippocampal neuronal cells treated with oxyglucose deprivation to establish an in-vitro ischemia model. A bioinformatic analysis and formaldehyde RNA immunoprecipitation (fRIP) were used to investigate the biological functions. A Western blot assay and reverse transcription polymerase chain reaction were used to explore the expression of the molecules involved. A cell proliferation and cytotoxicity assay was performed to detect neuronal apoptosis. TUG1 exhibits a localization-specific expression pattern in HT22 cells under OGD treatment. The bioinformatics analysis showed a strong correlation between the TUG1 and HuR as predicted, and this interaction was subsequently confirmed by fRIP-qPCR. We found that HuR was translocated from the nucleus to the cytoplasm after ischemia treatment and subsequently targeted and stabilized COX-2 mRNA, which led to elevated COX-2 mRNA levels and apoptosis of the HT22 cells. Furthermore, nuclear-specific disruption of TUG1 prevented the translocation of HuR to the cytoplasm and decreased COX-2 mRNA expression, resulting in increased cell viability and partially reversed apoptosis. In conclusion, it was demonstrated that TUG1 accelerates the process of apoptosis by promoting the transfer of HuR to the cytoplasm and stabilizing COX-2 mRNA. These results provide useful information concerning a therapeutic target for ischemic stroke.

Association of lncRNA H19 polymorphisms with cancer susceptibility: An updated meta-analysis based on 53 studies

The association between polymorphisms in lncRNA H19 and cancer susceptibility remains to be inconsistent. This study aimed to provide a more precise estimation of the relationship between lncRNA H19 polymorphisms and the risk of cancer based on all available published studies. 53 studies encompassing 32,376 cases and 43,659 controls were included in our meta-analysis by searching the Pubmed, Embase, Web of Science, WanFang, and China National Knowledge Infrastructure databases. Pooled ORs and their 95% CIs were used to estimate the strength between the SNPs in H19 (rs217727, rs2839698, rs2107425, rs3024270, rs2735971, rs3741216, and rs3741219) and cancer susceptibility. The results showed that H19 rs2839698 polymorphism was associated with increased cancer risk in all participants under three genetic models. However, no significant association was identified between the other six SNPs as well as an overall cancer risk. Stratification by ethnicity showed that rs2839698 mutation indicated to be an important hazardous factor for the Asian population. While rs2107425 mutation had a protective effect on the Caucasian population. Stratification by cancer type identified that rs217727 mutation was linked to increased susceptibility to oral squamous cell carcinoma, lung cancer, and hepatocellular carcinoma; whereas rs2839698 mutation was associated with an elevated risk of hematological tumor and digestive system tumor (p < 0.05). Besides, the rs2735971 mutation was connected with the digestive system tumor. In summary, the rs217727, rs2839698, rs2107425 and rs2735971 polymorphisms in H19 have associations with cancer susceptibility.

The Mutual Relationship between Glycosylation and Non-Coding RNAs in Cancer and Other Physio-Pathological Conditions

Glycosylation, which consists of the enzymatic addition of sugars to proteins and lipids, is one of the most important post-co-synthetic modifications of these molecules, profoundly affecting their activity. Although the presence of carbohydrate chains is crucial for fine-tuning the interactions between cells and molecules, glycosylation is an intrinsically stochastic process regulated by the relative abundance of biosynthetic (glycosyltransferases) and catabolic (glycosidases) enzymes, as well as sugar carriers and other molecules. Non-coding RNAs, which include microRNAs, long non-coding RNAs and circRNAs, establish a complex network of reciprocally interacting molecules whose final goal is the regulation of mRNA expression. Likewise, these interactions are stochastically regulated by ncRNA abundance. Thus, while protein sequence is deterministically dictated by the DNA/RNA/protein axis, protein abundance and activity are regulated by two stochastic processes acting, respectively, before and after the biosynthesis of the protein axis. Consequently, the worlds of glycosylation and ncRNA are closely interconnected and mutually interacting. In this paper, we will extensively review the many faces of the ncRNA-glycosylation interplay in cancer and other physio-pathological conditions.

Enhanced myogenesis through lncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter

The mammalian transcriptome comprises a vast family of long noncoding (lnc)RNAs implicated in physiologic processes such as myogenesis, through which muscle forms during embryonic development and regenerates in the adult. However, the specific molecular mechanisms by which lncRNAs regulate human myogenesis are poorly understood. Here, we identified a novel muscle-specific lncRNA, lncFAM71E1-2:2 (lncFAM), which increased robustly during early human myogenesis. Overexpression of lncFAM promoted differentiation of human myoblasts into myotubes, while silencing lncFAM suppressed this process. As lncFAM resides in the nucleus, chromatin isolation by RNA purification followed by mass spectrometry (ChIRP-MS) analysis was employed to identify the molecular mechanisms whereby it might promote myogenesis. Analysis of lncFAM-interacting proteins revealed that lncFAM recruited the RNA-binding protein HNRNPL to the promoter of MYBPC2, in turn increasing MYBPC2 mRNA transcription and enhancing production of the myogenic protein MYBPC2. These results highlight a mechanism whereby a novel ribonucleoprotein complex, lncFAM-HNRNPL, elevates MYBPC2 expression transcriptionally to promote myogenesis.

A review of current evidence about lncRNA MEG3: A tumor suppressor in multiple cancers

Long non-coding RNA (lncRNA) maternally expressed gene 3 (MEG3) is a lncRNA located at the DLK1-MEG3 site of human chromosome 14q32.3. The expression of MEG3 in various tumors is substantially lower than that in normal adjacent tissues, and deletion of MEG3 expression is involved in the occurrence of many tumors. The high expression of MEG3 could inhibit the occurrence and development of tumors through several mechanisms, which has become a research hotspot in recent years. As a member of tumor suppressor lncRNAs, MEG3 is expected to be a new target for tumor diagnosis and treatment. This review discusses the molecular mechanisms of MEG3 in different tumors and future challenges for the diagnosis and treatment of cancers through MEG3.

Construction of ceRNA network and key gene screening in cervical squamous intraepithelial lesions

BACKGROUND

This study aimed to construct an endogenous competition network for cervical squamous intraepithelial lesions using differential gene screening.

METHODS

GSE149763 was used to screen differentially expressed long non-coding RNAs (lncRNAs) and mRNAs to predict correlated microRNAs (miRNAs). The correlated miRNAs and GSE105409 were used to screen differentially expressed miRNAs for differential co-expression analysis, and the co-expressed differentially expressed miRNAs were used to predict correlated mRNAs. Differentially expressed mRNAs, miRNAs, and lncRNAs were visualized, and differential gene screening, enrichment, and pathway analysis were performed.

RESULTS

The ceRNA network of cervical squamous intraepithelial was successfully established and a potential differentially expressed network was identified. The key genes were VEGFA and FOS, and the key pathway was the MAPK signaling pathway.

CONCLUSIONS

The differential expression and potential effects of the lncRNA BACH1-IT1/miR-140-5p/VEGFA axis, key genes, VEGFA and FOS, and MAPK signaling in CIN were clarified, and the occurrence and potential effects of CIN were further clarified. The underlying molecular mechanism provides a certain degree of reference for subsequent treatments and experimental research.

