LNCcation: lncRNA localization and function

lncExACT1 and DCHS2 Regulate Physiological and Pathological Cardiac Growth

BACKGROUND

The heart grows in response to pathological and physiological stimuli. The former often precedes cardiomyocyte loss and heart failure; the latter paradoxically protects the heart and enhances cardiomyogenesis. The mechanisms underlying these differences remain incompletely understood. While long noncoding RNAs (lncRNAs) are important in cardiac development and disease, less is known about their roles in physiological hypertrophy or cardiomyogenesis.

METHODS

RNA sequencing was applied to hearts from mice after eight weeks voluntary exercise-induced physiological hypertrophy and cardiomyogenesis or transverse aortic constriction (TAC) for two or eight weeks to induce pathological hypertrophy or heart failure. The top lncRNA candidate was overexpressed in hearts with adeno-associated virus (AAV) vectors and inhibited with antisense locked nucleic acid (LNA)-GapmeRs to examine its function. Downstream effectors were identified through promoter analyses and binding assays. The functional roles of a novel downstream effector, dachsous cadherin-related 2 (DCHS2), were examined through transgenic overexpression in zebrafish and cardiac-specific deletion in Cas9-knockin mice.

RESULTS

We identified exercise-regulated cardiac lncRNAs, termed lncExACTs. lncExACT1 was evolutionarily conserved and decreased in exercised hearts but increased in human and experimental heart failure. Cardiac lncExACT1 overexpression caused pathological hypertrophy and heart failure, while lncExACT1 inhibition induced physiological hypertrophy and cardiomyogenesis, protecting against cardiac fibrosis and dysfunction. lncExACT1 functioned by regulating microRNA-222, calcineurin signaling, and Hippo/Yap1 signaling through DCHS2. Cardiomyocyte DCHS2 overexpression in zebrafish induced pathological hypertrophy and impaired cardiac regeneration, promoting scarring after injury. In contrast, murine DCHS2 deletion induced physiological hypertrophy and promoted cardiomyogenesis.

CONCLUSIONS

These studies identify lncExACT1-DCHS2 as a novel pathway regulating cardiac hypertrophy and cardiomyogenesis. lncExACT1-DCHS2 acts as a master switch toggling the heart between physiological and pathological growth to determine functional outcomes, providing a potentially tractable therapeutic target for harnessing the beneficial effects of exercise.

PACER lncRNA regulates COX-2 expression in lung cancer cells

Long noncoding RNAs (lncRNAs) are known to regulate gene expression; however, in many cases, the mechanism of this regulation is unknown. One novel lncRNA relevant to inflammation and arachidonic acid (AA) metabolism is the p50-associated COX-2 extragenic RNA (PACER). We focused our research on the regulation of PACER in lung cancer. While the function of PACER is not entirely understood, PACER is known to play a role in inflammation-associated conditions. Our data suggest that PACER is critically involved in COX-2 transcription and dysregulation in lung cancer cells. Our analysis of The Cancer Genome Atlas (TCGA) expression data revealed that PACER expression is significantly higher in lung adenocarcinomas than normal lung tissues. Additionally, we discovered that elevated PACER expression strongly correlates with COX-2 expression in lung adenocarcinoma patients. Specific siRNA-mediated knockdown of PACER decreases COX-2 expression indicating a direct relationship. Additionally, we show that PACER expression is induced upon treatment with proinflammatory cytokines to mimic inflammation. Treatment with prostaglandin E2 (PGE2) induces both PACER and COX-2 expression, suggesting a PGE2-mediated feedback loop. Inhibition of COX-2 with celecoxib decreased PACER expression, confirming this self-regulatory process. Significant overlap between the COX-2 promotor and the PACER promotor led us to investigate their transcriptional regulatory mechanisms. Treatment with pharmacologic inhibitors of NF-κB or AP-1 showed a modest effect on both PACER and COX-2 expression but did not eliminate expression. These data suggest that the regulation of expression of both PACER and COX-2 is complex and intricately linked.

Review of LINC00707: A Novel LncRNA and Promising Biomarker for Human Diseases

Long noncoding RNAs (lncRNAs) are a major type of noncoding RNA greater than 200 nucleotides in length involved in important regulatory processes. Abnormal expression of certain lncRNAs contributes to the pathogenesis of multiple diseases, including cancers. The lncRNA LINC00707 is located on chromosome 10p14 and is abnormally expressed in numerous disease types, and particularly in several types of cancer. High LINC00707 levels mediate a series of biological functions, including cell proliferation, apoptosis, metastasis, invasion, cell cycle arrest, inflammation, and even osteogenic differentiation. In this review, we discuss the main functions and underlying mechanisms of LINC00707 in different diseases and describe promising applications of LINC00707 in clinical settings.

