Emerging role of extracellular microRNAs and lncRNAs

LncRNA HOXA‑AS2 is a prognostic and clinicopathological predictor in patients with cancer: A meta‑analysis

Elevated expression of long non-coding RNA homeobox A cluster antisense RNA 2 (lncRNA HOXA-AS2) is known to have prognostic value in various solid tumors. The present meta-analysis aimed to comprehensively quantify its prognostic significance across a wider spectrum of malignancies and to provide an updated synthesis of evidence that could refine prognostic models. To achieve this aim, multiple databases were carefully searched for lncRNA HOXA-AS2-related articles published in the past 10 years. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to demonstrate the prognostic value of lncRNA HOXA-AS2 using Stata 15.0 software. The function of lncRNA HOXA-AS2 was inferred from its associations with key clinical outcomes such as lymph node metastasis, distant metastasis, tumor stage and tumor size, which may reflect its role in tumor biology. In the present systematic review and meta-analysis of 454 patients across 7 studies, it was found that high lncRNA HOXA-AS2 expression was significantly associated with a shorter overall survival (OS) time in patients with cancer (HR=2.14; 95% CI, 1.40-3.27; P<0.001). High lncRNA HOXA-AS2 expression was also associated with lymph node metastasis [odds ratio (OR)=2.06; 95% CI, 1.07-3.99; P=0.032], distant metastasis (OR=2.11; 95% CI, 1.15-3.88; P=0.016), advanced tumor stage (OR=2.71; 95% CI, 1.50-4.89; P=0.001) and larger tumor size (OR=2.02; 95% CI, 0.86-4.78; P=0.006). However, no significant association was observed with age (OR=1.00; 95% CI, 0.63-1.59; P=0.991) or sex (OR=1.55; 95% CI, 0.72-3.34; P=0.258). In conclusion, elevated expression of lncRNA HOXA-AS2 was significantly related to poor clinical outcomes in various cancer types, such as osteosarcoma, non-small cell lung cancer and papillary thyroid carcinoma, a finding that was further confirmed by the present study. Specifically, the potential of lncRNAHOXA-AS2 as a biomarker in assessing tumor stage, metastasis risk and OS in patients was demonstrated. However, the results of the present study also indicated that the expression of lncRNA HOXA-AS2 was not significantly associated with age or sex, suggesting its role in cancer progression might be independent of these factors. This insight may direct future research to place more focus on the relationship between lncRNA HOXA-AS2 and specific cancer types and clinical characteristics.

RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs

The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.

Temperament & Character account for brain functional connectivity at rest: A diathesis-stress model of functional dysregulation in psychosis

The human brain's resting-state functional connectivity (rsFC) provides stable trait-like measures of differences in the perceptual, cognitive, emotional, and social functioning of individuals. The rsFC of the prefrontal cortex is hypothesized to mediate a person's rational self-government, as is also measured by personality, so we tested whether its connectivity networks account for vulnerability to psychosis and related personality configurations. Young adults were recruited as outpatients or controls from the same communities around psychiatric clinics. Healthy controls (n = 30) and clinically stable outpatients with bipolar disorder (n = 35) or schizophrenia (n = 27) were diagnosed by structured interviews, and then were assessed with standardized protocols of the Human Connectome Project. Data-driven clustering identified five groups of patients with distinct patterns of rsFC regardless of diagnosis. These groups were distinguished by rsFC networks that regulate specific biopsychosocial aspects of psychosis: sensory hypersensitivity, negative emotional balance, impaired attentional control, avolition, and social mistrust. The rsFc group differences were validated by independent measures of white matter microstructure, personality, and clinical features not used to identify the subjects. We confirmed that each connectivity group was organized by differential collaborative interactions among six prefrontal and eight other automatically-coactivated networks. The temperament and character traits of the members of these groups strongly accounted for the differences in rsFC between groups, indicating that configurations of rsFC are internal representations of personality organization. These representations involve weakly self-regulated emotional drives of fear, irrational desire, and mistrust, which predispose to psychopathology. However, stable outpatients with different diagnoses (bipolar or schizophrenic psychoses) were highly similar in rsFC and personality. This supports a diathesis-stress model in which different complex adaptive systems regulate predisposition (which is similar in stable outpatients despite diagnosis) and stress-induced clinical dysfunction (which differs by diagnosis).