Unveiling the Vital Role of Long Non-Coding RNAs in Cardiac Oxidative Stress, Cell Death, and Fibrosis in Diabetic Cardiomyopathy

Diabetes mellitus is a burdensome public health problem. Diabetic cardiomyopathy (DCM) is a major cause of mortality and morbidity in diabetes patients. The pathogenesis of DCM is multifactorial and involves metabolic abnormalities, the accumulation of advanced glycation end products, myocardial cell death, oxidative stress, inflammation, microangiopathy, and cardiac fibrosis. Evidence suggests that various types of cardiomyocyte death act simultaneously as terminal pathways in DCM. Long non-coding RNAs (lncRNAs) are a class of RNA transcripts with lengths greater than 200 nucleotides and no apparent coding potential. Emerging studies have shown the critical role of lncRNAs in the pathogenesis of DCM, along with the development of molecular biology technologies. Therefore, we summarize specific lncRNAs that mainly regulate multiple modes of cardiomyopathy death, oxidative stress, and cardiac fibrosis and provide valuable insights into diagnostic and therapeutic biomarkers and strategies for DCM.

Extracellular vesicle-mediated transfer of lncRNA CLDN10-AS1 aggravates low-density lipoprotein-induced vascular endothelial injury

Oxidized low-density lipoprotein (ox-LDL) stimulation impairs the oxidation-reduction equilibrium in vascular endothelial cells (VECs) and contributes to atherosclerosis (AS). This study probed the mechanisms of extracellular vesicle (EV)-mediated transfer of lncRNA CLDN10 antisense RNA 1 (CLDN10-AS1) in ox-LDL-induced VEC injury. Initially, VEC injury models were established by treating human umbilical vein endothelial cells (HUVECs) with ox-LDL. EVs were isolated from HUVECs (HUVECs-EVs) and identified. CLDN10-AS1, microRNA (miR)-186, and Yin Yang 1 (YY1) expressions in ox-LDL-treated HUVECs and EVs derived from these cells (ox-EVs) were measured. HUVECs were incubated with EVs, after which the cell viability, apoptosis, and concentrations of proinflammatory cytokines and oxidative stress markers were measured. We discovered that CLDN10-AS1 and YY1 were upregulated in ox-LDL-treated HUVECs, whereas miR-186 was downregulated. ox-EVs treatment elevated CLDN10-AS1 expression in HUVECs and ox-EVs overexpressing CLDN10-AS1 promoted VEC injury. Besides, CLDN10-AS1 is competitively bound to miR-186 and promoted YY1 expression. Rescue experiments revealed that miR-186 overexpression or YY1 suppression partially reversed the roles of ox-EVs overexpressing CLDN10-AS1 in ox-LDL-induced VEC injury. Lastly, clinical serum samples were collected for verification. Overall, CLDN10-AS1 carried by HUVECs-EVs into HUVECs competitively bound to miR-186 to elevate YY1 expression, thereby aggravating ox-LDL-induced VEC injury.

Regulatory roles of noncoding RNAs in intervertebral disc degeneration as potential therapeutic targets (Review)

Intervertebral disc degeneration (IDD) is the leading cause of lower back pain, which is one of the primary factors that lead to disability and pose a serious economic burden. The key pathological processes involved are extracellular matrix degradation, autophagy, apoptosis, and inflammation of nucleus pulposus cells. Non-coding RNAs (ncRNAs), including microRNAs, long ncRNAs and circular RNAs, are key regulators of the aforementioned processes. ncRNAs are differentially expressed in tissues of the intervertebral disc between healthy individuals and patients and participate in the pathological progression of IDD via a complex pattern of gene regulation. However, the regulatory mechanisms of ncRNAs in IDD remain unclear. The present review summarizes the latest insights into the regulatory role of ncRNAs in IDD and sheds light on potentially novel therapeutic strategies for IDD that may be implemented in the future.

Molecular typing and prognostic model of lung adenocarcinoma based on cuprotosis-related lncRNAs

Background

Previous research has shown the heterogeneity of lung adenocarcinoma (LUAD) accounts for the different effects and prognoses of the same treatment. Cuprotosis is a newly discovered form of programmed cell death involved in the development of tumors. Therefore, it is important to study the long non-coding RNAs (lncRNAs) that regulate cuprotosis to identify molecular subtypes and predict survival of LUAD.

Methods

The expression profile, clinical, and mutation data of LUAD were downloaded from The Cancer Genome Atlas (TCGA), and the "ConsensusClusterPlus" package was used to cluster LUADs based on cuprotosis-related lncRNAs (CR-lncRNAs). The least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression were used to construct a prognostic model. CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were used for assessing immune cells infiltration and immune function. The tumor microenvironment (TME) score was calculated by ESTIMATE, and the tumor mutational burden (TMB) and Tumor Immune Dysfunction and Exclusion (TIDE) were used to evaluate the efficacy of immunotherapy.

Results

Firstly, 501 CR-lncRNAs were identified based on the co-expression relationship of 19 cuprotosis genes. And univariate Cox further obtained 34 prognosis-related CR-lncRNAs. The unsupervised consensus clustering divided LUAD samples into cluster A and cluster B, and showed cluster A had better prognosis, more immune cells infiltration, stronger immune function, and a higher TME score. Subsequently, we used Lasso Cox regression to construct a prognostic model, and univariate and multivariate Cox analyses showed the risk score could be an independent prognostic indicator. Immune cells infiltration, immune function, and TME score were increased markedly in the low-risk group, while TMB and TIDE suggested the efficacy of immunotherapy might be increased in high-risk group.

Conclusions

Our research identified two new molecular subtypes and constructed a novel prognostic model of LUAD which could provide new direction for its diagnosis, treatment, and prognosis.

The tumor therapeutic potential of long non-coding RNA delivery and targeting

Long non-coding RNAs (lncRNAs) is a type of RNA over 200 nt long without any protein coding ability, which has been investigated relating to crucial biological function in cells. There are many key lncRNAs in tumor/normal cells that serve as a biological marker or a new target for tumor treatment. However, compared to some small non-coding RNA, lncRNA-based drugs are limited in clinical application. Different from other non-coding RNA, like microRNAs, most lncRNAs have a high molecular weight and conserved secondary structure, making the delivery of lncRNAs more complex than the small non-coding RNAs. Considering that lncRNAs constitute the most abundant part of the mammalian genome, it is critical to further explore lncRNA delivery and the subsequent functional studies for potential clinical application. In this review, we will discuss the function and mechanism of lncRNAs in diseases, especially cancer, and different approaches for lncRNA transfection using multiple biomaterials.

