LncRNA DDX11-AS1: a novel oncogene in human cancer

Biological functions and affected signaling pathways by Long Non-Coding RNAs in the immune system

Recently, the various regulative functions of long non-coding RNAs (LncRNAs) have been well determined. Recently, the vital role of LncRNAs as gene regulators has been identified in the immune system, especially in the inflammatory response. All cells of the immune system are governed by a complex and ever-changing gene expression program that is regulated through both transcriptional and post-transcriptional processes. LncRNAs regulate gene expression within the cell nucleus by influencing transcription or through post-transcriptional processes that affect the splicing, stability, or translation of messenger RNAs (mRNAs). Recent studies in immunology have revealed substantial alterations in the expression of lncRNAs during the activation of the innate immune system as well as the development, differentiation, and activation of T cells. These lncRNAs regulate key aspects of immune function, including the manufacturing of inflammatory molecules, cellular distinction, and cell movement. They do this by modulating protein-protein interactions or through base pairing with RNA and DNA. Here we review the current understanding of the mechanism of action of lncRNAs as novel immune-related regulators and their impact on physiological and pathological processes related to the immune system, including autoimmune diseases. We also highlight the emerging pattern of gene expression control in important research areas at the intersection between immunology and lncRNA biology.

Construction and validation of a prognostic signature based on seven endoplasmic reticulum stress-related lncRNAs for patients with head and neck squamous cell carcinoma

Endoplasmic reticulum stress (ERS) occurs when misfolded or unfolded proteins accumulate in the endoplasmic reticulum (ER), and it is often observed in tumors, including head and neck squamous cell carcinoma (HNSCC). Relevant studies have demonstrated the prognostic significance of ERS-related long non-coding RNAs (lncRNAs) in various cancers. However, the relationship between ERS and lncRNAs in HNSCC has received limited attention in previous studies. In this study, we aimed to develop an ERS-related lncRNAs prognostic model using correlation analysis, Cox regression analysis, least absolute shrinkage, and selection operator (LASSO) regression analysis based on data from The Cancer Genome Atlas (TCGA) database. The survival and predictive ability of this model were evaluated using Kaplan-Meier analysis and time-dependent receiver operating characteristics (ROC), while nomograms and calibration curves were constructed. Then, functional enrichment analyses, tumor mutation burden (TMB), tumor infiltration of immune cells, single sample Gene Set Enrichment Analysis (ssGSEA), and drug sensitivity analysis were performed. Additionally, we conducted a consensus cluster analysis to compare differences between subtypes of tumors. Finally, we validated the expression of the ERS-related lncRNAs that constructed prognostic risk score model in HNSCC tissues through quantitative real-time PCR (qRT-PCR). We developed a prognostic signature based on seven ERS-related lncRNAs, which showed better predictive performance than other clinicopathological features. The high-risk poor prognosis group had a poorer prognosis in comparison to the low-risk good prognosis. The area under the ROC curve (AUC) predicted by this model for 3-year survival rates of HNSCC patients was 0.805. Enrichment analysis revealed that the differentially expressed genes were primarily enriched in pathways related to immune responses and signal transduction. Low-risk patients had lower TMB, more immune cell infiltrations, and enhanced anti-tumor immunity. Cluster analysis indicated that cluster 3 may have a better prognosis and immunotherapy effect. In addition, the result of qRT-PCR was consistent with our analysis. This prognostic model based on seven ERS-related lncRNAs is a promising tool for risk stratification, survival prediction, and immune cell infiltration status assessment.

The role of non-coding RNAs in the diagnosis of different stages (HCC, CHB, OBI) of hepatitis B infection

Despite the availability of an effective hepatitis B virus (HBV) vaccine and universal immunization schedules, HBV has remained a health problem in various stages such as occult hepatitis B infection (OBI), chronic hepatitis B (CHB), and hepatocellular carcinoma (HCC), which is considered one of the possible phases during chronic HBV infection. OBI is defined as the persistence of HBV genomes in hepatocytes of patients with a negative HBV surface antigen (HBsAg) test and detectable or undetectable HBV DNA in the blood. OBI is occasionally associated with infection caused by mutant viruses that produce a modified HBsAg that is undetected by diagnostic procedures or with replication-defective variations. Many aspects of HBV (OBI more than any other stage) including prevalence, pathobiology, and clinical implications has remained controversial. According to a growing body of research, non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been linked to the development and progression of a number of illnesses, including viral infectious disorders. Despite a shortage of knowledge regarding the expression and biological activities of lncRNAs and miRNAs in HBV infection, Hepatitis B remains a major global public health concern. This review summarizes the role of lncRNAs in the diagnosis and treatment of different stages of hepatitis B infection.