Linc01513 inhibits the malignant potential of Nasopharyngeal carcinoma by binding to PTBP1

LncRNAs are reported to be involved in tumor proliferation, invasion and metastasis, and are considered as potential biomarkers and therapeutic targets for human cancer, including head and neck cancer. In this study, we screened the differentially low-expressed linc01513 by bioinformatic to detect its expression and biological effect on nasopharyngeal carcinoma (NPC). MTT was used to evaluate the effect of linc01513 on the proliferation of NPC cells. Wound healing assay was used to determine the cells migration ability. The matrix transwell was used to further detect the role of linc01513 in cell invasion. Western blot was used to detect the expression of epithelial-mesenchymal transformation (EMT)-induced transcription factors E-cadherin, vimentin and Slug. The results showed that silence of linc01513 could promoted the proliferation, migration and invasion of NPC cells. The in vivo experiment showed that overexpression of linc01513 could inhibit the volume and weight of xenograft tumors. Database prediction, RNA pull-down and RIP experiments suggested that linc01513 may play an anti-tumor effect by inhibiting PTBP1 protein level. It is suggested that linc01513 directly binds to PTBP1 protein and mediates the EMT process and malignant biological behavior of NPC cells, which provides a new molecular marker for the prognosis and treatment of NPC.

Molecular Mechanisms of lncRNAs in the Dependent Regulation of Cancer and Their Potential Therapeutic Use

Deep whole genome and transcriptome sequencing have highlighted the importance of an emerging class of non-coding RNA longer than 200 nucleotides (i.e., long non-coding RNAs (lncRNAs)) that are involved in multiple cellular processes such as cell differentiation, embryonic development, and tissue homeostasis. Cancer is a prime example derived from a loss of homeostasis, primarily caused by genetic alterations both in the genomic and epigenetic landscape, which results in deregulation of the gene networks. Deregulation of the expression of many lncRNAs in samples, tissues or patients has been pointed out as a molecular regulator in carcinogenesis, with them acting as oncogenes or tumor suppressor genes. Herein, we summarize the distinct molecular regulatory mechanisms described in literature in which lncRNAs modulate carcinogenesis, emphasizing epigenetic and genetic alterations in particular. Furthermore, we also reviewed the current strategies used to block lncRNA oncogenic functions and their usefulness as potential therapeutic targets in several carcinomas.

LncRNA Expression Profiles in Systemic Lupus Erythematosus and Rheumatoid Arthritis: Emerging Biomarkers and Therapeutic Targets

Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are two common multisystem autoimmune diseases that share, among others, many clinical manifestations and serological features. The role of long non-coding RNAs (lncRNAs) has been of particular interest in the pathogenesis of autoimmune diseases. Here, we aimed to summarize the roles of lncRNAs as emerging novel biomarkers and therapeutic targets in SLE and RA. We conducted a narrative review summarizing original articles on lncRNAs associated with SLE and RA, published until November 1, 2021. Based on the studies on lncRNA expression profiles in samples (including PBMCs, serum, and exosomes), it was noted that most of the current research is focused on investigating the regulatory mechanisms of these lncRNAs in SLE and/or RA. Several lncRNAs have been hypothesized to play key roles in these diseases. In SLE, lncRNAs such as GAS5, NEAT1, TUG1, linc0949, and linc0597 are dysregulated and may serve as emerging novel biomarkers and therapeutic targets. In RA, many validated lncRNAs, such as HOTAIR, GAS5, and HIX003209, have been identified as promising novel biomarkers for both diagnosis and treatment. The shared lncRNAs, for example, GAS5, may participate in SLE pathogenesis through the mitogen-activated protein kinase pathway and trigger the AMP-activated protein kinase pathway in RA. Here, we summarize the data on key lncRNAs that may drive the pathogenesis of SLE and RA and could potentially serve as emerging novel biomarkers and therapeutic targets in the coming future.

The management of bone defect using long non-coding RNA as a potential biomarker for regulating the osteogenic differentiation process

Tissue engineered bone brings hope to the treatment of bone defects, and the osteogenic differentiation of stem cells is the key link. Inducing osteogenic differentiation of stem cells may be a potential approach to promote bone regeneration. In recent years, lncRNA has been studied in the field increasingly, which is believed can regulate cell cycle, proliferation, metastasis, differentiation and immunity, participating in a variety of physiology and pathology processes. At present, it has been confirmed that certain lncRNAs regulate the osteogenesis of stem cells and take part in mediating signaling pathways including Wnt/β-catenin, MAPK, TGF-β/BMP, and Notch pathways. Here, we provided an overview of lncRNA, reviewed its researches in the osteogenic differentiation of stem cells, emphasized the importance of lncRNA in bone regeneration, and focused on the roles of lncRNA in signaling pathways, in order to make adequate preparations for applying lncRNA to bone tissue Engineering, letting it regulate the osteogenic differentiation of stem cells for bone regeneration.