Dynamic landscape of long noncoding RNAs during leaf aging in Arabidopsis

Leaf senescence, the last stage of leaf development, is essential for whole-plant fitness as it marks the relocation of nutrients from senescing leaves to reproductive or other developing organs. Temporally coordinated physiological and functional changes along leaf aging are fine-tuned by a highly regulated genetic program involving multi-layered regulatory mechanisms. Long noncoding RNAs (lncRNAs) are newly emerging as hidden players in many biological processes; however, their contribution to leaf senescence has been largely unknown. Here, we performed comprehensive analyses of RNA-seq data representing all developmental stages of leaves to determine the genome-wide lncRNA landscape along leaf aging. A total of 771 lncRNAs, including 232 unannotated lncRNAs, were identified. Time-course analysis revealed 446 among 771 developmental age-related lncRNAs (AR-lncRNAs). Intriguingly, the expression of AR-lncRNAs was regulated more dynamically in senescing leaves than in growing leaves, revealing the relevant contribution of these lncRNAs to leaf senescence. Further analyses enabled us to infer the function of lncRNAs, based on their interacting miRNA or mRNA partners. We considered functionally diverse lncRNAs including antisense lncRNAs (which regulate overlapping protein-coding genes), competitive endogenous RNAs (ceRNAs; which regulate paired mRNAs using miRNAs as anchors), and mRNA-interacting lncRNAs (which affect the stability of mRNAs). Furthermore, we experimentally validated the senescence regulatory function of three novel AR-lncRNAs including one antisense lncRNA and two mRNA-interacting lncRNAs through molecular and phenotypic analyses. Our study provides a valuable resource of AR-lncRNAs and potential regulatory networks that link the function of coding mRNA and AR-lncRNAs. Together, our results reveal AR-lncRNAs as important elements in the leaf senescence process.

LncRNA TUG1 Promoted Stabilization of BAG5 by Binding DDX3X to Exacerbate Ketamine-Induced Neurotoxicity

As a clinically widely used anesthetic, ketamine (KET) has been reported to cause neurotoxicity in patients. Our work aimed to probe the function of long-chain non-coding RNA taurine-upregulated gene 1 (lncRNA TUG1) in KET-induced neurotoxicity. HT22 cells were subjected to KET to build the cell model. 3-(4, 5-Dimethylthiazolyl2)-2, 5-diphenyltetrazolium bromide (MTT) assay was employed to determine cell viability. Additionally, cell apoptosis was evaluated by flow cytometry. The binding relationships among TUG1, DEAD-box RNA helicase 3X (DDX3X), and Bcl-2-associated athanogene 5 (BAG5) were verified by RIP and RNA pull-down assays. Cell viability was impaired and cell apoptosis was increased in KET-treated HT22 cells accompanied by increased TUG1, DDX3X, and BAG5 expressions. TUG1 knockdown dramatically enhanced cell viability and repressed the of KET-induced apoptosis in HT22 cells, while TUG1 overexpression presented the opposite effects. In addition, we found that TUG1 promoted DDX3X expression via directly binding with DDX3X. As expected, DDX3X overexpression abolished the palliative effect of TUG1 knockdown on KET-induced neurotoxicity. Further research proved that TUG1 increased the stability of BAG5 through interacting with DDX3X. Finally, as expected, the moderating effect of TUG1 knockdown on KET-induced neuron injury was abolished by BAG5 overexpression. Taken together, TUG1 promoted BAG5 expression by binding DDX3X to exacerbate KET-induced neurotoxicity.

DANCR deletion retards the initiation and progression of hepatocellular carcinoma based on gene knockout and patient-derived xenograft in situ hepatoma mice model

Our previous study has demonstrated that the expression level of long noncoding RNA (lncRNA)-differentiation antagonizing non-protein coding RNA (DANCR) increases in hepatocellular carcinoma (HCC), contributing to the initiation and aggravation of such kind of malignant tumor, which is recognized as a promising therapeutic target for patients with HCC. To further investigate the effect of DANCR on HCC in preclinical models, we generated a Dancr knockout (KO) mice model by Cas9/gRNA technology and a patient-derived xenograft (PDX) in situ hepatoma mice model using immunodeficient mice and utilized adeno-associated virus 8 (AAV8) delivery DANCR-shRNA system to silence the expression of DANCR in xenograft tumor. Here, we reported that Dancr expression mainly occurred in hepatocytes and its depletion significantly alleviated hepatic fibrosis in mice and showed a prospective result with smaller tumor size and fewer number of tumors in HCC preclinical mice model. Additionally, we found that the expression of Dancr in mice cirrhotic liver was positively correlated with the content of Dancr in serum. Overall, DANCR KO can inhibit the occurrence and development of HCC and is a target worthy of further study in patients with HCC.

Comprehensive analysis of necroptosis-related long noncoding RNA to predict prognosis, immune status, and immunotherapeutic response in clear cell renal cell carcinoma

Background

Necroptosis has been found to be associated with tumorigenesis and tumor progression. However, the prognostic effect of long noncoding RNAs (lncRNAs) associated with necroptosis in clear cell renal cell carcinoma (ccRCC) is still unclear.

Methods

Pearson correlation analysis was used to identify necroptosis-related genes and lncRNAs obtained from The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) dataset. Least absolute shrinkage and selection operator (LASSO) regression and Cox regression analyses were used to identify a novel necroptosis-associated lncRNAs signature that significantly correlated with survival of ccRCC. Next, single sample gene set enrichment analysis (ssGSEA) was employed to assess the extent of infiltration with immune cells. Analyses to predict the half-maximal inhibitory concentration (IC50) of patients in different risk groups were also conducted. Moreover, follow-up data of an immunotherapy cohort were used to test for differences in the immunotherapeutic efficiency between two risk groups. Finally, patients with ccRCC were divided into two groups based on 6 prognostic lncRNAs.

Results

We developed a signature of necroptosis-related lncRNAs, which was verified as an independent prognostic factor that can predict prognosis up to 7 years. Patients with higher risk scores were shown to have higher immune suppressive cell infiltration levels and expression of immune checkpoint genes, which suggests that these patients were in a state of immunosuppression. Patients in the low-risk group were found to have an increased response to immunotherapy. A prognostic prediction nomogram was conducted to predict long-term survival of patients. Cluster A tumors were considered hot tumors, since they were correlated with higher levels of immune infiltration and were more sensitive to immunotherapy.

Conclusions

A comprehensive bioinformatics analysis was conducted, which found that the necroptosis-associated lncRNA signature might be a potent prognostic factor for patients with ccRCC, which could contribute to improved prognosis of these patients.

N6-methyladenosine Modification of Noncoding RNAs: Mechanisms and Clinical Applications in Cancer

N6-methyladenosine (m6A) modification remains the most pivotal epigenetic modification on RNA. As we know, m6A not only affects physiological processes but is also involved in carcinoma. Noncoding RNAs play an indispensable role in the occurrence and development of carcinoma. However, a large amount of research is focused on mRNA currently. Insufficient research has been done on the relationship between noncoding RNA (ncRNA) methylation and cancer. Therefore, this review aims to introduce the theoretical knowledge of m6A modification in noncoding RNA, discuss its function in tumorigenesis and progression, and ultimately summarize its potential clinical applications.