The Cuproptosis-Related Long Noncoding RNA Signature Predicts Prognosis and Immune Cell Infiltration in Hepatocellular Carcinoma

Background

Hepatocellular carcinoma (HCC), ranking as one of the most common malignant tumors, is one of the leading causes of cancer death, with a poor prognosis. Cuproptosis, a novel programmed cell death modality that has just been confirmed recently, may play an important role in HCC prognosis. Long noncoding RNA (LncRNA) is a key participant in tumorigenesis and immune responses. It may be of great significance to predict HCC based on cuproptosis genes and their related LncRNA.

Methods

The sample data on HCC patients were obtained from The Cancer Genome Atlas (TCGA) database. Combined with cuproptosis-related genes collected from the literature search, expression analysis was carried out to find cuproptosis genes and their related LncRNAs significantly expressed in HCC. The prognostic model was constructed by least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression. The feasibility of these signature LncRNAs used for the evaluation of the overall survival rate in HCC patients as independent factors was investigated. The expression profile of cuproptosis, immune cell infiltration, and the status of somatic mutation were analyzed and compared.

Results

A prognostic model of HCC consisting of seven cuproptosis gene-related LncRNA signatures was constructed. Multiple verification methods have showed that this model can accurately predict the prognosis of HCC patients. It was showed that the classified high-risk group under the risk score of this model had worse survival status, more significant expression of the immune function, and higher mutation frequency. During the analysis, the cuproptosis gene CDKN2A was found to be most closely related to LncRNA DDX11-AS1 in the expression profile of HCC patients.

Conclusion

The cuproptosis-related signature LncRNA in HCC was identified, on the basis of which a model was constructed, and it was verified that it can be used to predict the prognosis of HCC patients. The potential role of these cuproptosis-related signature LncRNAs as new targets for disease therapy in antagonizing HCC development was discussed.

LncRNA LOXL1-AS1 expression in cancer prognosis: A meta-analysis

BACKGROUND

Several studies showed that LncRNA LOXL1 antisense RNA 1 (LOXL1-AS1) is overexpressed in a variety of cancers and plays a role as an oncogene in cancer. The present meta-analysis aims to elucidate the relationship between LOXL1-AS1 expression and prognosis and clinicopathological features among cancer patients.

METHODS

PubMed, Web of Science, Cochrane Library, and EMBASE database were comprehensively and systematically searched. Pooled odds ratios (ORs) and hazard ratios with a 95% confidence interval (CI) were employed to assess the relationship between LOXL1-AS1 expression and clinical outcomes and clinicopathological features in cancer patients.

RESULTS

The present study finally enrolled 8 studies which included 657 cancer patients. The combined results indicated that the overexpression of LOXL1-AS1 was significantly associated with shorter overall survival (pooled hazard ratio = 1.99, 95% CI 1.49-2.65, P < .00001). Meanwhile, regarding clinicopathology of cancer patients, the upregulation of LOXL1-AS1 expression was closely related to lymph node metastasis (yes vs no OR = 4.01, 95% CI: 2.02-7.96, P < .0001) and distant metastasis (yes vs no OR = 3.04, 95% CI: 1.82-5.06, P < .0001), respectively.

CONCLUSION

High expression of LOXL1-AS1 in some cancers predicts shorter overall survival, distant metastasis, and lymph node metastasis. LOXL1-AS1 shows great promise as a prognostic biomarker in cancer patients.

LncRNAs-associated to genomic instability: A barrier to cancer therapy effectiveness

Although a large part of the genome is transcribed, only 1.9% has a protein-coding potential; most of the transcripts are non-coding RNAs such as snRNAs, tRNAs, and rRNAs that participate in mRNA processing and translation. In addition, there are small RNAs with a regulatory role, such as siRNAs, miRNAs, and piRNAs. Finally, the long non-coding RNAs (lncRNAs) are transcripts of more than 200 bp that can positively and negatively regulate gene expression (both in cis and trans), serve as a scaffold for protein recruitment, and control nuclear architecture, among other functions. An essential process regulated by lncRNAs is genome stability. LncRNAs regulate genes associated with DNA repair and chromosome segregation; they are also directly involved in the maintenance of telomeres and have recently been associated with the activity of the centromeres. In cancer, many alterations in lncRNAs have been found to promote genomic instability, which is a hallmark of cancer and is associated with resistance to chemotherapy. In this review, we analyze the most recent findings of lncRNA alterations in cancer, their relevance in genomic instability, and their impact on the resistance of tumor cells to anticancer therapy.

