Long Non-Coding RNAs: Novel Players in Regulation of Immune Response Upon Herpesvirus Infection

RNA-Seq and miRNA-Seq data from Epstein-Barr virus-infected tree shrews reveal a ceRNA network contributing to immune microenvironment regulation

Epstein-Barr virus (EBV) infection in humans is ubiquitous and associated with various diseases. Remodeling of the immune microenvironment is the primary cause of EBV infection and pathogenesis; however, the underlying mechanism has not been fully elucidated. In this study, we used whole-transcriptome RNA-Seq to detect mRNAs, long non-coding RNAs (lncRNA), and microRNA (miRNA) profiles in the control group, 3 days, and 28 days after EBV infection, based on the tree shrew model that we reported previously. First, we estimated the proportion of 22 cell types in each sample using CIBERSORT software and identified 18 high-confidence DElncRNAs related to immune microenvironment regulation after EBV infection. Functional enrichment analysis of these differentially expressed lncRNAs primarily focused on the autophagy, endocytosis, and ferroptosis signalling pathways. Moreover, EBV infection affects miRNA expression patterns, and many miRNAs are silenced. Finally, three competing endogenous RNA regulatory networks were built using lncRNAs that significantly correlated with immune cell types, miRNAs that responded to EBV infection, and potentially targeted the mRNA of the miRNAs. Among them, MRPL42-AS-5 might act as an hsa-miR-296-5p "sponge" and compete with target mRNAs, thus increasing mRNA expression level, which could induce immune cell infiltration through the cellular senescence signalling pathway against EBV infection. Overall, we conducted a complete transcriptomic analysis of EBV infection in vivo for the first time and provided a novel perspective for further investigation of EBV-host interactions.

Long non-coding RNAs and immune cells: Unveiling the role in viral infections

Viral infections present significant challenges to human health, underscoring the importance of understanding the immune response for effective therapeutic strategies. Immune cell activation leads to dynamic changes in gene expression. Numerous studies have demonstrated the crucial role of long noncoding RNAs (lncRNAs) in immune activation and disease processes, including viral infections. This review provides a comprehensive overview of lncRNAs expressed in immune cells, including CD8 T cells, CD4 T cells, B cells, monocytes, macrophages, dendritic cells, and granulocytes, during both acute and chronic viral infections. LncRNA-mediated gene regulation encompasses various mechanisms, including the modulation of viral replication, the establishment of latency, activation of interferon pathways and other critical signaling pathways, regulation of immune exhaustion and aging, and control of cytokine and chemokine production, as well as the modulation of interferon-stimulated genes. By highlighting specific lncRNAs in different immune cell types, this review enhances our understanding of immune responses to viral infections from a lncRNA perspective and suggests potential avenues for exploring lncRNAs as therapeutic targets against viral diseases.

A comprehensive overview of exosome lncRNAs: emerging biomarkers and potential therapeutics in endometriosis

Endometriosis is a gynecological condition that significantly impacting women's daily lives. In recent years, the incidence of endometriosis has been rising yearly and is now an essential contributor to female infertility. Exosomes are extracellular vesicles (EVs) that carry long noncoding RNA (lncRNA) and shield lncRNA from the outside environment thanks to their vesicle-like structure. The role of exosome-derived lncRNAs in endometriosis is also receiving more study as high-throughput sequencing technology develops. Several lncRNAs with variable expression may be crucial to the emergence and growth of endometriosis. The early diagnosis of endometriosis will be considerably improved by further high specificity and sensitivity Exosome lncRNA screening. Exosomes assist lncRNAs in carrying out their roles, offering a new target for creating endometriosis-specific medications. In order to serve as a reference for clinical research on the pathogenesis, diagnosis, and treatment options of endometriosis, this paper covers the role of exosome lncRNAs in endometriosis and related molecular mechanisms.

Long Noncoding RNA: A Novel Insight into the Pathogenesis of Acute Lung Injury

Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), represent an acute stage of lung inflammation where the alveolar epithelium loses its functionality. ALI has a devastating impact on the population as it not only has a high rate of incidence, but also has high rates of morbidity and mortality. Due to the involvement of multiple factors, the pathogenesis of ALI is complex and is not fully understood yet. Long noncoding RNAs (lncRNAs) are a group of non-protein-coding transcripts longer than 200 nucleotides. Growing evidence has shown that lncRNAs have a decisive role in the pathogenesis of ALI. LncRNAs can either promote or hinder the development of ALI in various cell types in the lungs. Mechanistically, current studies have found that lncRNAs play crucial roles in the pathogenesis of ALI via the regulation of small RNAs (e.g., microRNAs) or downstream proteins. Undoubtedly, lncRNAs not only have the potential to reveal the underlying mechanisms of ALI pathogenesis but also serve as diagnostic and therapeutic targets for the therapy of ALI.