Functional analysis of differently expressed ferroptosis-related genes in patients with mitral valve prolapse

Background: The prevalence of mitral valve prolapse (MVP) in heart valvular diseases is globally increasing. However, the understanding of its etiology and pathogenesis is limited. So far, the relationship between ferroptosis-related genes and long non-coding RNAs (lncRNAs) in MVP remains unexplored. This study investigates the potential pathogenesis of ferroptosis-related genes in MVP and provides a therapeutic target for the disease. Methods: Blood samples from patients with MVP and healthy volunteers were collected for transcriptomic sequencing to analyze the expression of ferroptosis-related differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElncRNAs Co-expression network of ferroptosis-related DEGs and DElncRNAs. Furthermore, this work conducted GO and KEGG enrichment analyses. Results: CDKN2A, SLC1A4, ATF3, and other core genes related to the mitral valve prolapse were screened out. CDKN2A, SLC1A4, and ATF3 genes were at the core position of the network, regulated by numerous lncRNAs. Notably, these genes are primarily involved in the extracellular region and p53 signaling pathway. Conclusion: In summary, CDKN2A, SLC1A4, and ATF3 regulate the pathophysiological process of MVP and are potential therapeutic targets.

Noncoding RNAs Are Promising Therapeutic Targets for Diabetic Retinopathy: An Updated Review (2017-2022)

Diabetic retinopathy (DR) is the most common complication of diabetes. It is also the main cause of blindness caused by multicellular damage involving retinal endothelial cells, ganglial cells, and pigment epithelial cells in adults worldwide. Currently available drugs for DR do not meet the clinical needs; thus, new therapeutic targets are warranted. Noncoding RNAs (ncRNAs), a new type of biomarkers, have attracted increased attention in recent years owing to their crucial role in the occurrence and development of DR. NcRNAs mainly include microRNAs, long noncoding RNAs, and circular RNAs, all of which regulate gene and protein expression, as well as multiple biological processes in DR. NcRNAs, can regulate the damage caused by various retinal cells; abnormal changes in the aqueous humor, exosomes, blood, tears, and the formation of new blood vessels. This study reviews the different sources of the three ncRNAs-microRNAs, long noncoding RNAs, and circular RNAs-involved in the pathogenesis of DR and the related drug development progress. Overall, this review improves our understanding of the role of ncRNAs in various retinal cells and offers therapeutic directions and targets for DR treatment.

Tumour-derived exosomal lncRNA SNHG16 induces telocytes to promote metastasis of hepatocellular carcinoma via the miR-942-3p/MMP9 axis

BACKGROUND

Hepatocellular carcinoma (HCC) cell-derived exosomal LncRNA SNHG16 is highly expressed and associated with poor overall survival of patients. Telocytes (TCs), as novel interstitial cells, have been reported to promote HCC metastasis. Therefore, in our study, we investigated whether a molecular interaction occurred between exosomal LncSNHG16 and TCs in the tumor microenvironment.

METHODS

LncSNHG16 expression in HCC tissues and cell lines was measured, and bioinformatics analysis was performed. Exosomes were isolated and purified from HCC cells with LncSNHG16 overexpression/knockdown vectors and cocultured with TCs. Then, markers of the LncSNHG16/miR-942-3p/MMP9 axis were tested in TCs. Transwell assays and cell wound healing assays were designed to examine the invasion and migration of HCC cells after coincubation with TCs. RNA immunoprecipitation (RIP) assays and dual-luciferase gene reporter assays were performed to verify the binding effect of LncSNHG16, miR-942-3p, and MMP9 mRNA. In vivo, experimental animal models were established to confirm the effect of exosomal LncSNHG16-induced MMP9 expression on HCC metastasis.

RESULTS

Exosomal LncSNHG16 was phagocytized by TCs and downregulated miR-942-3p, which induced targeted MMP9 upregulation, and it had specific binding sites with miR-942-3p in TCs to facilitate the migration of HCC cells in vitro and in vivo. Exosomal LncSNHG16 was found to act as a competing endogenous RNA of the miR-942-3p/MMP9 axis in TCs.

CONCLUSION

Tumour-derived exosomal LncSNHG16 modulates MMP9 via competitively binding to miR-942-3p in TCs, thus promoting the metastasis of HCC.

Bioinformatics analysis and in vivo validation of ferroptosis-related genes in ischemic stroke

Ischemic stroke (IS) is a neurological condition associated with high mortality and disability rates. Although the molecular mechanisms underlying IS remain unclear, ferroptosis was shown to play an important role in its pathogenesis. Hence, we applied bioinformatics analysis to identify ferroptosis-related therapeutic targets in IS. IS-related microarray data from the GSE61616 dataset were downloaded from the Gene Expression Omnibus (GEO) database and intersected with the FerrDb database. In total, 33 differentially expressed genes (DEGs) were obtained and subjected to functional enrichment and protein-protein interaction (PPI) network analyses. Four candidate genes enriched in the HIF-1 signaling pathway (HMOX1, STAT3, CYBB, and TLR4) were selected based on the hierarchical clustering of the PPI dataset. We also downloaded the IR-related GSE35338 dataset and GSE58294 dataset from the GEO database to verify the expression levels of these four genes. ROC monofactor analysis demonstrated a good performance of HMOX1, STAT3, CYBB, and TLR4 in the diagnosis of ischemic stroke. Transcriptional levels of the above four genes, and translational level of GPX4, the central regulator of ferroptosis, were verified in a mouse model of middle cerebral artery occlusion (MCAO)-induced IS by qRT-PCR and western blotting. Considering the regulation of the HIF-1 signaling pathway, dexmedetomidine was applied to the MCAO mice. We found that expression of these four genes and GPX4 in MCAO mice were significantly reduced, while dexmedetomidine reversed these changes. In addition, dexmedetomidine significantly reduced MCAO-induced cell death, improved neurobehavioral deficits, and reduced the serum and brain levels of inflammatory factors (TNF-α and IL-6) and oxidative stress mediators (MDA and GSSG). Further, we constructed an mRNA-miRNA-lncRNA network based on the four candidate genes and predicted possible transcription factors. In conclusion, we identified four ferroptosis-related candidate genes in IS and proposed, for the first time, a possible mechanism for dexmedetomidine-mediated inhibition of ferroptosis during IS. These findings may help design novel therapeutic strategies for the treatment of IS.

Inflammatory mechanisms of Ginkgo Biloba extract in improving memory functions through lncRNA-COX2/NF-κB pathway in mice with status epilepticus

PURPOSE

This study was to explore whether Ginkgo biloba extract (GBE) improve memory impairment by alleviating neuroinflammation signaling in mice with status epilepticus.

METHODS

The status epilepticus (SE) mice model was established by pilocarpine and treated with 100 mg / kg of GBE for 14 days. Spontaneous alternation of Y-maze and new object recognition were used to explore memory impairment. To examine glial cell activation, we performed immunohistochemistry and immunofluorescence staining. The activation of NF-κB signaling and the expression level of lncRNA-COX2 were detected by Western blot and qRT-PCR, respectively. Adeno-associated virus lncRNA-COX2 was injected into mice for overexpression of lncRNA-COX2.