The Long Non-Coding RNA Nostrill Regulates Transcription of Irf7 Through Interaction With NF-κB p65 to Enhance Intestinal Epithelial Defense Against Cryptosporidium parvum

The cells of the intestinal epithelium establish the frontline for host defense against pathogens in the gastrointestinal tract and play a vital role in the initiation of the immune response. Increasing evidence supports the role of long non-coding RNAs (lncRNAs) as critical regulators of diverse cellular processes, however, their role in antimicrobial host defense is incompletely understood. In this study, we provide evidence that the lncRNA Nostrill is upregulated in the intestinal epithelium following infection by Cryptosporidium parvum, a globally prevalent apicomplexan parasite that causes significant diarrheal disease and an important opportunistic pathogen in the immunocompromised and AIDS patients. Induction of Nostrill in infected intestinal epithelial cells was triggered by NF-κB signaling and was observed to enhance epithelial defense by decreasing parasitic infection burden. Nostrill participates in the transcriptional regulation of C. parvum-induced Irf7 expression through interactions with NF-κB p65, and induction of Nostrill promotes epigenetic histone modifications and occupancy of RNA polymerase II at the Irf7 promoter. Our data suggest that the induction of Nostrill promotes antiparasitic defense against C. parvum and enhances intestinal epithelial antimicrobial defense through contributions to transcriptional regulation of immune-related genes, such as Irf7.

The emerging role of long non-coding RNAs in schizophrenia

Schizophrenia (SZ) is a severe psychiatric disorder which is contributed by both genetic and environmental factors. However, at present, its specific pathogenesis is still not very clear, and there is a lack of objective and reliable biomarkers. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) are involved in the pathophysiology of several psychiatric disorders, including SZ, and hold promise as potential biomarkers and therapeutic targets for psychiatric disorders. In this review, we summarize and discuss the role of lncRNAs in the pathogenesis of SZ and their potential value as biomarkers and therapeutic targets.

LncRNAs as the Regulators of Brain Function and Therapeutic Targets for Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common type of dementia and a serious threat to the health and safety of the elderly population. It has become an emerging public health problem and a major economic and social burden. However, there is currently no effective treatment for AD. Although the mechanism of AD pathogenesis has been investigated substantially, the full range of molecular factors that contribute to its development remain largely unclear. In recent years, accumulating evidence has revealed that long non-coding RNAs (lncRNAs), a type of non-coding RNA longer than 200 nucleotides, play important roles in multiple biological processes involved in AD pathogenesis. With the further exploration of genomics, the role of lncRNA in the pathogenesis of AD has been phenotypically or mechanistically studied. Herein, we systematically review the current knowledge about lncRNAs implicated in AD and elaborate on their main regulatory pathways, which may contribute to the discovery of novel therapeutic targets and drugs for AD.

RT-qPCR as a screening platform for mutational and small molecule impacts on structural stability of RNA tertiary structures

The exponential increase in the discovery and characterization of RNA tertiary structures has highlighted their active role in a variety of human diseases, yet often their interactome and specific function remain unknown. Small molecules offer opportunities to both decode these cellular roles and develop therapeutics, however there are few examples of small molecules that target biologically relevant RNA tertiary structures. While RNA triple helices are a particularly attractive target, discovery of triple helix modulators has been hindered by the lack of correlation between small molecule affinity and effect on structural modulation, thereby limiting the utility of affinity-based screening as a primary filtering method. To address this challenge, we developed a high-throughput RT-qPCR screening platform that reports on the effect of mutations and additives, such as small molecules, on the stability of triple helices. Using the 3′-end of the oncogenic long non-coding RNA MALAT1 as a proof-of-concept, we demonstrated the applicability of both a two-step and a one-pot method to assess the impact of mutations and small molecules on the stability of the triple helix. We demonstrated the adaptability of the assay to diverse RNA tertiary structures by applying it to the SARS-CoV-2 pseudoknot, a key viral RNA structure recently identified as an attractive therapeutic target for the development of antivirals. Employment of a functional high-throughput assay as a primary screen will significantly expedite the discovery of probes that modulate the structural landscape of RNA structures and, consequently, help gain insight into the roles of these pervasive structures.

RT-qPCR can be harnessed as a small molecule screening platform to read out the effect of small molecules on the structural stability of a variety of RNA targets.

Comprehensive Diagnostics of Diabetic Nephropathy by Transcriptome RNA Sequencing

BACKGROUND

Diabetic nephropathy (DN) is a primary driver of end-stage renal disease. Given the heterogeneity of renal lesions and the complex mechanisms of DN, the present-day diagnostic approach remains highly controversial. We aimed to design a diagnostic model by bioinformatics methods for discriminating DN patients from normal subjects.

METHODS

In this study, transcriptome sequencing was performed on 6 clinical samples (3 from DN patients and 3 from healthy volunteers) from the Second Affiliated Hospital of Kunming Medical University. Construction of a competing endogenous RNA (ceRNA) network based on differentially expressed (DE)-mRNAs and -long noncoding RNAs (lncRNAs). Subsequently, the CytoHubba plugin was used to identify hub genes from DE-mRNAs in the ceRNA network and to perform functional enrichment analysis on them. The least absolute shrinkage and selection operator (LASSO) regression analysis was responsible for screening the diagnostic biomarkers from hub genes and assessing their diagnostic power using ROC curves. The pathways involved in hub genes were revealed by single-gene Gene Set Enrichment Analysis (GSEA). Moreover, we verified the expression levels of diagnostic biomarkers by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot.