Combined proteomics and transcriptomics identifies serpin family C member 1 associated protein as a biomarker of endometriosis

OBJECTIVE

To explore potential biomarkers indicating endometriosis (EM).

MATERIALS AND METHODS

A proteomics method and combined quantitative transcriptomics were adopted to highlight markers in the EM. Venn analysis was used to integrate the ribonucleic acid sequencing (RNA-seq) and protein profiles. Promising candidate markers were tested by enzyme-related immunosorbent assay.

RESULTS

A sum of 979 mRNAs and 39 proteins were tested to be significantly differentially expression in the standard cluster compared with the EM cluster. Venn analysis showed a filtered signature of only two down-regulated molecules in the EM group, i.e. fetuin B (FETUB) and serpin family C member 1 (SERPINC1); the latter showed a big variance between the control category and the EM set in the authentication test.

CONCLUSION

SERPINC1 may be a useful possible biomarker for the analysis of EM.

Long non-coding RNAs: The modulators of innate and adaptive immune cells

Before very sensitive current genomics platforms were discovered, long non-coding RNAs (lncRNAs) as controllers of gene expression, were thought to be accumulated genetic garbage. The past few years have seen a lot of interest in a large classification of non-coding transcripts with an indeterminate length of more than 200 nucleotides [1]. lncRNAs' association with immunity and disease progression has been revealed by a growing body of experimental research. Only a limited subset of lncRNAs, however, has solid proof of their role. It is also clear that various immune cells express lncRNAs differently. In this review, we concentrated on the role of lncRNA expression in the regulation of immune cell function and response to pathological conditions in macrophages, dendritic cells, natural killer (NK) cells, neutrophils, Myeloid-derived suppressor cells (MDSCs), T cells, and B cells. The innate and adaptive immune response systems may be significantly regulated by lncRNAs, according to emerging research. To discover possible therapeutic targets for the therapy of different diseases, it may be helpful to have a better realization of the molecular mechanisms beyond the role of lncRNAs in the immune response. Therefore, it is crucial to investigate lncRNA expression and comprehend its significance for the immune system.

A tumor immune microenvironment-related integrated signature can predict the pathological response and prognosis of esophageal squamous cell carcinoma following neoadjuvant chemoradiotherapy: A multicenter study in China

BACKGROUND

Currently, there are insufficient indicators for the reliable assessment of treatment response following neoadjuvant chemoradiotherapy (nCRT) in patients with esophageal squamous cell carcinoma (ESCC). Considering the essential role of protein-coding and non-coding RNAs in gene regulation and cellular processes, we systematically explored the molecular features and clinical significance of mRNA and lncRNA in 249 pretreatment biopsies from four hospitals in three districts with a high incidence of ESCC patients in China.

METHODS

During the discovery phrase, 13 differentially expressed genes were identified and validated between samples with a complete pathological response (pCR) and those with an incomplete pathological response (<pCR). Subsequently, we constructed a predictive mRNA and lncRNA signature (SERPINE1, LINC00592, and PRKAG2-AS1) using Fisher's linear discriminant analysis (FLDA) with stepwise variant-selection, followed by validation of its predictive ability in both internal and external cohorts.

RESULTS

Our signature showed great value in predicting the response to nCRT among ESCC samples and acted as an independent predictive indicator, in addition to demonstrating great potential in estimating patient prognosis. Interestingly, we found that patients with a high signature score had lower PD-L1 and IDO1 expression levels but higher CD8⁺ T cells infiltration, suggesting that PD-L1 and IDO1 are negatively correlated with a high signature score and further associated with pCR and a better prognosis.

CONCLUSION

The present study identified a promising three-gene-based predictive signature that has powerful clinical implications for the identification of pCR and a good prognosis among patients with ESCC. Further immune-related exploration may provide an opportunity for future therapeutic combination.