RESULTS

After GBE treatment, the spontaneous alternation rate and the recognition coefficient in SE mice were both increased. Moreover, activation of glial cells, NF-κB signaling and lncRNA-COX2 were significantly decreased in SE mice. In the GBE-treated SE mice with lncRNA-COX2 overexpression, NF-κB signaling was up-regulated again; the reduced level of inflammation factors was reversed; the GBE-rescued spontaneous alternation rate of Y-maze was eliminated.

CONCLUSION

Our results suggested that GBE reduces the hippocampal inflammation by down-regulating lncRNA-COX2 / NF-κB signaling in the SE mice, leading to the decrease of neuronal damage and the improvement of memory functions.

Noncoding RNA in the Regulation of Acute Aortic Dissection: From Profile to Mechanism

Aortic dissection is a life-threatening condition caused by a tear in the intimal layer of the aorta or bleeding within the aortic wall, resulting in the separation of the layers of the aortic wall. As Nienaber reported, aortic dissection is most common in people 65-75 years old and has an incidence of 35 cases per 100,000 people per year in this population. Many pathogenic factors are involved in aortic dissection, including hypertension, dyslipidemia, and abnormality of the aortic intima caused by genetic variation. However, with the development of gene sequencing and transgenic technology, genetic methods are being used for the diagnosis and treatment of diseases, including acute aortic dissection. Genetic research on acute aortic dissection began around 2006. Recently, research on acute aortic dissection has mainly focused on microRNA (miRNA). Studies have found that miRNA plays a critical regulatory role in the occurrence and development of acute aortic dissection. By regulating miRNA expression, acute aortic dissection can be prevented and treated.

LncRNA NALT1 promotes colorectal cancer progression via targeting PEG10 by sponging microRNA-574-5p

Colorectal cancer (CRC) is currently one of the commonest tumors and the main reason for cancer-related deaths worldwide. It has been reported that long non-coding RNAs (lncRNAs) act as important indicators and regulators in various cancers. There is an urgent need to explore new lncRNA biomarkers in CRC, as well as their functions and molecular mechanisms. NALT1 has been implicated in the occurrence of gastric cancer (GC). However, the detailed function and mechanism of NALT1 in CRC progress have not been reported. In this study, RT-qPCR was conducted to detect the expression of NALT1 in 76 CRC patients ranging from stages I through IV. To assess the biological function of NALT1, loss- and gain-of-function experiments were conducted both in vivo and in vitro. Moreover, RNA-seq, bioinformatics analysis, RNA pulldown assay, dual-luciferase reporter, Ago2-RIP, quantitative PCR, Western blot assays, and rescue experiments were performed to reveal the molecular mechanisms of competitive endogenous RNAs (ceRNAs). It was observed that high expression of NALT1 was markedly correlated with advanced cancer stage in the clinic. Functionally, NALT1 downregulation inhibited cell proliferation, migration and invasion, whereas NALT1 overexpression exhibited an opposite trend both in vivo and in vitro. Bioinformatics analysis, RNA pulldown, Ago2-RIP, and luciferase reporter assays showed that miRNA-574-5p was a target of NALT1. Additionally, dual-luciferase reporter assays, Ago2-RIP, and rescue experiments indicated that miRNA-574-5p could target the PEG10 gene directly. Our results suggested that NALT1 promoted CRC proliferation and migration by sponging miRNA-574-5p to upregulate PEG10 expression, and implied that NALT1 might act as a promising biomarker and therapeutic target for CRC.

ALKBH5-mediated m6A modification of lincRNA LINC02551 enhances the stability of DDX24 to promote hepatocellular carcinoma growth and metastasis

As the most important RNA epigenetic regulation in eukaryotic cells, N6-metheyladenosine (m⁶A) modification has been demonstrated to play significant roles in cancer progression. However, this modification in long intergenic non-coding RNAs (lincRNAs) and the corresponding functions remain elusive. Here, we showed a lincRNA LINC02551 was downregulated by AlkB Homolog 5 (ALKBH5) overexpression in a m⁶A-dependent manner in hepatocellular carcinoma (HCC). Functionally, LINC02551 was required for the growth and metastasis of HCC. Mechanistically, LINC02551, a bona fide m⁶A target of ALKBH5, acted as a molecular adaptor that blocked the combination between DDX24 and a E3 ligase TRIM27 to decrease the ubiquitination and subsequent degradation of DDX24, ultimately facilitating HCC growth and metastasis. Thus, ALKBH5-mediated LINC02551 m⁶A methylation was required for HCC growth and metastasis.

Effect of long noncoding RNA NONHSAT070806 on the apoptosis, proliferation, migration, invasion and tumorigenesis of bladder cancer

Background

Bladder cancer (BC) is the most common malignancy of the urinary tract in China, and the extent of tumor invasion negatively correlates with prognosis. The mechanism of tumor invasion in BC has been unclear until recent studies revealed the critical role of long noncoding RNAs (lncRNAs) in the proliferation and invasion of tumors. Several lncRNAs have been reported to be associated with pathogenesis in BC, but not specifically.

Methods

We used a microarray to screen the candidate lncRNAs with different expressions in BC. The expression of the lncRNAs in BC tissues or cells was identified by reverse transcription polymerase chain reaction (RT-PCR) or quantitative real-time PCR (qRT-PCR), and their ectopic expressions were measured via transfection experiment. The function of the lncRNAs was investigated by flow cytometry, caspase-3 enzyme linked immunosorbent assay (ELISA), Cell Counting Kit-8 (CCK-8), wound healing, transwell and colony formation experiments in vitro and xenograft experiments in vivo.

Results

We identified a novel sense lncRNA, NONHSAT070806, that was downregulated in BC tissues and cells and negatively correlated with level of tumor invasion in patients. Furthermore, overexpression of NONHSAT070806 induced apoptosis of T24 and 5637 cells, inhibited the proliferation, migration and invasion of BC cells, and attenuated the tumorigenesis of BC cells both in vitro and in vivo.

Conclusions

NONHSAT070806 may act as a suppressor of BC and is a potential indicator of the invasiveness of BC.

Genetic and environmental perturbations alter the rhythmic expression pattern of a circadian long non-coding RNA, Per2AS, in mouse liver

Background: Long non-coding RNAs (lncRNAs) play a wide variety of biological roles without encoding a protein. Although the functions of many lncRNAs have been uncovered in recent years, the regulatory mechanism of lncRNA expression is still poorly understood despite that the expression patterns of lncRNAs are much more specific compared to mRNAs. Here, we investigated the rhythmic expression of Per2AS, a novel lncRNA that regulates circadian rhythms. Given that Per2AS expression is antiphasic to Period2 ( Per2), a core circadian clock gene, and transcribed from the antisense strand of Per2, we hypothesized that the rhythmic Per2AS expression is driven either by its own promoter or by the rhythmic Per2 transcription via transcriptional interference. Methods: We leveraged existing circadian RNA-seq datasets and analyzed the expression patterns of Per2AS and Per2 in response to the genetic or environmental disruption of the circadian rhythm in mouse liver. We tested our hypotheses by comparing the changes in the expression patterns of Per2AS and Per2. Conclusions: We found that, in some cases, Per2AS expression is independently controlled by other circadian transcription factors. In other cases, the pattern of expression change is consistent with both transcriptional interference and independent regulation hypotheses. Although additional experiments will be necessary to distinguish these possibilities, findings from this work contribute to a deeper understanding of the mechanism of how the expression of lncRNA is regulated.