RESULTS

A total of 10 hub genes were screened from the ceRNA network, which appeared to be associated with the viral infection, kidney development, and regulation of immune and inflammatory responses. Subsequently, LASSO regression analysis established a diagnostic model consisting of DDX58, SAMD9L, and TLR6 with a robust diagnostic potency (AUC = 1). Similarly, single-gene GSEA showed a strong association of these diagnostic biomarkers with the viral infection. Furthermore, PCR and Western blot demonstrated showed that DDX58, SAMD9L, and TLR6 were upregulated in DN patients at both transcriptome and protein levels compared to healthy controls.

CONCLUSION

We confirmed that differentially expressed hub genes may be novel diagnostic biomarkers in DN.

Long Noncoding RNAs and Mitochondrial Homeostasis in the Development of Diabetic Retinopathy

Retinopathy is one of the most devastating complications of diabetes, which a patient fears the most. Hyperglycemic environment results in many structural, functional, molecular and biochemical abnormalities in the retina, and overproduction of mitochondrial superoxide, induced by hyperglycemic milieu, is considered to play a central role in the development of diabetic retinopathy. Expression of many genes associated with maintaining mitochondrial homeostasis is also altered. Recent research has shown that several long noncoding RNAs, RNAs with more than 200 nucleotides but without any reading frames, are aberrantly expressed in diabetes, and altered expression of these long noncoding RNAs is now being implicated in the development of diabetes and its complications including retinopathy. This review focuses the role of long noncoding RNAs in the development of diabetic retinopathy, with a special emphasis on the maintenance of mitochondrial homeostasis.

LncRNA <i>SNHG16</i> promotes colorectal cancer proliferation by regulating ABCB1 expression through sponging miR-214-3p

Mounting evidence indicates that long non-coding RNAs (lncRNAs) have critical roles in colorectal cancer (CRC) progression, providing many potential diagnostic biomarkers, prognostic biomarkers, and treatment targets. Here, we sought to investigate the role and underlying regulatory mechanism of lncRNA small nucleolar RNA host gene 16 (SNHG16) in CRC. The expressions of SNHG16 in CRC were identified by RNA-sequencing and quantitative reverse transcription PCR. The functions of SNHG16 were explored by a series of in vitro and in vivo assays (colony formation assay, flow cytometry assay, and xenograft model). Bioinformatics analysis, RNA fluorescencein situ hybridization and luciferase reporter assay were used to investigate the regulatory mechanism of effects of SNHG16. SNHG16 was found to be significantly elevated in human CRC tissues and cell lines. Functional studies suggested that SNHG16 promoted CRC cell growth both in vitro and in vivo. Mechanistically, we identified that SNHG16 is expressed predominantly in the cytoplasm. SNHG16 could interact with miR-214-3p and up-regulated its target ABCB1. This study indicated that SNHG16 plays an oncogenic role in CRC, suggesting it could be a novel biomarker and therapeutic target in CRC.

Knockdown of long non-coding RNA NEAT1 relieves inflammation of ulcerative colitis by regulating the miR-603/FGF9 pathway

Ulcerative colitis (UC) is a significant threat to human life. Hence, there is an urgent requirement to understand the mechanism of UC progression and to develop novel therapeutic interventions for the treatment of UC. The present study aimed to evaluate the potential significance of long non-coding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1) in the progression of UC. NEAT1 expression was detected in colonic mucosa samples from patients with UC and healthy individuals. Fetal human cells (FHCs) were treated with different concentrations of lipopolysaccharides (LPS) to induce UC-caused inflammatory injury, and the effects of NEAT1 knockdown were investigated on cytokines production, cell apoptosis and viability. Furthermore, the correlation and regulation between NEAT1 and microRNA (miRNA/miR)-603 and the fibroblast growth factor 9 (FGF9) pathway were investigated. The results demonstrated that NEAT1 expression was upregulated in the colonic mucosa tissues of patients with UC. In addition, significant cell injury was observed in FHCs treated with different concentrations of LPS, with decreased cell viability, and increased apoptosis and inflammatory cytokines production. Conversely, NEAT1 knockdown significantly reduced LPS-induced cell injury in FHCs, which was achieved through negative regulation of miR-603 expression. Furthermore, FGF9 was negatively regulated by miR-603, and thus, FGF9 was identified as a potential target of miR-603. Notably, FGF9 knockdown reversed the suppressing effects of miR-603 on LPS-induced injury in FHCs. Taken together, the results of the present study suggest that NEAT1 contributes to the development of UC by regulating the miR-603/FGF9 pathway.