LncRNA-ANAPC2 and lncRNA-NEFM positively regulates the inflammatory response via the miR-451/npr2/ hdac8 axis in grass carp

In grass carp (Ctenopharyngodon idella), septicemia is a systemic inflammatory response to bacterial infection and could be leaded to lethality. MiR-451 involved in septicemia progression has been reported. However, the underlying mechanism of miR-451 in septicemia induced inflammatory response remains to be revealed. In the present study, miR-451 was highly expressed in Aeromonas hydrophila induced CIK cells, opposite to lncRNA-ANAPC2 and lncRNA-NEFM expression. Furthermore, we found that miR-451 interacted with lncRNA-ANAPC2 and lncRNA-NEFM, also targeted the 3' UTR of npr2 and hdac8. In CIK cells, the inhibition of npr2 and hdac8 were down-regulated by lncRNA-ANAPC2 and lncRNA-NEFM knockdown, while downstream proinflammatory factors were inhibited. In a word, this study indicates that lncRNA-ANAPC2 and lncRNA-NEFM regulation the LPS-induced progression of inflammatory response by modulating miR-451/npr2/hdac8 axis.

The Role of Latency-Associated Transcripts in the Latent Infection of Pseudorabies Virus

Pseudorabies virus (PRV) can cause neurological, respiratory, and reproductive diseases in pigs and establish lifelong latent infection in the peripheral nervous system (PNS). Latent infection is a typical feature of PRV, which brings great difficulties to the prevention, control, and eradication of pseudorabies. The integral mechanism of latent infection is still unclear. Latency-associated transcripts (LAT) gene is the only transcriptional region during latent infection of PRV which plays the key role in regulating viral latent infection and inhibiting apoptosis. Here, we review the characteristics of PRV latent infection and the transcriptional characteristics of the LAT gene. We also analyzed the function of non-coding RNA (ncRNA) produced by the LAT gene and its importance in latent infection. Furthermore, we provided possible strategies to solve the problem of latent infection of virulent PRV strains in the host. In short, the detailed mechanism of PRV latent infection needs to be further studied and elucidated.

Understanding pathogen–host interplay by expression profiles of lncRNA and mRNA in the liver of Echinococcus multilocularis-infected mice

Almost all Echinococcus multilocularis (Em) infections occur in the liver of the intermediate host, causing a lethal zoonotic helminthic disease, alveolar echinococcosis (AE). However, the long non-coding RNAs (lncRNAs) expression profiles of the host and the potential regulatory function of lncRNA during Em infection are poorly understood. In this study, the profiles of lncRNAs and mRNAs in the liver of mice at different time points after Em infection were explored by microarray. Thirty-one differentially expressed mRNAs (DEMs) and 68 differentially expressed lncRNAs (DELs) were found continuously dysregulated. These DEMs were notably enriched in “antigen processing and presentation”, “Th1 and Th2 cell differentiation” and “Th17 cell differentiation” pathways. The potential predicted function of DELs revealed that most DELs might influence Th17 cell differentiation and TGF-β/Smad pathway of host by trans-regulating SMAD3, STAT1, and early growth response (EGR) genes. At 30 days post-infection (dpi), up-regulated DEMs were enriched in Toll-like and RIG-I-like receptor signaling pathways, which were validated by qRT-PCR, Western blotting and downstream cytokines detection. Furthermore, flow cytometric analysis and serum levels of the corresponding cytokines confirmed the changes in cell-mediated immunity in host during Em infection that showed Th1 and Th17-type CD4+ T-cells were predominant at the early infection stage whereas Th2-type CD4+ T-cells were significantly higher at the middle/late stage. Collectively, our study revealed the potential regulatory functions of lncRNAs in modulating host Th cell subsets and provide novel clues in understanding the influence of Em infection on host innate and adaptive immune response.

Research Progress on the Inflammatory Effects of Long Non-coding RNA in Traumatic Brain Injury

Globally, traumatic brain injury (TBI) is an acute clinical event and an important cause of death and long-term disability. However, the underlying mechanism of the pathophysiological has not been fully elucidated and the lack of effective treatment a huge burden to individuals, families, and society. Several studies have shown that long non-coding RNAs (lncRNAs) might play a crucial role in TBI; they are abundant in the central nervous system (CNS) and participate in a variety of pathophysiological processes, including oxidative stress, inflammation, apoptosis, blood-brain barrier protection, angiogenesis, and neurogenesis. Some lncRNAs modulate multiple therapeutic targets after TBI, including inflammation, thus, these lncRNAs have tremendous therapeutic potential for TBI, as they are promising biomarkers for TBI diagnosis, treatment, and prognosis prediction. This review discusses the differential expression of different lncRNAs in brain tissue during TBI, which is likely related to the physiological and pathological processes involved in TBI. These findings may provide new targets for further scientific research on the molecular mechanisms of TBI and potential therapeutic interventions.