Integrative pan-cancer analysis indicates the prognostic importance of long noncoding RNA SNHG17 in human cancers

BACKGROUND

Cancer is one of the most widespread causes of death today. Early diagnosis can dramatically reduce cancer-related mortality. Studies have shown that the lncRNA Small Nucleolar RNA Host Gene 17 (SNHG17) is aberrantly expressed in various types of solid tumors. Nevertheless, its prognostic value remains to be elucidated. The main objective of this meta-analysis was to elucidate whether SNHG17 can be considered as a potential prognostic biomarker for a variety of cancers.

METHODS

Correlational studies were screened from Cochrane, Embase, PubMed, and Web of Science. Hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs) were pooled, and the role of SNHG17 in cancer was analyzed. The Cancer Genome Atlas (TCGA) database was employed to verify the results.

RESULTS

Seventeen original papers including 1451 patients were included in the meta-analysis. SNHG17 expression was upregulated in various cancers. Overexpression of SNHG17 was significantly correlated with worse overall survival (OS) (HR = 1.92, 95% CI 1.55-2.37, P < 0.001) and relapse-free survival (RFS) (HR = 1.87, 95% CI 1.06-3.30, P = 0.030). Furthermore, overexpression of SNHG17 was predictive of earlier lymph node metastasis (LNM) (OR = 2.94, 95% CI 2.29-3.78, P < 0.001), more advanced tumor-node-metastases (TNM) stage (OR = 3.56, 95% CI 2.22-5.68, P < 0.001), larger tumor size (OR = 2.18, 95% CI 1.65-2.88, P < 0.001), worse differentiation grade (OR = 1.69, 95% CI 1.26-2.25, P < 0.001), and earlier distant metastasis (DM) (OR = 1.63, 95% CI 1.03-2.56, P = 0.033) in human cancers. Moreover, further inquiry based on TCGA dataset validated that SNHG17 was high expression in various tumors and foresaw unfavorable clinical prognosis.

CONCLUSIONS

Overexpression of SNHG17 correlates with poor prognosis and advanced clinicopathological features in cancer patients and may be a potential prognostic indicator and a therapeutic target for cancer treatment.

LncRNA OR2A1-AS1 index predicts survival in germinal center-like diffuse large B-cell lymphoma

BACKGROUND

Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive form of non-Hodgkin lymphoma. Long noncoding RNA (lncRNA) has been evaluated as prognostic markers in various carcinomas. However, the prognostic value of the lncRNA index in DLBCL has not been fully understood. Hence, this study aimed to identify the prognostic value of lncRNA olfactory receptor family 2 subfamily A member 1-antisense RNA 1 (OR2A1-AS1) in DLBCL.

METHODS

The Gene Expression Omnibus (GEO) database was used to obtain the GSE97336 dataset comprising lncRNA expression profiles. Quantitative reverse transcription polymerase chain reaction (QRT-PCR) was conducted to evaluate the expression of OR2A1-AS1 in 98 cases of DLBCL.

RESULTS

OR2A1-AS1 expression was considerably reduced in DLBCL patients, reduced OR2A1-AS1 expression was linked to a shorter overall survival (OS) and progression-free survival (PFS) in DLBCL patients, especially those with the germinal center B-cell-like subtype (GCB). Multivariate analysis (MVA) revealed that the OR2A1-AS1 index had prognostic significance. Patients with low OR2A1-AS1 expression have a poor prognosis.

CONCLUSIONS

OR2A1-AS may represent an effective predictor of patients' outcomes with DLBCL.