Network Integration Analysis and Immune Infiltration Analysis Reveal Potential Biomarkers for Primary Open-Angle Glaucoma

Primary open-angle glaucoma (POAG) is a progressive optic neuropathy and its damage to vision is irreversible. Therefore, early diagnosis assisted by biomarkers is essential. Although there were multiple researches on the identification of POAG biomarkers, few studies systematically revealed the transcriptome dysregulation mechanism of POAG from the perspective of pre- and post-transcription of genes. Here, we have collected multiple sets of POAG's aqueous humor (AH) tissue transcription profiles covering long non-coding RNA (lncRNA), mRNA and mircoRNA (miRNA). Through differential expression analysis, we identified thousands of significant differentially expressed genes (DEGs) between the AH tissue of POAG and non-glaucoma. Further, the DEGs were used to construct a competing endogenous RNA (ceRNA) regulatory network and 1,653 qualified lncRNA-miRNA-mRNA regulatory units were identified. Two ceRNA regulatory subnets were identified based on the random walk algorithm and revealed to be involved in the regulation of multiple complex diseases. At the pre-transcriptional regulation level, a transcriptional regulatory network was constructed and three transcription factors (FOS, ATF4, and RELB) were identified to regulate the expression of multiple genes and participate in the regulation of T cells. Moreover, we revealed the immune desert status of AH tissue for POAG patients based on immune infiltration analysis and identified a specific AL590666.2-hsa-miR-339-5p-UROD axis can be used as a biomarker of POAG. Taken together, the identification of regulatory mechanisms and biomarkers will contribute to the individualized diagnosis and treatment for POAG.

Prognostic Risk Model and Tumor Immune Environment Modulation of m5C-Related LncRNAs in Pancreatic Ductal Adenocarcinoma

RNA methylation modification is a key process in epigenetics that regulates posttranscriptional gene expression. With advances in next-generation sequencing technology, 5-methylcytosine (m5C) modification has also been found in multiple RNAs. Long non-coding RNAs (lncRNAs) were proved to have a key role in cancer progression and closely related to the tumor immune microenvironment. Thus, based on the PDAC patients' clinical information and genetic transcriptome data from the TCGA database, we performed a detailed bioinformatic analysis to establish a m5C-related lncRNA prognostic risk model for PDAC patients and discovered the relationship between the risk model and PDAC immune microenvironment. Pearson correlation coefficient analysis was applied to conduct a m5C regulatory gene and m5C-related lncRNA co-expression network. Expression of m5C-related lncRNAs screened by univariate regression analysis with prognostic value showed a significant difference between pancreatic cancer and normal tissues. The least absolute shrinkage and selection operator (LASSO) Cox regression method was applied to determine an 8-m5C-related lncRNA prognostic risk model. We used principal component analysis to indicate that the risk model could distinguish all the samples clearly. The clinical nomogram also accurately predicted 1-, 1.5-, 2-, and 3-year survival time among PDAC patients. Additionally, this risk model was validated in the entire group and sub-test groups using KM analysis and ROC analysis. Combined with the clinical characteristics, the risk score was found to be an independent factor for predicting the survival of PDAC patients. Furthermore, the association between the risk model and tumor immune microenvironment was evaluated via the ESTIMATE R package and CIBERSORT method. Consequently, the results indicated that immune cells were associated with m5C-related lncRNA risk model scores and had different distribution in the high- and low-risk groups. Based on all these analyses, the m5C-related lncRNA risk model could be a reliable prognostic tool and therapeutic target for PDAC patients.

Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN

The majority of lncRNAs and a small fraction of mRNAs localize in the cell nucleus to exert their functions. A SIRLOIN RNA motif was previously reported to drive its nuclear localization by the RNA-binding protein hnRNPK. However, the underlying mechanism remains unclear. Here, we report crystal structures of hnRNPK in complex with SIRLOIN, and with the nuclear import receptor (NIR) Impα1, respectively. The protein hnRNPK bound to SIRLOIN with multiple weak interactions, and interacted Impα1 using an independent high-affinity site. Forming a complex with hnRNPK and Impα1 was essential for the nuclear import and stress granule localization of SIRLOIN in semi-permeabilized cells. Nuclear import of SIRLOIN enhanced with increasing NIR concentrations, but its stress granule localization peaked at a low NIR concentration. Collectively, we propose a mechanism of SIRLOIN localization, in which NIRs functioned as drivers/regulators, and hnRNPK as an adaptor.

Long non-coding RNA RP11-465L10.10 promotes vascular smooth muscle cells phenotype switching and MMP9 expression via the NF-κB pathway

Background

Thoracic aortic aneurysm/dissection (TAA/D) are complicated vascular disorders with rapid development and high mortality. Vascular smooth muscle cells (VSMCs) phenotype switching plays an important role in the pathological process of TAA/D. Previous studies have indicated a potential correlation between long non-coding RNA (lncRNA) RP11-465L10.10 and matrix metallopeptidase 9 (MMP9) involved in the development of TAA/D. This study aims to investigate the role of lncRNA RP11-465L10.10 in VSMCs phenotype switching and the molecular mechanism in regulating MMP9 expression.