BMSC-EV-derived lncRNA NORAD Facilitates Migration, Invasion, and Angiogenesis in Osteosarcoma Cells by Regulating CREBBP via Delivery of miR-877-3p

Bone marrow mesenchymal stem cells (BMSCs) can boost osteosarcoma (OS) cell proliferation and invasion, yet the function of extracellular vesicles (EVs) derived from BMSCs on OS is scarcely known. This study is aimed at examining the role of BMSC-EVs in OS cells. BMSCs and BMSC-EVs were isolated and identified. The effect of EVs and EVs-si-NORAD on OS cell proliferation, invasion, migration, and angiogenesis was determined. Expressions of NORAD, miR-877-3p, and CREBBP were detected. The binding relationship among NORAD, miR-877-3p, and CREBBP was verified. The miR-877-3p inhibitor or pc-CREBBP was delivered into OS cells treated with EVs-si-NORAD for in vitro analysis. The nude mouse model of the subcutaneous tumor xenograft was established for in vivo analysis. BMSC-EVs promoted OS cell proliferation, invasion, migration, and angiogenesis. BMSC-EVs carried NORAD into OS cells and upregulated CREBBP by sponging miR-877-3p. miR-877-3p downregulation or CREBBP overexpression partly inverted the inhibitory effect of EVs by silencing NORAD on OS cell proliferation, invasion, migration, and angiogenesis. In vivo experiments validated that BMSC-EV-derived NORAD facilitated tumor growth by upregulating CREBBP via miR-877-3p. To conclude, BMSC-EV-derived NORAD facilitated OS cell proliferation, invasion, migration, and angiogenesis by modulating CREBBP via miR-877-3p, which may offer new insights into OS treatment.

IGFBP7-AS1 is a p53-responsive long noncoding RNA downregulated by Epstein-Barr virus that contributes to viral tumorigenesis

Epstein-Barr virus (EBV) is closely related to the development of several malignancies, such as B-cell lymphoma (B-CL), by the mechanism through which these malignancies develop remains largely unknown. We previously observed downregulation of the long noncoding RNA (lncRNA) IGFBP7-AS1 in response to EBV infection. However, the role of IGFBP7-AS1 in EBV-associated cancers has not been clarified. Here, we found that expression of IGFBP7-AS1, as well as its sense gene IGFBP7, is decreased in EBV-positive B-CL cells and clinical tissues. IGFBP7-AS1 stabilizes IGFBP7 mRNA by forming a duplex based on their overlapping regions. The tumour suppressor p53 transcriptionally activates IGFBP7-AS1 expression by binding to the promoter region of the lncRNA gene. The IGFBP7-AS1 expression is able to be rescued in EBV-positive cells in wild-type (wt) p53-dependent manner. IGFBP7-AS1 inhibits the proliferation and promotes the apoptosis of B-CL cells. Moreover, tumorigenic properties due to the depletion of IGFBP7-AS1 were restored by exogenous expression of IGFBP7 or wt-p53. Furthermore, the functional p53/IGFBP7-AS1/IGFBP7 axis facilitates apoptosis by suppressing the production and secretion of the NPPB signal peptide and further regulating the cGMP-PKG signalling pathway. This study demonstrates that EBV promotes tumorigenesis, particularly in B-CL progression, by downregulating the novel p53-responsive lncRNA IGFBP7-AS1.

lncRNA-SUMO3 and lncRNA-HDMO13 modulate the inflammatory response by binding miR-21 and miR-142a-3p in grass carp

Septicemia is a systemic inflammatory response to bacterial infection in grass carp (Ctenopharyngodon idella). It could lead to lethality. There is increasing evidence that long noncoding RNAs are involved in the regulation of inflammatory response. In the present study, we firstly confirmed that lncRNA-SUMO3 and lncRNA-HDMO13 could involve in the inflammatory response following infection with Aeromonas hydrophila. Dual-luciferase reporter assays and lncRNA expression profiling confirmed that lncRNA-SUMO3 and lncRNA-HDMO13 contains a functional miR-21 and miR-142a-3p binding site. Meanwhile, transfection with lncRNAs mimics and inhibitors affected the expression of miRNAs and its target genes, including jnk, ccr7, glut3 and tnfaip2. Moreover, the downstream proinflammatory factors of miR-21 and miR-142a-3p were also regulated by lncRNA-SUMO3 and lncRNA-HDMO13. Our results provide a theoretical basis for exploring the molecular mechanism of grass carp lncRNAs regulating inflammation.