Comprehensive analysis of m5C-Related lncRNAs in the prognosis and immune landscape of hepatocellular carcinoma

5-Methyladenosine (m5C) is a type of epigenetic modification involved in the progression of various cancers. To investigate the role of m5C-related long non-coding RNAs (lncRNAs) in the prognosis and immune cell infiltration in hepatocellular carcinoma (HCC), we obtained patients' clinical information and transcriptome data of HCC from the Cancer Genome Atlas (TCGA) database. We applied Pearson correlation analysis to construct an m5C-related lncRNA-messenger RNA (mRNA) co-expression network. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analysis were employed to establish an m5C-related lncRNA prognostic risk model. We then verified the model using Kaplan-Meier analysis, principal component analysis, as well as univariate and multivariate Cox analyses. The expression of m5C-related lncRNAs was validated in HCC tissues and different cell lines. Combining the risk score and clinicopathological features, a nomogram was established for predicting the overall survival (OS) of HCC patients. Furthermore, gene set enrichment analysis (GSEA) revealed that some tumor-associated pathways were significantly enriched in the high-risk group. Immune cell infiltration analysis demonstrated that the levels of Treg cells, neutrophils, and M2 macrophages were higher in the high-risk group. In addition, patients with high tumor mutation burden (TMB) had worse OS than those with low TMB. We also assessed the immune checkpoint level and chemotherapeutic agent sensibility. Then in vitro experiments were performed to examine the biological function of MKLN1-AS in HCC cells and found that knockdown of MKLN1-AS suppressed the proliferation, migration, and invasion. In conclusion, m5C-related lncRNAs played a critical role in predicting the prognosis of patients with HCC and may serve as new therapeutic targets for HCC patients.

Glycation-Associated Diabetic Nephropathy and the Role of Long Noncoding RNAs

The glycation of various biomolecules is the root cause of many pathological conditions associated with diabetic nephropathy and end-stage kidney disease. Glycation imbalances metabolism and increases renal cell injury. Numerous therapeutic measures have narrowed down the adverse effects of endogenous glycation, but efficient and potent measures are miles away. Recent advances in the identification and characterization of noncoding RNAs, especially the long noncoding RNAs (lncRNAs), have opened a mammon of new biology to explore the mitigations for glycation-associated diabetic nephropathy. Furthermore, tissue-specific distribution and condition-specific expression make lncRNA a promising key for second-generation therapeutic interventions. Though the techniques to identify and exemplify noncoding RNAs are rapidly evolving, the lncRNA study encounters multiple methodological constraints. This review will discuss lncRNAs and their possible involvement in glycation and advanced glycation end products (AGEs) signaling pathways. We further highlight the possible approaches for lncRNA-based therapeutics and their working mechanism for perturbing glycation and conclude our review with lncRNAs biology-related future opportunities.

Integrated analysis of lncRNA-mediated ceRNA network involved in immune regulation in the spleen of Meishan piglets

Meishan pigs are a famous local pig breed in China, with high fertility and early sexual maturity, and stronger immunity compared to other breeds. The spleen is the largest lymphoid organ in pigs and performs essential functions, such as those relating to immunity and haematopoiesis. The invasion of many pathogenic microorganisms in pigs is associated with spleen damage. Long non-coding RNAs participate in a broad range of biological processes and have been demonstrated to be associated with splenic immune regulation. However, the expression network of mRNAs and lncRNAs in the spleen of Meishan pigs remains unclear. This study collected spleen tissues from Meishan piglets at three different ages as a model, and mRNA and lncRNA transcripts were profiled for each sample. Additionally, 1,806 differential mRNAs and 319 differential lncRNAs were identified. A complicated interaction between mRNAs and lncRNAs was identified via WGCNA, demonstrating that lncRNAs are a crucial regulatory component in mRNA. The results show that the modules black and red have similar mRNA and lncRNA transcription patterns and are mainly involved in the process of the immune defense response. The core genes (DHX58 and IFIT1) and key lncRNAs (TCONS-00002102 and TCONS-00012474) of piglet spleen tissue were screened using the ceRNA network. The expression of these genes is related to the immune response of pigs. Our research may contribute to a further understanding of mRNA and lncRNA expression in the spleen of piglets, and provide new ideas to improve the disease resistance of piglets.

Targeting lncRNA/Wnt axis by flavonoids: A promising therapeutic approach for colorectal cancer

Despite the dramatic advances in our understanding of the etiology of colorectal cancer (CRC) in recent decades, effective therapeutic strategies are still urgently needed. Oncogenic mutations in the Wnt/β-Catenin pathway are hallmarks of CRC. Moreover, long non-coding RNAs (lncRNAs) as molecular managers are involved in the initiation, progression, and metastasis of CRC. Therefore, it is important to further explore the interaction between lncRNAs and Wnt/β-Catenin signaling pathway for targeted therapy of CRC. Natural phytochemicals have not toxicity and can target carcinogenesis-related pathways. Growing evidences suggest that flavonoids are inversely associated with CRC risk. These bioactive compounds could target carcinogenesis pathways of CRC and reduced the side effects of anti-cancer drugs. The review systematically summarized the progress of flavonoids targeting lncRNA/Wnt axis in the investigations of CRC, which will provide a promising therapeutic approach for CRC and develop nutrition-oriented preventive strategies for CRC based on epigenetic mechanisms. In the field, more epidemiological and clinical trials are required in the future to verify feasibility of targeting lncRNA/Wnt axis by flavonoids in the therapy and prevention of CRC.

Transcriptome Sequencing Analysis of lncRNA and mRNA Expression Profiles in Bone Nonunion

Background

Bone nonunion is a serious complication of fracture. This study explored the differentially expressed lncRNAs (DELs) and mRNAs (DEGs) and identified potential lncRNA-mRNA interactions in bone nonunion.

Methods

We extracted total RNA from three bone nonunion and three bone union patient tissue samples. RNA sequencing was performed to detect DELs and DEGs between bone nonunion and union tissue samples. The lncRNAs and genes with absolute log2-fold change (log2FC) > 1 and adjusted p value < 0.05 were further chosen for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. lncRNA and targeted mRNA interaction networks were constructed.

Results

We observed 179 DELs and 415 DEGs between the bone nonunion and union tissue samples. GO analysis indicated that DELs and DEGs were mainly enriched in the chondroitin sulfate proteoglycan biosynthetic process. DELs and DEGs were enriched in “ECM-receptor interaction” and “Staphylococcus aureus infection” KEGG pathways. Several potential lncRNA-mRNA interactions were also predicted.

Conclusions

This study identified bone nonunion-associated lncRNAs and mRNAs using deep sequencing that may be useful as potential biomarkers for bone nonunion.