Methods

The expression of RP11-465L10.10 in vascular tissues and in VMSCs was detected by RT-qPCR. To investigate the role of RP11-465L10.10 on VSMCs phenotype switching, an RP11-465L10.10-overexpressed lentiviral vector was constructed and transfected into VSMCs. Through EdU staining, migration assay, flow cytometry analysis, the roles of RP11-465L10.10 were estimated. Bioinformatics indicated that RP11-465L10.10 upregulating MMP9 expression via NF-κB signaling, and SN50 (a specific inhibitor of NF-κB pathway) was used to inhibit the NF-κB pathway activation, then the expression of MMP9 was detected in RP11-465L10.10 overexpressed VMSCs.

Results

In this study, we found RP11-465L10.10 and MMP9 were highly increased in TAD patient tissues, which was consistent in angiotensin II-induced VSMCs phenotype switching. RP11-465L10.10 overexpression facilitated VSMCs phenotype switching and MMP9 expression. Mechanismly, NF-κB signal pathway was involved in RP11-465L10.10 induced VSMCs phenotype switching and MMP9 expression by transcriptome data analysis and experimental confirm.

Conclusion

This study demonstrated that RP11-465L10.10 induces VSMCs phenotype switching and MMP9 expression via the NF-κB signal pathway, suggesting that RP11-465L10.10 might be a potential therapeutic target for TAA/D treatment.

Focally amplified long non-coding RNA in epithelial cancer as a potential biomarker and therapeutic target

Deregulation of long non-coding RNAs (lncRNAs) has been implicated in tumorigenesis. FALEC is a lncRNA upregulated in multiple cancer types. FALEC functions as an oncogene through various mechanisms, such as competitively binding miRNAs and regulation of PI3K/AKT, Tp53 and phosphatase and tensin homolog signaling pathways. Pertinent to clinical practice, the use of FALEC as a putative biomarker has been identified. These findings suggested that FALEC might play a pivotal role in human cancers. Further studies are warranted to examine the diagnostic and prognostic performance of FALEC as a noninvasive biomarker in liquid biopsy samples and promote its development to be a clinically utilizable prognostic cancer biomarker and molecular therapeutic target.

Competitive Endogenous Role of the LINC00511/miR-185-3p Axis and miR-301a-3p From Liquid Biopsy as Molecular Markers for Breast Cancer Diagnosis

Breast cancer (BC) is the leading cause of female cancer-related mortalities. Evidence has illustrated the role of long non-coding RNAs (lncRNA) and microRNAs (miRNA) as promising pool of protein non-coding regulators, for tuning the aggressiveness of several malignancies. This research aims to unravel the expression pattern and the emphases of the diagnostic value of the long intergenic ncRNA00511 (LINC00511) and its downstream microRNA (miR-185-3p) and the pathogenic significance of the onco-miR-301a-3p in naïve BC patients. LINC00511 was chosen and validated, and its molecular binding was confirmed using bioinformatics. LINC00511 was measured in 25 controls and 70 patients using qPCR. The association between the investigated ncRNA’s expression and the BC patients’ clinicopathological features was assessed. Receiver operating characteristic (ROC) curve was blotted to weigh out their diagnostic efficacy over the classical tumor markers (TMs). Bioinformatics and Spearman correlation were used to predict the interaction between LINC00511, miR-185-3p, and miR-301a-3p altogether to patients’ features. LINC00511 and miR-301a-3p, in BC patients’ blood, were overexpressed, and their median levels increased significantly, while miR-185-3p was, in contrast, downregulated, being decreased fourfold. LINC00511 was elevated in BC early stages, when compared to late stages (p < 0.0003). LINC00511, miR-185-3p, and miR-301a-3p showed AUC superior to classical TMs, allowing us to conclude that the investigated ncRNAs, in BC patients’ liquid biopsy, are novel diagnostic molecular biomarker signatures. Lymph node metastasis (LNM) and advanced tumor grade were directly correlated with LINC00511 significantly. Additionally, both LINC00511 and miR-301a-3p were positively correlated with the aggressiveness of BC, as manifested in patients with larger tumors (>2 cm) at (p < 0.001). Therefore, these findings aid our understanding of BC pathogenesis, in the clinical setting, being related in part to the LINC00511/miR axis, which could be a future potential therapeutic target.

Microarray analysis of long non-coding RNAs related to osteogenic differentiation of human dental pulp stem cells

Background/purpose

Dental pulp stem cells (DPSCs) are candidate seed cells for bone tissue engineering, but the molecular regulation of osteogenic differentiation in DPSCs is not fully understood. Long non-coding RNAs (lncRNAs) are important regulators of gene expression, and whether they play roles in osteogenic differentiation of DPSCs requires more study.