Identification and characterization of a novel Epstein-Barr Virus-encoded circular RNA from LMP-2 Gene

Epstein-Barr virus (EBV) has been recently found to generate novel circular RNAs (circRNAs) through backsplicing. However, comprehensive catalogs of EBV circRNAs in other cell lines and their functional characterization are still lacking. In this study, we have identified a list of putative EBV circRNAs in GM12878, an EBV-transformed lymphoblastoid cell line, with a significant majority encoded from the EBV latent genes. A novel EBV circRNA derived from the exon 5 of LMP-2 gene which exhibited highest prevalence, was further validated using RNase R assay and Sanger sequencing. This circRNA, which we term circLMP-2_e5, can be universally detected in a panel of EBV-positive cell lines modelling different latency programs. It ranges from lower expression in nasopharyngeal carcinoma (NPC) cells to higher expression in B cells, and is localized to both the cytoplasm and the nucleus. We provide evidence that circLMP-2_e5 is expressed concomitantly with its cognate linear LMP-2 RNA upon EBV lytic reactivation, and may be produced as a result of exon skipping, with its circularization possibly occurring without the involvement of cis elements in the short flanking introns. Furthermore, we show that circLMP-2_e5 is not involved in regulating cell proliferation, host innate immune response, its linear parental transcripts, or EBV lytic reactivation. Taken together, our study expands the current repertoire of putative EBV circRNAs, broadens our understanding of the biology of EBV circRNAs, and lays the foundation for further investigation of their function in the EBV life cycle and disease development.

Long noncoding RNAs in respiratory viruses: A review

Long noncoding RNAs (lncRNAs) are defined as RNA molecules longer than 200 nucleotides that can regulate gene expression at the transcriptional or post‐transcriptional levels. Both human lncRNAs and lncRNAs encoded by viruses can modulate the expression of host genes which are critical for viral replication, latency, activation of signalling pathways, cytokine and chemokine production, RNAi processing, expression of interferons (IFNs) and interferon‐stimulated genes (ISGs). Studies on lncRNAs as key regulators of host‐virus interactions may give new insights into therapeutic strategies for the treatment of related diseases. This current review focuses on the role of lncRNAs, and their interactions with respiratory viruses including influenza A virus (IAV), respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2).

Viral Manipulation of the Host Epigenome as a Driver of Virus-Induced Oncogenesis

Tumorigenesis due to viral infection accounts for a high fraction of the total global cancer burden (15–20%) of all human cancers. A comprehensive understanding of the mechanisms by which viral infection leads to tumor development is extremely important. One of the main mechanisms by which viruses induce host cell proliferation programs is through controlling the host’s epigenetic machinery. In this review, we dissect the epigenetic pathways through which oncogenic viruses can integrate their genome into host cell chromosomes and lead to tumor progression. In addition, we highlight the potential use of drugs based on histone modifiers in reducing the global impact of cancer development due to viral infection.

Herpesvirus latency

Herpesviruses infect virtually all humans and establish lifelong latency and reactivate to infect other humans. Latency requires multiple functions: maintaining the herpesvirus genome in the nuclei of cells; partitioning the viral genome to daughter cells in dividing cells; avoiding recognition by the immune system by limiting protein expression; producing noncoding viral RNAs (including microRNAs) to suppress lytic gene expression or regulate cellular protein expression that could otherwise eliminate virus-infected cells; modulating the epigenetic state of the viral genome to regulate viral gene expression; and reactivating to infect other hosts. Licensed antivirals inhibit virus replication, but do not affect latency. Understanding of the mechanisms of latency is leading to novel approaches to destroy latently infected cells or inhibit reactivation from latency.

Regulation of Host Innate Immunity by Non-Coding RNAs During Dengue Virus Infection

An estimated 3.9 billion individuals in 128 nations (about 40% of global population) are at risk of acquiring dengue virus infection. About 390 million cases of dengue are reported each year with higher prevalence in the developing world. A recent modeling-based report suggested that half of the population across the globe is at risk of dengue virus infection. In any given dengue outbreak, a percentage of infected population develops severe clinical manifestations, and this remains one of the “unsolved conundrums in dengue pathogenesis”. Although, host immunity and virus serotypes are known to modulate the infection, there are still certain underlying factors that play important roles in modulating dengue pathogenesis. Advanced genomics-based technologies have led to identification of regulatory roles of non-coding RNAs. Accumulating evidence strongly suggests that viruses and their hosts employ non-coding RNAs to modulate the outcome of infection in their own favor. The foremost ones seem to be the cellular microRNAs (miRNAs). Being the post-transcriptional regulators, miRNAs can be regarded as direct switches capable of turning “on” or “off” the viral replication process. Recently, role of long non-coding RNAs (lncRNAs) in modulating viral infections via interferon dependent or independent signaling has been recognized. Hence, we attempt to identify the “under-dog”, the non-coding RNA regulators of dengue virus infection. Such essential knowledge will enhance the understanding of dengue virus infection in holistic manner, by exposing the specific molecular targets for development of novel prophylactic, therapeutic or diagnostic strategies.