LINC00958 Inhibits Autophagy of Bladder Cancer Cells via Sponge Adsorption of miR-625-5p to Promote Tumor Angiogenesis and Oxidative Stress

Objective

This study further explored LINC00958's role in promoting tumor angiogenesis (AG) and oxidative stress (OS) development by inhibiting BC cell autophagy through sponge adsorption of miR-625-5p.

Methods

BC patients and healthy controls who visited our hospital between June 2017 and February 2019 were selected as the research group (RG) and the control group (CG), respectively, with a total of 133 study subjects. Peripheral blood LINC00958 and miR-625-5p in both cohorts of participants were detected. Additionally, human bladder transitional cell carcinoma cells (T24 and J82) and human normal urothelial cells (SV-HUC-1) were purchased. Alterations in cell biological behavior were observed after transfecting miR-625-5p-mimics, miR-625-5p-inhibition, and miR-625-5p-NC sequences into these cells, respectively. Besides, ELISA was performed to quantify inflammatory factors (IFs), AG indicators, and OS indexes in cells. Subsequently, a double luciferase reporter (DLR) assay was performed to verify the targeting relationship between LINC00958 and miR-625-5p. Finally, BALB/c-nu nude mice were purchased, and T24 cells transfected with silenced LINC00958 and miR-625-5p expression sequences were used to establish subcutaneous tumors to observe tumor growth and pathological changes.

Results

RG exhibited higher LINC00958 and lower miR-625-5p than CG. LINC00958 and miR-625-5p were strongly linked to myometrial invasion (MI), lymph node metastasis (LNM), distant metastasis (DM), and histology in BC patients, and the increase of LINC00958 and the decrease of miR-625-5p predicted an increased risk of prognostic death in such patients. After miR-625-5p inhibition, the capacity of BC cells to proliferate, invade, and migrate enhanced and the AG, inflammatory response, and OS injury increased, while the apoptosis rate and autophagy ability decreased. The DLR assay revealed inhibited LINC00958WT fluorescence activity by miR-625-5p-mimics, while the biological behavior of BC cells cotransfected with sh-LINC00958 and miR-625-5p-inhibition had no difference with the functions of sh-control and miR-625-5p-NC cotransfected cells. Finally, the nude mouse tumorigenesis experiment showed that the tumor mass, volume, and histopathological features of the sh-LINC00958 group were decreased compared with the sh-control group, while those of the miR-625-5p-inhibition group were increased versus miR-625-5p-NC.

Conclusions

In BC, LINC00958 is highly expressed while miR-625-5p is underexpressed. LINC00958 can inhibit cell autophagy to enhance cell activity; promote OS, inflammation, and AG; and regulate tumor immunity by targeting miR-625-5p, thus participating in the development of BC.

The Crucial Role of AR-V7 in Enzalutamide-Resistance of Castration-Resistant Prostate Cancer

Simple Summary

Androgen receptor splice variant 7 (AR-V7) has always been considered a key driver for triggering enzalutamide resistance of castration-resistant prostate cancer (CRPC). In recent years, both the homeostasis of AR-V7 protein and AR-V7’s relationship with LncRNAs have gained great attention with in-depth studies. Starting from protein stability and LncRNA, the paper discusses and summarizes the mechanisms and drugs that affect the CRPC patients’ sensitivity to enzalutamide by regulating the protein or transcriptional stability of AR-V7, hoping to provide therapeutic ideas for subsequent research to break through the CRPC therapeutic bottleneck.

Abstract

Prostate cancer (PCa) has the second highest incidence of malignancies occurring in men worldwide. The first-line therapy of PCa is androgen deprivation therapy (ADT). Nonetheless, most patients progress to castration-resistant prostate cancer (CRPC) after being treated by ADT. As a second-generation androgen receptor (AR) antagonist, enzalutamide (ENZ) is the current mainstay of new endocrine therapies for CRPC in clinical use. However, almost all patients develop resistance during AR antagonist therapy due to various mechanisms. At present, ENZ resistance (ENZR) has become challenging in the clinical treatment of CRPC. AR splice variant 7 (AR-V7) refers to a ligand-independent and constitutively active variant of the AR and is considered a key driver of ENZR in CRPC. In this review, we summarize the mechanisms and biological behaviors of AR-V7 in ENZR of CRPC to contribute novel insights for CRPC therapy.

Aberrant lncRNA–mRNA expression profile and function networks during the adipogenesis of mesenchymal stem cells from patients with ankylosing spondylitis

Objective: We have already demonstrated that mesenchymal stem cells from patients with ankylosing spondylitis (ASMSCs) exhibited greater adipogenic differentiation potential than those from healthy donors (HDMSCs). Here, we further investigated the expression profile of long noncoding RNA (lncRNA) and mRNA, aiming to explore the underlying mechanism of abnormal adipogenic differentiation in ASMSCs.

Methods: HDMSCs and ASMSCs were separately isolated and induced with adipogenic differentiation medium for 10 days. Thereafter, lncRNAs and mRNAs that were differentially expressed (DE) between HDMSCs and ASMSCs were identified via high-throughput sequencing and confirmed by quantitative real-time PCR (qRT–PCR) assays. Then, the DE genes were annotated and enriched by GO analysis. In addition, protein interaction network was constructed to evaluate the interactions between DE mRNAs and to find hub nodes and study cliques. Besides, co-expression network analysis was carried out to assess the co-expressions between DE mRNA and DE lncRNAs, and competing endogenous RNA (ceRNA) network analysis were conducted to predict the relationships among lncRNAs, mRNAs and miRNAs. The signaling pathways based on the DE genes and the predicted DE genes were enriched by KEGG analysis.

Results: A total of 263 DE lncRNAs and 1376 DE mRNAs were found during adipogenesis in ASMSCs. qRT–PCR indicated that the expression of the top 20 mRNAs and the top 10 lncRNAs was consistent with the high-throughput sequencing data. Several lncRNAs (NR_125386.1, NR_046473.1 and NR_038937.1) and their target genes (SPN and OR1AIP2), together with the significantly co-expressed pairs of DE lncRNAs and DE mRNAs (SLC38A5-ENST00000429588.1, TMEM61-ENST00000400755.3 and C5orf46-ENST00000512300.1), were closely related to the enhanced adipogenesis of ASMSCs by modulating the PPAR signaling pathway.

Conclusion: Our study analyzed the expression profiles of DE lncRNAs and DE mRNAs during adipogenesis in ASMSCs and HDMSCs. Several DE lncRNAs, DE mRNAs and signaling pathways that probably participate in the aberrant adipogenesis of ASMSCs were selected for future study. These results will likely provide potential targets for our intervention on fat metaplasia and subsequent new bone formation in patients with AS in the future.

The effect of long non-coding RNAs in joint destruction of rheumatoid arthritis

Rheumatoid arthritis (RA) is a systemic autoimmune disease accompanied with joint destruction. Serious joint destruction will eventually lead to disability and the decline of life quality in RA patients. At present, the therapeutic effect of drugs to alleviate joint destruction in RA is limited. Recently, accumulating evidences have shown that long non-coding RNAs (lncRNAs) play an important role in the pathogenesis of joint diseases. Therefore, this paper reviews the expression change and the action mechanism of lncRNAs in joint destruction of RA in recent years. A more comprehensive understanding of the role of lncRNAs in joint destruction will help the treatment of RA.