Therapeutic Implications of the Drug Resistance Conferred by Extracellular Vesicles Derived from Triple-Negative Breast Cancer Cells

Anticancer drug resistance is a significant impediment in current cancer treatment. Extracellular vesicles (EVs) derived from cancer cells were recently acknowledged as a critical mechanism of drug resistance, tumor progression, and metastasis. EVs are enveloped vesicles comprising a lipid bilayer that transfers various cargo, including proteins, nucleic acids, lipids, and metabolites, from an originating cell to a recipient cell. Investigating the mechanisms whereby EVs confer drug resistance is still in the early stages. In this review, I analyze the roles of EVs derived from triple-negative breast cancer cells (TNBC-EVs) in anticancer drug resistance and discuss strategies to overcome TNBC-EV-mediated drug resistance.

Prognostic Value and Potential Regulatory Mechanism of H19 in Stomach Adenocarcinoma

The first lncRNA discovered, H19, has been found to participate in the regulation of diverse biological processes, including the pathogenesis of stomach adenocarcinoma. In addition to its oncogenic function in tumor formation, a high level of H19 in tumor tissues has also been reported to be an indicator for poor prognosis. However, although many previous works have investigated the level of H19 as an independent indicator for prognosis, the real value of H19 in predicting survival has rarely been evaluated. In this study, we established a prognostic model and nomogram for stomach adenocarcinoma by combining the expression level of H19 with traditional indices, which showed the value of H19 in predicting the survival rates of patients. In addition, we investigated the mechanism underlying the correlation of the H19 level in cancer tissue with poor prognosis in patients. Our results showed that H19 could function as ceRNA by sponging five miRNAs, which may promote the progression of cancer.

Circulating Noncoding RNAs in Pituitary Neuroendocrine Tumors-Two Sides of the Same Coin

Pituitary neuroendocrine tumors (PitNET) are common intracranial neoplasms. While in case of hormone secreting tumors pituitary hormone measurements can be used for monitoring the disease, in non-functional tumors there is a need to discover non-invasive biomarkers. Non-coding RNAs (ncRNAs) are popular biomarker candidates due to their stability and tissue specificity. Among ncRNAs, miRNAs, lncRNAs and circRNAs have been investigated the most in pituitary tumor tissues and in circulation. However, it is still not known whether ncRNAs are originated from the pituitary, or whether they are casually involved in the pathophysiology. Additionally, there is strong diversity among different studies reporting ncRNAs in PitNET. Therefore, to provide an overview of the discrepancies between published studies and to uncover the reasons why despite encouraging experimental data application of ncRNAs in clinical routine has not yet taken hold, in this review available data are summarized on circulating ncRNAs in PitNET. The data on circulating miRNAs, lncRNAs and circRNAs are organized according to different PitNET subtypes. Biological (physiological and pathophysiological) factors behind intra- and interindividual variability and technical aspects of detecting these markers, including preanalytical and analytical parameters, sample acquisition (venipuncture) and type, storage, nucleic acid extraction, quantification and normalization, which reveal the two sides of the same coin are discussed.

Functional Intricacy and Symmetry of Long Non-Coding RNAs in Parasitic Infections

RNAs are a class of molecules and the majority in eukaryotes are arbitrarily termed non- coding transcripts which are broadly classified as short and long non-coding RNAs. Recently, knowledge of the identification and functions of long non-coding RNAs have continued to accumulate and they are being recognized as important molecules that regulate parasite-host interface, parasite differentiation, host responses, and disease progression. Herein, we present and integrate the functions of host and parasite long non-coding RNAs during infections within the context of epigenetic re-programming and molecular crosstalk in the course of host-parasite interactions. Also, the modular range of parasite and host long non-coding RNAs in coordinated parasite developmental changes and host immune dynamic landscapes are discussed. We equally canvass the prospects of long non-coding RNAs in disease diagnosis and prognosis. Hindsight and suggestions are offered with the aim that it will bolster our understanding for future works on host and parasite long non-coding RNAs.