LncRNA MEG8 Attenuates Cerebral Ischemia After Ischemic Stroke Through Targeting miR-130a-5p/VEGFA Signaling

MEG8 is involved in ischemia stroke, however, its role in ischemia stroke remains unknown. The current research aimed to investigate the effects and mechanisms of MEG8 in ischemic stroke. Mouse brain microvascular endothelial cells (BMECs) were treated by oxygen-glucose deprivation (OGD). Then, the expressions of MEG8 and miR-130a-5p were detected by quantitative reverse transcription-polymerase chain reaction (q-PCR). Cell counting kit-8 (CCK-8), wound-healing, tube formation, Western blot, and q-PCR assays were performed to detect the effects of MEG8 and miR-130a-5p on cell viability, migration, and angiogenesis and VEGFA expression. Bioinformatics, dual-luciferase reporter assay, and RNA immunoprecipitation analysis were carried out to investigate the targeting relationship between MEG8 and miR-130a-5p, and between miR-130a-5p and VEGFA. Then, rat middle cerebral artery occlusion (MCAO) model and MEG8 overexpression MCAO model were established, and neurological deficit and infarct volume of the model rats were evaluated. Finally, Western blot and q-PCR were carried out to detect the expressions of MEG8, miR-130a-5p, and VEGFA. MEG8 was upregulated and miR-130a-5p was downregulated in OGD-treated BMECs. MiR-130a-5p was found to be a target of MEG8, and VEGFA was predicted to be a potential target of miR-130a-5p. Downregulation of MEG8 inhibited the cell viability, migration, and angiogenesis and the expression of VEGFA via negatively regulating miR-130a-5p of BMECs treated by OGD/non-OGD. In addition, MEG8 reduced cerebral ischemia, neurological score and miR-130a-5p expression, and increased VEGFA expression of MCAO rat. Our findings proved that MEG8 regulates angiogenesis and attenuates cerebral ischemia after ischemic stroke via miR-130a-5p/VEGFA signaling.

Downregulation of Cancer-Associated lncRNAs in Peripheral Blood of Multiple Sclerosis Patients

Recent studies have shown contribution of long non-coding RNAs (lncRNAs) in the pathogenesis of immune-related disorders including multiple sclerosis (MS). Based on the role of these transcripts in the regulation of immune response, peripheral levels of lncRNAs can reflect the level of immune activation. In the present study, we quantified expression of four lncRNAs namely SPRY4-IT1, HOXA-AS2, LINC-ROR, and MEG3 in venous blood of MS patients and controls using quantitative real-time PCR method. Relative expressions of SPRY4-IT1, HOXA-AS2, LINC-ROR, and MEG3 were significantly lower in female MS patients compared with female healthy subjects. For MEG3, this pattern of expression was also observed in male subjects. However, for other lncRNAs, no significant difference was detected between male patients and male controls. Expression of HOXA-AS2 was correlated with progression index (r = 0.36, P < 0.001). Besides, there was a significant correlation between expression of this lncRNA and expression of LINC-ROR in MS patients (r = 0.44, P < 0.0001). There was no other correlation between expression of lncRNAs and clinical data in MS patients. In control group, expressions of none of lncRNAs were correlated with age of persons. Notably, significant correlations were demonstrated between expression levels of all lncRNAs in healthy subjects with r values ranging from 0.23 to 0.42. The current investigation shows dysregulation of lncRNAs in MS patients in a sex-specific manner and warrants further studies to unravel the clinical and therapeutic implications of such dysregulation.

SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Background

Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis.

Methods

In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus.

Results

A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.

lncRNA Mtss1 promotes inflammatory responses and secondary brain injury after intracerebral hemorrhage by targeting miR-709 in mice