LncRNA OSTM1-AS1 acts as an oncogenic factor in Wilms' tumor by regulating the miR-514a-3p/MELK axis

Wilms' tumor (WT) is the most typical basic renal tumor in children and is associated with a high recurrence rate and improper diagnosis. Long noncoding RNAs (lncRNAs) play important roles in WT development. However, the impact of the OSTM1 antisense RNA 1 (OSTM1-AS1) lncRNA on WT remains largely unexplored. Differential expression of OSTM1-AS1, miR-514a-3p and maternal embryonic leucine zipper kinase (MELK) in mice with WT cells was assessed via quantitative reverse transcription-PCR and western blotting. Changes in the proliferation, migration and apoptosis of WT cells after OSTM1-AS1, miR-514a-3p or MELK knockdown were assessed using the cell counting kit-8, Transwell and caspase-3 activity assays, respectively. Additionally, the tumorigenicity of WT cells after OSTM1-AS1 knockdown in vivo was analyzed using a xenograft tumor assay. The association among OSTM1-AS1, MELK and miR-514a-3p was confirmed using the RNA binding protein immunoprecipitation and luciferase reporter assays. OSTM1-AS1 and MELK were upregulated in WT cells, whereas miR-514a-3p was downregulated. OSTM1-AS1 was mostly observed in the cytoplasm, and its knockout suppressed WT cell migration and proliferation in vitro , triggered apoptosis and attenuated tumor development in vivo . MiR-514a-3p was sponged by OSTM1-AS1, and miR-514a-3p interference counteracted the tumoricidal effect of OSTM1-AS1 knockdown. MiR-514a-3p reduced WT progression by downregulating the expression of MELK, which is the target gene of miR-514a-3p. lncRNA OSTM1-AS1 acts as an oncogenic factor in WT by releasing MELK through sponging miR-514a-3p and could be a useful target for WT diagnosis and therapy.

LncRNA-ENST00000543604 exerts a tumor-promoting effect via miRNA 564/AEG-1 or ZNF326/EMT and predicts the prognosis of and chemotherapeutic effect in colorectal cancer

Objectives

Colorectal cancer(CRC) is a common malignant tumor. Recent studies have found that lncRNAs play an important role in the occurrence and development of colorectal cancer.

Methods

Based on high-throughput sequencing results of fresh CRC tissues and adjacent tissues, we identified lncRNA-ENST00000543604 (lncRNA 604) as the research object by qRT-PCR in CRC tissues and cells. We explored the mechanism of lncRNA 604 action by using luciferin reporter, qRT-PCR and Western blot assays. Kaplan-Meier survival analysis and a Cox regression model were used to analyze the correlation of lncRNA 604 and its regulatory molecules with the prognosis of and chemotherapy efficacy in CRC patients.

Results

In this study, we found that the expression levels of lncRNA 604 were increased in CRC. LncRNA 604 could promote CRC cell proliferation and metastasis through the miRNA 564/AEG-1 or ZNF326/EMT signaling axis in vivo and in vitro. LncRNA 604 could predict the prognosis of CRC and was an independent negative factor. LncRNA 604 exerted a synergistic effect with miRNA 564 or ZNF326 on the prognosis of CRC. LncRNA 604 could improve chemoresistance by increasing the expression of AEG-1, NF-κB, and ERCC1.

Conclusions

Our study demonstrated that lncRNA 604 could promote the progression of CRC via the lncRNA 604/miRNA 564/AEG-1/EMT or lncRNA 604/ZNF326/EMT signaling axis. LncRNA 604 could improve chemoresistance by increasing drug resistance protein expression.

FOXP4-AS1 May be a Potential Prognostic Biomarker in Human Cancers: A Meta-Analysis and Bioinformatics Analysis

Background

Cancer is one of the leading causes of death worldwide. Early diagnosis can significantly lower cancer-related mortality. Studies have shown that the lncRNA Forkhead box P4 antisense RNA 1 (FOXP4-AS1) is aberrantly expressed in various solid tumors. A meta-analysis was performed to evaluate the correlation of FOXP4-AS1 with the prognosis of cancer patients and determine the clinical value of FOXP4-AS1 as a potential diagnostic marker.

Methods

Correlational studies from the Web of Science, Embase, OVID, Cochrane and PubMed databases were screened (up to April 1, 2021). Meta-analysis was performed using Stata SE12.0 software.