Long Noncoding RNA CTD-2245E15.3 Promotes Anabolic Enzymes ACC1 and PC to Support Non-Small Cell Lung Cancer Growth

Long noncoding RNAs (lncRNA) have been shown to play critical regulatory roles in the onset and progression of human cancers. However, the functions of a large proportion of lncRNAs are still unexplored. Here we describe a novel lncRNA, CTD-2245E15.3, that promotes lung tumorigenesis by regulating the anabolic enzymes acetyl-CoA carboxylase 1 (ACC1, encoded by the ACACA gene) and pyruvate carboxylase (PC). Differentially expressed lncRNAs between non-small cell lung cancer (NSCLC) and paired adjacent nontumor tissues were identified by a microarray and validated using quantitative real-time polymerase chain reaction. CTD-2245E15.3 was significantly upregulated in NSCLC and was mainly located in the cytoplasm. Knockdown of CTD-2245E15.3 by specific antisense oligonucleotides suppressed cell growth in vitro and in vivo, largely due to cell-cycle arrest and induction of apoptosis. Overexpression of CTD-2245E15.3 in an orthotopic model of lung cancer led to a significant increase in total tumor burden. CTD-2245E15.3 exerted its oncogenic function by binding ACC1 and PC, which are key anabolic factors for biomolecule synthesis in rapidly proliferating tumor cells. Knockdown of CTD-2245E15.3 increased phosphorylation of ACC1 at an inhibitory site for enzymatic activity and promoted PC degradation via ubiquitination. Supplements of palmitate or oxaloacetate, products of ACC1 and PC, alleviated the suppression of cell growth caused by loss of CTD-2245E15.3. These findings reveal the important role of CTD-2245E15.3 as an oncogenic lncRNA in the anabolic process for tumor growth. SIGNIFICANCE: These findings demonstrate a novel lncRNA CTD-2245E15.3 that binds and positively regulates anabolic enzymes ACC1 and PC to promote tumor growth. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/13/3509/F1.large.jpg.

Caspase-3 Cleaves Extracellular Vesicle Proteins During Auditory Brainstem Development

Sound localization requires extremely precise development of auditory brainstem circuits, the molecular mechanisms of which are largely unknown. We previously demonstrated a novel requirement for non-apoptotic activity of the protease caspase-3 in chick auditory brainstem development. Here, we used mass spectrometry to identify proteolytic substrates of caspase-3 during chick auditory brainstem development. These auditory brainstem caspase-3 substrates were enriched for proteins previously shown to be cleaved by caspase-3, especially in non-apoptotic contexts. Functional annotation analysis revealed that our caspase-3 substrates were also enriched for proteins associated with several protein categories, including proteins found in extracellular vesicles (EVs), membrane-bound nanoparticles that function in intercellular communication. The proteome of EVs isolated from the auditory brainstem was highly enriched for our caspase-3 substrates. Additionally, we identified two caspase-3 substrates with known functions in axon guidance, namely Neural Cell Adhesion Molecule (NCAM) and Neuronal-glial Cell Adhesion Molecule (Ng-CAM), that were found in auditory brainstem EVs and expressed in the auditory pathway alongside cleaved caspase-3. Taken together, these data suggest a novel developmental mechanism whereby caspase-3 influences auditory brainstem circuit formation through the proteolytic cleavage of extracellular vesicle (EV) proteins.

LINC00460-miR-149-5p/miR-150-5p-Mutant p53 Feedback Loop Promotes Oxaliplatin Resistance in Colorectal Cancer

Oxaliplatin resistance is a major challenge in the clinical treatment for advanced colorectal cancer (CRC). Long non-coding RNAs (lncRNAs) are involved in tumorigenesis and progression as critical regulators, while their potential roles in chemoresistance are poorly understood. In this study, we report that the LINC00460-miR-149-5p/miR-150-5p-mutant p53 feedback loop is responsible for oxaliplatin resistance in CRC. First, LINC00460 was found to exhibit higher expression in oxaliplatin-resistant CRC (CRC/OxR) cells compared with parental oxaliplatin-sensitive ones, and this expression pattern depends on mutant p53 (SW480/OxR), not wild-type p53 (HCT116/OxR). Oxaliplatin-induced LINC00460 in SW480/OxR cells was mainly located in the cytoplasm and was associated with AGO2 protein. LINC00460 functions as a competing endogenous RNA (ceRNA) to promote oxaliplatin resistance through sequestering miR-149-5p/miR-150-5p and upregulating the expression of the microRNA (miRNA) target p53. Knockdown of LINC00460 sensitized SW480/OxR cells to oxaliplatin by modulating p53 in vitro and in vivo. In turn, mutant p53 positively regulated the expression of LINC00460, thus forming a feedback loop. Clinical data showed that LINC00460 was upregulated in CRC tissues compared with paired normal tissues and was significantly correlated with clinical stage and node (N) status. Our findings uncover a mechanism for the LINC00460-miR-149-5p/miR-150-5p-mutant p53 feedback loop in oxaliplatin resistance of CRC, and they provide potential therapeutic targets for tumor chemoresistance.