Secondary brain injuries following intracerebral hemorrhage (ICH) are mediated by inflammatory pathway activation. The present study aimed to characterize long noncoding RNAs (lncRNAs) that are differentially expressed in cerebral tissues during ICH pathogenesis and to investigate their pathogenic functions. An ICH mouse model established by collagenase injection was used to obtain differentially expressed lncRNAs for deep sequencing. A cellular inflammation model was established by treating mouse microglia with lipopolysaccharide. Expression of lncRNA and miRNA was assessed by quantitative RT-PCR, and protein abundance was measured by western blot. Cytokine levels in mouse serum and cell culture supernatants were analyzed using enzyme-linked immunosorbent assay. Cerebral injury was evaluated by hematoxylin-eosin and Nissl staining, the ratio of brain dry weight/brain wet weight, and neurobehavior scoring. Ionized calcium-binding adaptor molecule 1 (IBA1) expression in the brain sections was assessed using immunohistochemistry. A total of 3681 lncRNAs were differentially expressed in the brain tissue of the ICH mice group compared with the Sham group. Of these, lncRNA metastasis suppressor-1 (Mtss1) expression was increased. Mtss1 knockdown by siRNA in the cellular model strongly suppressed TIR-domain-containing adapter-inducing interferon-β (TRIF) expression, P65 phosphorylation, and tumor necrosis factor (TNF)-α and interleukin (IL)-1β secretion. Mtss1 knockdown in ICH mice inhibited secondary brain injury and decreased IBA1, TNF-α, and IL-1β. Mtss1 was predicted to bind miR-709, and Mtss1 knockdown elevated miR-709 expression in the cellular inflammation model and ICH mice. High expression of Mtss1 promoted inflammatory brain injuries after ICH by enhancing inflammatory cytokine secretion and targeting miR-709 expression.

Long noncoding RNAs involvement in Epstein-Barr virus infection and tumorigenesis

The Epstein-Barr virus (EBV) is a ubiquitous γ-herpesvirus related to various types of cancers, including epithelial nasopharyngeal carcinoma, gastric carcinoma, and lymphoma. Long noncoding RNAs (lncRNAs) are expressed extensively in mammalian cells and play crucial roles in regulating various cellular processes and multiple cancers. Cellular lncRNAs can be differentially expressed induced by EBV infection. The dysregulated lncRNAs probably modulate the host immune response and other biological functions. At present, lncRNAs have been found to be significantly increased or decreased in EBV-infected cells, exosomes and EBV-associated cancers, suggesting their potential function and clinical application as biomarkers. In addition, EBV-encoded lncRNAs, BART and BHLF1 lncRNAs, may play roles in the viral oncogenesis. Analysis of the specific lncRNAs involved in interactions with the EBV machinery will provide information on their potential mechanism of action during multiple steps of EBV tumorigenesis. Here, we review the current knowledge regarding EBV-related lncRNAs and their possible roles in the pathogenesis of EBV-associated cancers.

PAN RNA: transcriptional exhaust from a viral engine

Kaposi’s sarcoma-associated herpesvirus (KSHV), also designated human herpesvirus 8 (HHV-8), has been linked to Kaposi’s sarcoma, as well as to primary effusion lymphoma (PEL), and a subset of multicentric Castleman’s disease. KSHV genomes are maintained as episomes within infected cells and the virus exhibits a biphasic life cycle consisting of a life-long latent phase during which only a few viral genes are expressed and no viral progeny are produced and a transient lytic reactivation phase, in which a full repertoire of ~ 80 lytic genes are activated in a temporally regulated manner culminating in the release of new virions. Lytic replication is initiated by a single viral protein, K-Rta (ORF50), which activates more than 80 viral genes from multiple resident viral episomes (i.e., viral chromosomes). One of the major targets of K-Rta is a long non-coding nuclear RNA, PAN RNA (polyadenylated nuclear RNA), a lncRNA that accumulates to exceedingly high levels in the nucleus during viral reactivation. K-Rta directly binds to the PAN RNA promoter and robustly activates PAN RNA expression. Although PAN RNA has been known for over 20 years, its role in viral replication is still incompletely understood. In this perspective, we will briefly review the current understanding of PAN RNA and then describe our current working model of this RNA. The model is based on our observations concerning events that occur during KSHV lytic reactivation including (i) a marked accumulation of RNA Pol II at the PAN promoter, (ii) genomic looping emanating from the PAN locus, (iii) interaction of a second viral lytic protein (ORF57) with K-Rta, PAN RNA and RNA Pol II, (iv) the essential requirement for PAN RNA expression in cis for optimal transcriptional execution needed for the entire lytic program, and (v) ORF57 recruitment of RNA Pol II to the PAN genomic locus. Together our results generate a model in which the PAN locus serves as a hub for sequestration/trapping of the cellular transcriptional machinery proximal to viral episomes. Sequestration at the PAN locus facilitates high levels of viral transcription throughout the viral genome during lytic replication. ORF57 acts as a transcription-dependent transactivator at the PAN locus by binding to both Rta and PAN to locally trap RNA Pol II. The resulting accumulation of high levels of nuclear PAN RNA created by this process is an inducible enhancer-derived (eRNA) by-product that litters the infected cell nucleus.