Results

Eleven original studies with 1,332 patients who were diagnosed with a solid cancer (nasopharyngeal carcinoma, hepatocellular carcinoma, colorectal cancer, gastric cancer, osteosarcoma, mantle cell lymphoma, prostate cancer, and pancreatic ductal adenocarcinoma) were included in the meta-analysis. High expression of FOXP4-AS1 was correlated with poor overall survival (OS) (HR = 1.77, 95% CI 1.29-2.44, P < 0.001) and shorter disease-free survival (DFS) (HR = 1.66, 95% CI 1.01-2.72, P = 0.044). Subgroup analysis based on sample size, follow-up time and Newcastle-Ottawa Scale (NOS) score revealed significant differences between FOXP4-AS1 levels and OS (P < 0.05). However, the expression level of FOXP4-AS1 was not significantly correlated with the OS of gastric cancer patients (P = 0.381). High expression of FOXP4-AS1 was predictive of a larger tumor size (OR = 3.82, 95% CI 2.3-6.3, P < 0.001).

Conclusions

Overexpression of FOXP4-AS1 correlates with poor prognosis of cancer patients, and is a potential prognostic biomarker and therapeutic target.

Systematic Review Registration

PROSPERO, identifier CRD42021245267.

Long non-coding RNA DDX11-AS1 promotes the proliferation and migration of glioma cells by combining with HNRNPC

Glioma is a malignant tumor of the central nervous system with complex pathogenesis, difficult operation, and a high postoperative recurrence rate. At present, there is still a lack of effective treatment. Long non-coding RNA DDX11 antisense RNA 1 (DDX11-AS1) has been shown to promote tumor development, such as hepatocellular carcinoma, esophageal cancer, etc. However, its molecular mechanism in glioma is poorly understood. In this study, we found that the expression of DDX11-AS1 was elevated in glioma tissues, and patients with high expression of DDX11-AS1 had poor prognosis. DDX11-AS1 was a potential prognostic marker. Functionally, DDX11-AS1 promoted glioma cell proliferation and migration. Mechanistically, DDX11-AS1 interacted with RNA-binding protein heterogeneous nuclear ribonucleoprotein C (HNRNPC) to promote Wnt/β-catenin and AKT pathways and the epithelial-mesenchymal transition process. In summary, our study manifests that the DDX11-AS1/HNRNPC axis may play a vital part in the occurrence and development of glioma, which provides new ideas and therapeutic targets for the diagnosis, treatment, and prognosis of glioma.

LncRNA MNX1-AS1: A novel oncogenic propellant in cancers

To date, recent studies have shown that long non-coding RNAs (lncRNAs) are key players in gene regulation processes involved in cancer pathogenesis. In general, Motor neuron and pancreas homeobox 1-antisense RNA1 (MNX1-AS1) is highly expressed in all cancers as reported so far and exerts oncogenic effects through different mechanisms. In this review, we comprehensively summarize the detailed mechanisms of potential functions of MNX1-AS1 in different cancer types as well as the latest knowledge highlighting the potential of MNX1-AS1 as a therapeutic target for cancer. Aberrant expression of MNX1-AS1 closely correlates with clinicopathological parameters. such as lymphatic metastasis, tumor size, tumor stage, OS and DFS. Thus, MNX1-AS1 can be used as a diagnostic and prognostic biomarker or even a therapeutic prognostic target. This article reviews its function, molecular mechanism and clinical prognosis in various malignancies.

Noncoding RNAs and their therapeutics in paclitaxel chemotherapy: Mechanisms of initiation, progression, and drug sensitivity

The identification of agents that can reverse drug resistance in cancer chemotherapy, and enhance the overall efficacy is of great interest. Paclitaxel (PTX) belongs to taxane family that exerts an antitumor effect by stabilizing microtubules and inhibiting cell cycle progression. However, PTX resistance often develops in tumors due to the overexpression of drug transporters and tumor-promoting pathways. Noncoding RNAs (ncRNAs) are modulators of many processes in cancer cells, such as apoptosis, migration, differentiation, and angiogenesis. In the present study, we summarize the effects of ncRNAs on PTX chemotherapy. MicroRNAs (miRNAs) can have opposite effects on PTX resistance (stimulation or inhibition) via influencing YES1, SK2, MRP1, and STAT3. Moreover, miRNAs modulate the growth and migration rates of tumor cells in regulating PTX efficacy. PIWI-interacting RNAs, small interfering RNAs, and short-hairpin RNAs are other members of ncRNAs regulating PTX sensitivity of cancer cells. Long noncoding RNAs (LncRNAs) are similar to miRNAs and can modulate PTX resistance/sensitivity by their influence on miRNAs and drug efflux transport. The cytotoxicity of PTX against tumor cells can also be affected by circular RNAs (circRNAs) and limitation is that oncogenic circRNAs have been emphasized and experiments should also focus on onco-suppressor circRNAs.