Nucleus-specific RNAi nanoplatform for targeted regulation of nuclear lncRNA function and effective cancer therapy

In the context of cancer therapy, a recently identified therapeutic target is represented by the essential subtype of RNA transcripts - the long noncoding RNAs (lncRNA). While this is the case, it is especially difficult to successfully regulate the expression of this subtype in vivo, particularly due to the protection granted by the nuclear envelope of nuclear lncRNAs. This study documents the development of a nucleus-specific RNA interference (RNAi) nanoparticle (NP) platform for the targeted regulation of the nuclear lncRNA function, in order to effectuate successful cancer therapy. An NTPA (nucleus-targeting peptide amphiphile) and an endosomal pH-responsive polymer make up the novel RNAi nanoplatform in development, which is capable of complexing siRNA. The nanoplatform is capable of accumulating greatly in the tumor tissues and being internalized by tumor cells, following intravenous administration. The exposed complexes of the NTPA/siRNA may conveniently escape from the endosome with the pH-triggered NP disassociation, following which it can target the nucleus by specifically interacting with the importin α/β heterodimer. In orthotopic and subcutaneous xenograft tumor models, this would result in a notable suppression of the expression of nuclear lncNEAT2 as well as greatly impede the growth of tumors in liver cancer.

Oxidative stress-induced lncRNA CYLD-AS1 promotes RPE inflammation via Nrf2/miR-134-5p/NF-κB signaling pathway

Oxidative stress-induced damage to and dysfunction of retinal pigment epithelium (RPE) cells are important pathogenetic factors of age-related macular degeneration (AMD); however, the underlying molecular mechanism is not fully understood. Long noncoding RNAs (lncRNAs) have important roles in various biological processes. In this study, using an oxidative damage model in RPE cells, we identified a novel oxidation-related lncRNA named CYLD-AS1. We further revealed that the expression of CYLD-AS1 was increased in RPEs during oxidative stress. Depletion of CYLD-AS1 promoted cell proliferation and mitochondrial function and protected RPE cells against hydrogen peroxide (H₂ O₂ )-induced damage. Mechanistically, CYLD-AS1 also regulated the expression of NRF2, which is related to oxidative stress, and NF-κB signaling pathway members, which are related to inflammation. Remarkably, these two signaling pathways were mediated by the CYLD-AS1 interactor miR-134-5p. Moreover, exosomes secreted by CYLD-AS1 knockdown RPE cells had a lower proinflammatory effect than those secreted by control cells. In summary, our study revealed that CYLD-AS1 affects the oxidative stress-related and inflammatory functions of RPE cells by sponging miR-134-5p to mediate NRF2/NF-κB signaling pathway activity, suggesting that targeting CYLD-AS1 could be a promising strategy for the treatment of AMD and related diseases.

SIPA1 Regulates LINC01615 to Promote Metastasis in Triple-Negative Breast Cancer

Simple Summary

Breast cancer is a malignant tumor that often endangers women. After undergoing surgery and supplementary chemotherapy, however, tumor recurrence has not been well researched. The primary cause is high metastatic rates. Hence, bioinformatic and functional analyses were performed to indicate the effect of LINC01615 on breast cancer. We revealed that LINC01615 is regulated by the transcription factor SIPA1 in promoting breast cancer cell malignancy.

Abstract

Long non-coding RNAs (lncRNAs) are reported to play an important regulatory effect in carcinogenesis and malignancy. We found by high-throughput sequencing that LINC01615 is upregulated in breast cancer patients and reduces patients’ overall survival. In vivo and in vitro experiments, we clarified that overexpression of LINC01615 can promote breast cancer cell metastasis ability. The expression of LINC01615 is regulated by the transcriptional activator SIPA1, thereby promoting carcinogenesis in breast cancer cells. Our research clarified that LINC01615 can act as an oncogenic factor in promoting the development of breast cancer.

Unveiling caspase-2 regulation by non-coding RNAs

Non-coding RNAs (ncRNAs) are a group of RNA molecules, such as small nucleolar RNAs, circular RNAs (circRNAs), microRNAs (miRNAs) and long-noncoding RNAs (ncRNAs), that do not encode proteins. Although their biofunctions are not well-understood, many regulatory ncRNAs appear to be highly involved in regulating the transcription and translation of several genes that have essential biological roles including cell differentiation, cell death, metabolism, tumorigenesis and so on. A growing number of studies have revealed the associations between dysregulated ncRNAs and caspases involved in cell death in numerous human diseases. As one of the initiator and executor caspases, caspase-2 is the most evolutionally conserved caspase in mammals, exerting both apoptotic and non-apoptotic functions. A great deal of studies has shown the involvement of caspase-2 as a tumor suppressor in multiple oncogene-driven cancers, and yet a comprehensive understanding of its biological roles remains largely unknown. In this review, we highlight a compilation of studies focused on the interaction between caspase-2 and miRNAs/lncRNAs in the context of different diseases in order to deepen our knowledge on the regulatory biofunctions of caspase-2 and, furthermore, provide more insight into understanding the role that ncRNAs/caspase-2 axis plays in the development of human diseases.

lncRNA MPFAST Promotes Proliferation and Fatty Acid Synthesis of Bovine Mammary Epithelial Cell by Sponging miR-103 Regulating PI3K-AKT Pathway

Long noncoding RNAs (lncRNAs) have an essential role in mammary gland development and lactation. Our earlier study showed that the lncRNA mammary proliferation and fatty acid synthesis-associated transcript (MPFAST) is highly expressed in the Holstein cow mammary gland during the middle lactation period compared to the dry period, which indicates its potential role in lactation. Therefore, gain- and loss-of-function experiments were performed on bovine mammary epithelial cells (BMECs) by cell counting kit 8 (CCK8), 5-ethynyl-2'-deoxyuridine (EdU), real-time quantitative polymerase chain reaction (RT-qPCR), and western blot. The results indicated that MPFAST promoted the viability and proliferation of BMECs. The oil red O staining and cellular triglyceride assay further showed that MPFAST promoted the number of lipid droplets and cellular triglyceride synthesis in BMECs. Bioinformatics analysis showed that MPFAST could act as a molecular sponge for miR-103, and PIK3R1 was a potential target of miR-103, which was further confirmed by the dual-luciferase reporter assay, RT-qPCR, and western blot. The overexpression of MPFAST promoted the expression of PIK3R1 at mRNA and protein levels. It also significantly increased the mRNA relative expression levels of AKT, mTOR, and SREBP1, and the protein relative expression levels of AKT and p-AKT in the PI3K-AKT signaling pathway. In contrast, the inhibition of MPFAST resulted in the downregulation of the PI3K-AKT signaling pathway genes. These results indicated that MPFAST regulates the expression of the genes in the PI3K-AKT signaling pathway through sponging miR-103 and promotes the proliferation and synthesis of fatty acids of BMECs. Our results would provide a new direction for further exploring the regulatory mechanism of lncRNA in the mammary gland.