Comparative analysis of dsRNA-induced lncRNAs in three kinds of insect species

Long noncoding RNAs (lncRNAs) that have immune responses to various stimuli have been identified in some insects. One type of pathogen-associated molecular pattern, double-stranded RNA (dsRNA), can trigger the RNA interference (RNAi) pathway and immune response. Interestingly, there has been no research into characterizing the relationship between lncRNA and dsRNA-induced RNAi pathways. In this study, dsRNA-induced lncRNAs were investigated in two species of lepidopteran insects, Helicoverpa armigera and Plutella xylostella, and one species of coleopteran insects, Tribolium castaneum. Between untreated group and dsRNA-induced group; 3,463 H. armigera, 6,245 P. xylostella, and 3,067 T. castaneum differentially expressed lncRNAs were identified while 156 H. armigera, 247 P. xylostella, 415 T. castaneum lncRNAs and their putative target genes showed consistent changes in gene expression. In T. castaneum, most target genes of the differentially expressed lncRNAs are enriched in the cyclic adenosine monophosphate signaling pathway, ABC transporters, and Janus kinase-signal transducers and activators of the transcription signaling pathway. Conversely, in H. armigera and P. xylostella, the differentially expressed lncRNAs were mainly enriched in the metabolic, digestive, and synthetic signaling pathways. This result indicates that dsRNA-induced lncRNA is species-dependent. We also found that both Dicer-2 and the lncRNA that targets Dicer-2 were significantly upregulated after dsRNA treatment in P. xylostella, indicating that some lncRNAs may be involved in the regulation of the core RNAi pathway in insects. Our results are the first to identify a relationship between lncRNAs and dsRNA in various insect species with different RNAi efficiencies. These results provide a reference for future study of the dsRNA-induced RNAi pathway and different RNAi efficiencies among insect species.

Endometriosis-related ceRNA network to identify predictive biomarkers of endometrial receptivity

AIM

As RNA, which plays a role in the regulation of endometrial receptivity, can be modulated via ceRNA mechanisms, we constructed a ceRNA network to explore potential RNA/ceRNA biomarkers indicating endometrial receptivity associated with endometriosis.

MATERIALS & METHODS

RNA sequencing was performed on eutopic endometrium from eight patients with and without endometriosis. Bioinformatics algorithms were used to predict ceRNA network and pathway analysis.

RESULTS

We identified an endometriosis-associated ceRNA network involving 45 pathways and four ceRNAs as potential predictive biomarkers for endometrial receptivity. Patients with endometriosis presented lower levels of progesterone receptor type B expression.

CONCLUSION

Differentially expressed RNAs and lower progesterone receptors type B levels in endometriosis might be related to the impairment of endometrial receptivity.

Non-coding RNAs Function as Immune Regulators in Teleost Fish

Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.

SNHG12 Promotes Angiogenesis Following Ischemic Stroke via Regulating miR-150/VEGF Pathway

The promotion of angiogenesis is a promising therapeutic strategy for ischemic stroke. Many long noncoding RNAs (lncRNAs) are related to angiogenesis following ischemic stroke. LncRNA small nucleolar RNA host gene 12 (SNHG12) was upregulated in oxygen-glucose deprivation (OGD)-exposed primary brain microvascular endothelial cells and in microvessel from middle cerebral artery occlusion (MCAO) animal brains. However, the role and underlying mechanism of SNHG12 in ischemic stroke especially associated with angiogenesis process remain unknown. The expression of SNHG12 and miR-150 was determined in OGD-stimulated mouse brain microvascular endothelial (bEnd.3) cells. The role and mechanism of SNHG12 in the angiogenesis after ischemic stroke were investigated using gain- and loss-of function approaches both in OGD-exposed bEnd.3 cells and in MCAO mouse models. We found SNHG12 expression was elevated, whereas miR-150 reduced in OGD-exposed bEnd.3 cells. Upregulation of SNHG12 elevated, and SNHG12 knockdown suppressed the capillary-like tube formation, viability, migration, and VEGF expression in OGD-injured bEnd.3 cells. miR-150 mimic reversed, whereas anti-miR-150 further strengthened the effect of SNHG12 upregulation on the angiogenesis in bEnd.3 cells. Furthermore, we found that SNHG12 functioned as a competing endogenous RNA for miR-150 to regulate VEGF expression. Additionally, overexpression of SNHG12 improved the recovery of neurological function, reduced infarct volume and miR-150 expression, increased vascular density and VEGF expression in the infarct border zone of MCAO mice. In conclusion, SNHG12 promotes the angiogenesis following ischemic stroke via miR-150/VEGF pathway, which further clarified the mechanism of angiogenesis after ischemic stroke and provides a target for the treatment of this disease.