LncRNA GATA2-AS1 suppresses esophageal squamous cell carcinoma progression via the mir-940/PTPN12 axis

Esophageal squamous cell carcinoma (ESCC) is a common malignant tumor worldwide. Long noncoding RNAs (lncRNAs) exhibit a regulatory role in the progression of ESCC. Our research was performed to investigate the potential molecular mechanism of lncRNA GATA2-AS1 in ESCC.

METHODS

The expression of GATA2-AS1 was identified by qRT-PCR. Cell function assays explored the potential effect of GATA2-AS1 on ESCC progression. The subcellular hierarchical localization method was executed to identify the subcellular localization of GATA2-AS1 in ESCC cells. A prediction website was utilized to discover the relationships among GATA2-AS1, miR-940 and PTPN12. Dual luciferase reporter gene, pull-down assays and RIP assays were executed to verify the binding activity among GATA2-AS1, miR-940 and PTPN12. Xenograft tumor experiments were performed to evaluate ESCC cell growth in vivo.

RESULTS

The expression of GATA2-AS1 and PTPN12 was reduced, while miR-940 expression was enhanced in ESCC tissues and cell lines. In vivo experiments showed that GATA2-AS1 inhibited the progression of ESCC cells toward malignancy. Bioinformatics analysis, dual luciferase and RIP assays revealed that GATA2-AS1 upregulated PTPN12 expression by competitively targeting miR-940. miR-940 reversed the inhibitory effect of GATA2-AS1 on the biological behavior of ESCC cells.

CONCLUSION

Our findings suggested that GATA2-AS1, expressed at low levels in ESCC, plays a crucial role in the progression of ESCC by targeting the miR-940/PTPN12 axis and could be a potential drug target to treat ESCC patients.

Clinicopathological and prognostic significance of long non-coding RNA EWSAT1 in human cancers: A review and meta analysis

Background

Ewing sarcoma-associated transcript 1 (lncRNA EWSAT1) is reported to have a close relationship with the overall survival in many cancers. However, the role of its prognosis and correlations with the clinicopathological features in different cancers haven’t been explored yet. Herein, we intend to assess the prognostic value and correlations with the clinicopathological features in several cancers.

Methods

PubMed, Embase, Web of Science, and The Cochrane Library were searched for literature review from inception to October 25, 2021. Valid data was extracted to make forest and sensitivity analysis plots using Review Manager 5.4 and Stata software. Hazard ratio (HR) or odds ratio (OR) with 95% confidence interval (CI) was used to evaluate the relationship between different expression of EWSAT1 and patients’ prognosis and clinicopathological features.

Results

7 studies were screened for this review, including 550 samples. Meta-analysis showed that high expression of lncRNA EWSAT1 was associated with poor overall survival (OS) (HR = 2.10, 95% CI, 1.60–2.75, p < 0.0001) in cancers reported. In addition, patients in high expression group of EWAST1 tended to have more metastasis (OR = 2.20, 95% CI 1.47–3.31, p = 0.0001), and higher TNM stage (I+II vs. III: OR = 0.34, 95% CI 0.21–0.56, p < 0.0001), but in the same time with higher differentiation (well + moderate vs. Poor: OR = 2.21, 95% CI 1.02–4.76, p = 0.04). Age (OR = 1.47, 95% CI 0.94–2.30, p = 0.09) was not significantly different in patients with aberrant expression of EWSAT1.

Conclusions

Our study shows that high expression of EWSAT1 may indicate poor overall survival and associated with several clinicopathological features, which can be used as a potential prognosis biomarker for multiple cancers.