Materials and methods

DPSCs were isolated and cultured. The mRNA and lncRNA expression profiles were compared through microarray assay between osteo-differentiated DPSCs and non-differentiated DPSCs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, Gene ontology (GO) analyses, and the mRNA-lncRNA co-expression analyses were performed for functional annotation of differentially expressed RNAs. Small interfering RNA (siRNA) was used to interfere the expression of lncRNA ENST00000533992 (also named smooth muscle-induced lncRNA or SMILR), a candidate regulator, then the osteogenic differentiation potential of DPSCs was analyzed.

Results

DPSCs were isolated and cultured successfully. The expression of 273 mRNAs and 184 lncRNAs changed significantly in DPSCs after osteogenic induction. KEGG analyses and GO analyses showed that the differentially expressed RNAs were enriched in several pathways and biological processes. The mRNA-lncRNA co-expression network was constructed to reveal the potential relationships between mRNAs and lncRNAs. The osteogenic differentiation potential of DPSCs decreased when SMILR was interfered.

Conclusion

The present study provides clues for seeking for lncRNAs that participate in the regulation of osteogenic differentiation in DPSCs. LncRNA SMILR could play a role in regulating osteogenic differentiation of DPSCs.

The nomogram based on the 6-lncRNA model can promote the prognosis prediction of patients with breast invasive carcinoma

Long non-coding RNA (lncRNA) is a prognostic biomarker for many types of cancer. Here, we aimed to study the prognostic value of lncRNA in Breast Invasive Carcinoma (BRCA). We downloaded expression profiles from The Cancer Genome Atlas (TCGA) datasets. Subsequently, we screened the differentially expressed genes between normal tissues and tumor tissues. Univariate Cox, LASSO regression, and multivariate Cox regression analysis were used to construct a lncRNA prognostic model. Finally, a nomogram based on the lncRNAs model was developed, and weighted gene co-expression network analysis (WGCNA) was used to predict mRNAs related to the model, and to perform function and pathway enrichment. We constructed a 6-lncRNA prognostic model. Univariate and multivariate Cox regression analysis showed that the 6-lncRNA model could be used as an independent prognostic factor for BRCA patients. We developed a nomogram based on the lncRNAs model and age, and showed good performance in predicting the survival rates of BRCA patients. Also, functional pathway enrichment analysis showed that genes related to the model were enriched in cell cycle-related pathways. Tumor immune infiltration analysis showed that the types of immune cells and their expression levels in the high-risk group were significantly different from those in the low-risk group. In general, the 6-lncRNA prognostic model and nomogram could be used as a practical and reliable prognostic tool for invasive breast cancer.

A novel lncRNA linc-AhRA negatively regulates innate antiviral response in murine microglia upon neurotropic herpesvirus infection

Microglia are the primary cellular source of type I interferons (I-IFNs) in the brain upon neurotropic virus infection. Although the I-IFN-based antiviral innate immune response is crucial for eliminating viruses, overproduction led to immune disorders. Therefore, the relatively long-lasting I-IFNs must be precisely controlled, but the regulatory mechanism for the innate antiviral response in microglia remains largely unknown. Long non-coding RNAs (lncRNAs) are being recognized as crucial factors in numerous diseases, but their regulatory roles in the innate antiviral response in microglia are undefined.

Methods: The high-throughput RNA sequencing was performed to obtain differentially expressed lncRNAs (DELs) in primary microglia infected with or without the neurotropic herpes simplex virus type 1 (HSV-1). We selected four DELs ranked in the top 15 in basic level and their fold change induced by HSV-1, i.e., FPKM_HSV-1/FPKM_Cells.We subsequently found a key lncRNA affecting the innate antiviral response of microglia significantly. We next used dual-luciferase reporter assays, bioinformatical tools, and truncation mutants of both lncRNA and targeted proteins to elucidate the downstream and upstream mechanism of action of lncRNA. Further, we established microglia-specific knock-in (KI) mice to investigate the role of lncRNA in vivo.

Results: We identified a long intergenic non-coding RNA, linc-AhRA, involved in regulating the innate antiviral response in murine microglia. linc-AhRA is activated by aryl hydrocarbon receptor (AhR) and restricts I-IFN production in microglia upon neurotropic herpesvirus infection and innate immune stimulation. Mechanistically, linc-AhRA binds to both tripartite motif-containing 27 (TRIM27) and TANK-binding kinase 1 (TBK1) through its conserved 117nt fragment as a molecular scaffold to enhance TRIM27-TBK1 interaction. This interaction facilitates the TRIM27-mediated ubiquitination of TBK1 and results in ubiquitin-proteasome-dependent degradation of TBK1. Consequently, linc-AhRA suppresses I-IFN production through facilitating TBK1 degradation and limits the microglial innate immune response against neurotropic herpesvirus infection. Microglia-specific KI of linc-AhRA mice shows a weakened antiviral immune response upon neurotropic herpesvirus challenge due to a reduction of TBK1 in microglia.