Therapeutic potential of extracellular vesicle-associated long noncoding RNA

Both extracellular vesicles (EVs) and long noncoding RNAs (lncRNAs) have been increasingly investigated as biomarkers, pathophysiological mediators, and potential therapeutics. While these two entities have often been studied separately, there are increasing reports of EV-associated lncRNA activity in processes such as oncogenesis as well as tissue repair and regeneration. Given the powerful nature and emerging translational impact of other noncoding RNAs such as microRNA (miRNA) and small interfering RNA, lncRNA therapeutics may represent a new frontier. While EVs are natural vehicles that transport and protect lncRNAs physiologically, they can also be engineered for enhanced cargo loading and therapeutic properties. In this review, we will summarize the activity of lncRNAs relevant to both tissue repair and cancer treatment and discuss the role of EVs in enabling the potential of lncRNA therapeutics.

The PGC-1α/NRF1/miR-378a axis protects vascular smooth muscle cells from FFA-induced proliferation, migration and inflammation in atherosclerosis

BACKGROUND AND AIMS

Atherosclerosis (AS) is the leading cause of cardiovascular diseases. PGC-1α is a key regulator of cellular energy homeostasis, but its role in AS remains debatable.

METHODS AND RESULTS

In our study, PGC-1α was shown to be significantly decreased in the media of human atherosclerotic vessels. To explore whether miRNAs might be regulated by PGC-1α in vascular smooth muscle cells (VSMCs), microarray analysis was performed. Microarray and Pearson's correlation analysis showed that PGC-1α and miR-378a were positively correlated in vivo and in vitro. As an upstream co-activator, PGC-1α was found to regulate miR-378a through binding to the transcriptional factor NRF1 in VSMCs. Therefore, the decreased expression of PGC-1α might account for suppression of miR-378a in VSMCs in AS. Furthermore, IGF1 and TLR8, two genes known to be aberrantly up-regulated in atherogenic vessels, were identified as direct targets of miR-378a. In vitro up-regulation of miR-378a markedly inhibited free fatty acid (FFA)-induced VSMC proliferation, migration and inflammation through targeting IGF1 and TLR8.

CONCLUSIONS

These findings highlight the protective role of the PGC-1α/NRF1/miR-378a regulatory axis in AS progression and suggest miR-378a as potential therapeutic target for AS treatment.

An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients

Colorectal cancer (CRC) is one of the most common cancers worldwide, whose morbidity and mortality gradually increased. Here, we aimed to identify and access prognostic long non-coding RNAs (lncRNAs) associated with overall survival (OS) in CRC. Firstly, RNA expression profiles were obtained from The Cancer Genome Atlas (TCGA) database, and 439 CRC patients were enrolled as a training set. Univariate Cox analysis and the least absolute shrinkage and selection operator analysis (LASSO) were performed to identify the prognostic lncRNAs. Multivariable Cox regression analysis was used to establish a prognostic risk formula including three lncRNAs (AP003555.2, AP006284.1, and LINC01602). The low-risk group had a better OS than the high-risk group (P < 0.0001), and the areas under the receiver operating characteristic curve (AUCs) of 3- and 5-year OS were 0.712 and 0.674, respectively. Then, we evaluated the signature in a clinical validation set which were collected from the Affiliated Hospital of Jiangnan University. Compared with the low-risk group, patients' OS were found to be significantly worse in the high-risk group (P = 0.0057). The AUCs of 3- and 5-year OS were 0.701 and 0.694, respectively. Finally, we constructed an lncRNA–microRNA (miRNA)–messenger RNA (mRNA) competing endogenous RNA (ceRNA) network to explore the potential function of three differentially expressed lncRNAs (DElncRNAs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DElncRNAs were involved with several cancer-related pathways. In summary, our data provide evidence that the three-lncRNA signature could serve as an independent biomarker to predict prognosis in CRC. This study will also suggest that these three lncRNAs potentially participate in the progression of CRC.