Gliomas with Downregulation of lncRNA SLC25A21-AS1 Carry a Dismal Prognosis and an Accelerated Progression in Cell Proliferation, Migration and Invasion

Glioma is one type of primary intracranial carcinoma with a relatively poor prognosis. We investigated the level of SLC25A21-AS1 in gliomas and the association with survival and progression in patients with glioma. Specimens of gliomas from patients were assessed by quantitative real-time polymerase chain reaction analysis of the SLC25A21-AS1 level (117 specimens). For prognostic value assessment, χ² test, Kaplan-Meier method with the log-rank test, and Multivariate survival analysis were performed. The direct targets for SLC25A21-AS1 were explored. The biological roles of SLC25A21-AS1 were investigated by manipulating the expression level of SLC25A21-AS1 in glioma cells. SLC25A21-AS1 was significantly downregulated in glioma specimens and cell lines compared to non-cancerous ones. Significant associations were found between SLC25A21-AS1 downregulation and WHO stage, IDH status, poor disease-free survival/overall survival. miR-221-3p/miR-222-3p were the target miRNAs for SLC25A21-AS1. Overexpression of SLC25A21-AS1 inhibited glioma cell growth, invasion, and migration while miR-221-3p/miR-222-3p-overexpressed groups could offset this effect. Downregulation of SLC25A21-AS1 in gliomas carries a universally poor prognosis. Overexpression of SLC25A21-AS1 inhibited glioma progression via miR-221-3p/miR-222-3p.

lncRNA ACTA2-AS1 inhibits malignant phenotypes of gastric cancer cells

Gastric cancer (GC) is one of the most common malignancies in digestive system. Accumulating evidence reveals the critical role of long noncoding RNAs (lncRNAs) in GC development. The study aimed to explore the functions and mechanism of lncRNA actin alpha 2, smooth muscle antisense RNA 1 (ACTA2-AS1) in GC. Reverse transcription-quantitative polymerase chain reaction analyses and subcellular fractionation assays showed that ACTA2-AS1 was lowly expressed in GC cells and was mainly distributed in the cytoplasm. Overexpressed ACTA2-AS1 inhibited GC cell viability, proliferation, migration, invasion, and epithelial-mesenchymal transition process, as suggested by cell counting kit-8 assays, colony formation assays, wound healing assays, Transwell assays and Western blot analyses. Mechanistically, ACTA2-AS1 served as a competing endogenous RNA (ceRNA) to bind with miR-378a-3p and thereby, antagonized the inhibitory effect of miR-378a-3p on the expression of messenger RNA phosphatidylinositol specific phospholipase C X domain containing 2 (PLCXD2). The binding capacity between miR-378a-3p and ACTA2-AS1 (or PLCXD2) was detected by RNA pulldown assays, luciferase reporter assays and RNA immunoprecipitation assays. Moreover, PLCXD2 knockdown rescued the inhibitory effect of ACTA2-AS1 overexpression on malignant behaviors of GC cells. Overall, ACTA2-AS1 inhibits malignant phenotypes of GC cells by acting as a ceRNA to target miR-378a-3p/PLCXD2 axis.

Silencing long non-coding RNA LINC00960 inhibits osteosarcoma proliferation by sponging miR-107 to downregulate SALL4

long non-coding RNAs (lncRNAs), as tumor suppressors or oncogenes, have been identified to play key roles in tumorigenesis. The present study explored the roles and potential mechanisms of LINC00960 in osteosarcoma (OS). In vitro study showed that silencing LINC00960 inhibited proliferation, migration and invasion of 143B and MG63. In vivo study demonstrated that knockdown of LINC00960 repressed tumor growth. Further investigation revealed that LINC00960 could regulate SALL4 by sponging miR-107 to promote the progression of OS. Together, LINC00960 is a tumor oncogene in the development and prognosis of OS, which may be a new therapeutic target for OS.

Knockdown of lncRNA AL928768.3 inhibits multiple myeloma cell proliferation by inducing cell cycle arrest in G0/G1 phase

Background

Multiple myeloma (MM) is a B-lymphocyte-derived malignancy. It ranks as the second most common hematological malignancy, with relatively high morbidity and mortality. However, the molecular mechanisms of MM occurrence and development remain elusive. This study found that long non-coding RNA AL928768.3 (lncRNA AL) was abnormally expressed in MM samples. However, the effect and molecular mechanism of lncRNA AL on the occurrence and development of MM remains unclear.

Methods

Bone marrow fluids of MM patients (n=54) and volunteers (n=13) were collected and CD138⁺ cells were isolated. The expression level of lncRNA AL in MM cells was detected by quantitative real-time polymerase chain reaction (qRT-PCR), and the correlation between the expression level of lncRNA AL and the clinicopathological features of patients was analyzed. Lentiviral vectors targeting lncRNA AL knockdown were constructed and transfected into cells. After transfection, the effects of lncRNA AL knockdown on MM cell proliferation and the cell cycle were detected by the CCK-8 assay, clone formation assay, and flow cytometry. The effect of lncRNA AL knockdown on MM cell cycle-related proteins was detected by Western blot. In addition, tumorigenicity experiments were performed in nude mice to detect the effect of lncRNA AL knockdown on MM cell proliferation in vivo.