Conclusion: Our findings indicate that linc-AhRA is a negative regulator of I-IFN production in microglia to avoid excessive autoimmune responses. These findings uncover a previously unappreciated role for lncRNA conserved fragments in the innate antiviral response, providing a strong foundation for developing nucleotide drugs based on conserved functional fragments within lncRNAs.

Multidimensional Mechanistic Spectrum of Long Non-coding RNAs in Heart Development and Disease

With the large-scale genome-wide sequencing, long non-coding RNAs (lncRNAs) have been found to compose of a large portion of the human transcriptome. Recent studies demonstrated the multidimensional functions of lncRNAs in heart development and disease. The subcellular localization of lncRNA is considered as a key factor that determines lncRNA function. Cytosolic lncRNAs mainly regulate mRNA stability, mRNA translation, miRNA processing and function, whereas nuclear lncRNAs epigenetically regulate chromatin remodeling, structure, and gene transcription. In this review, we summarize the molecular mechanisms of cytosolic and nuclear lncRNAs in heart development and disease separately, and emphasize the recent progress to dictate the crosstalk of cytosolic and nuclear lncRNAs in orchestrating the same biological process. Given the low evolutionary conservation of most lncRNAs, deeper understanding of human lncRNA will uncover a new layer of human regulatory mechanism underlying heart development and disease, and benefit the future clinical treatment for human heart disease.

Regulatory roles of nucleolus organizer region-derived long non-coding RNAs

The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly associated with responses to different types of cellular stresses. Recently, several long non-coding RNAs (lncRNAs) were found to be part of the regulatory network that modulate nucleolar functions. Several of these lncRNAs are encoded in the ribosomal DNA (rDNA) repeats or are transcribed from the genomic regions that are located near the nucleolus organizer regions (NORs). In this review, we first discuss the current understanding of the sequence of the NORs and variations between different NORs. We then focus on the NOR-derived lncRNAs in mammalian cells and their functions in rRNA transcription and the organization of nucleolar structure under different cellular conditions. The identification of these lncRNAs reveals great potential of the NORs in harboring novel genes involved in the regulation of nucleolar functions.

From Junk to Function: LncRNAs in CNS Health and Disease

Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.

Role of LncRNAs in the Epithelial-Mesenchymal Transition in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a type of primary liver cancer with a high incidence and mortality rate. HCC develops insidiously, and most newly diagnosed cases are in the middle and advanced stages. The epithelial-mesenchymal transition (EMT) is a vital mechanism underlying metastasis in patients with advanced HCC. EMT is a multistep and complex procedure. The promotion and inhibition of EMT directly affect the migration and invasion of HCC. LncRNAs are involved in the epigenetic modification of genes, regulation of gene transcription, and posttranslational modification of proteins. LncRNAs also play important roles in regulating EMT progression in HCC and are promising biomarkers and therapeutic targets. This review focused on summarizing the mechanism by which lncRNAs regulate EMT in HCC. In particular, lncRNAs were reported to primarily act as RNA sponges, and the regulation of EMT involves major signaling pathways. Finally, we reviewed the mechanisms by which lncRNAs are involved in drug resistance and discussed the clinical prospects and potential challenges of utilizing lncRNAs to treat HCC.

Novel biomarkers for post-contrast acute kidney injury identified from long non-coding RNA expression profiles

Background: Post-contrast acute kidney injury (PC-AKI) is a severe complication of cardiac catheterization. Emerging evidence indicated that long non-coding RNAs (lncRNAs) could serve as biomarkers for various diseases. However, the lncRNA expression profile and potential biomarkers in PC-AKI remain unclear. This study aimed to investigate novel lncRNA biomarkers for the early detection of PC-AKI. Methods: lncRNA profile in the kidney tissues of PC-AKI rats was evaluated through RNA sequencing. Potential lncRNA biomarkers were identified through human-rat homology analysis, kidney and blood filtering in rats and verified in 112 clinical samples. The expression patterns of the candidate lncRNAs were detected in HK-2 cells and rat models to evaluate their potential for early detection. Results: In total, 357 lncRNAs were found to be differentially expressed in PC-AKI. We identified lnc-HILPDA and lnc-PRND were conservative and remarkably upregulated in both kidneys and blood from rats and the blood of PC-AKI patients; these lncRNAs can precisely distinguish PC-AKI patients (area under the curve (AUC) values of 0.885 and 0.875, respectively). The combination of these two lncRNAs exhibited improved accuracy for predicting PC-AKI, with 100% sensitivity and 83.93% specificity. Time-course experiments showed that the significant difference was first noted in the blood of PC-AKI rats at 12 h for lnc-HILPDA and 24 h for lnc-PRND. Conclusion: Our study revealed that lnc-HILPDA and lnc-PRND may serve as the novel biomarkers for early detection and profoundly affect the clinical stratification and strategy guidance of PC-AKI.