Results

LncRNA AL was highly expressed in MM patient samples and cell lines, and was significantly correlated with the disease stage of patients. Knockdown of lncRNA AL significantly inhibited the proliferation and colony formation of MM cells and induced cell cycle arrest in G0/G1 phase. Western blot analysis showed that knockdown of lncRNA AL significantly inhibited the expression of CDK2 and cyclin D1 and promoted the expression of cyclin suppressor p21. Knockdown of lncRNA AL significantly inhibited the proliferation of MM cells in nude mice.

Conclusions

LncRNA AL was highly expressed in MM patients. Knockdown of this gene significantly inhibited the proliferative ability of MM cells and induced cell cycle arrest in G0/G1 phase. Therefore, lncRNA AL may be a novel biological target molecule for the early diagnosis, treatment, and prognostic evaluation of MM patients.

Clinical Potential of lncRNA PPP1R26-AS1 in Breast Cancer and Its Contribution to Cancer Progression

Breast cancer has become the most leading diagnosed tumor worldwide in 2020. In this study, the biomarker potential and influence on the cellular function of lncRNA PPP1R26-AS1 was investigated in breast cancer. Expression levels of lncRNA PPP1R26-AS1 in breast tissues and cells were detected by RT-qPCR. Association between lncRNA PPP1R26-AS1 level and clinical parameters was investigated by Chi-square analysis. The prognostic potential was assessed by Kaplan-Meier and multivariate Cox regression analysis. Knockdown of lncRNA PPP1R26-AS1 was subjected to study the effect on cell proliferation, invasion, and migration by CCK-8 and transwell assay. The bind between PPP1R26-AS1 and miR-1226-3p was investigated. LncRNA PPP1R26-AS1 was highly expressed in breast tissues and cell lines. This upregulation was correlated with pTNM, positive ER status, luminal B subtype, positive nodal status, and shorter overall survival in breast cancer patients. Significant decreases in proliferation, migration, and invasion activity were observed upon knockdown of lncRNA PPP1R26-AS1. lncRNA PPP1R26-AS1 could act as ceRNA to bind with miR-1226-3p in breast cancer. LncRNA PPP1R26-AS1, as oncogenic lncRNA, could provide a new perspective on the development of prognostic biomarkers and a new approach in tailoring the treatment personalized in breast cancer.

Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs

Glioblastoma is the most common brain cancer in adults. Nevertheless, the median survival time is 15 months, if treated with at least a near total resection and followed by radiotherapy in association with temozolomide. In glioblastoma (GBM), variations of non-coding ribonucleic acid (ncRNA) expression have been demonstrated in tumor processes, especially in the regulation of major signaling pathways. Moreover, many ncRNAs present in their sequences an Open Reading Frame (ORF) allowing their translations into proteins, so-called alternative proteins (AltProt) and constituting the “ghost proteome.” This neglected world in GBM has been shown to be implicated in protein–protein interaction (PPI) with reference proteins (RefProt) reflecting involvement in signaling pathways linked to cellular mobility and transfer RNA regulation. More recently, clinical studies have revealed that AltProt is also involved in the patient’s survival and bad prognosis. We thus propose to review the ncRNAs involved in GBM and highlight their function in the disease.

An lncRNA Model for Predicting the Prognosis of Hepatocellular Carcinoma Patients and ceRNA Mechanism

Liver cancer is a highly malignant tumor. Notably, recent studies have found that long non-coding RNAs (lncRNAs) play a prominent role in the prognosis of patients with liver cancer. Herein, we attempted to construct an lncRNA model to accurately predict the survival rate in liver cancer. Based on The Cancer Genome Atlas (TCGA) database, we first identified 1066 lncRNAs with differential expression. The patient data obtained from TCGA were divided into the experimental group and the verification group. According to the difference in lncRNAs, we used single-factor and multi-factor Cox regression to select the genes needed to build the model in the experimental group, which were verified in the verification group. The results showed that the model could accurately predict the survival rate of patients in the high and low risk groups. The reliability of the model was also confirmed by the area under the receiver operating characteristic curve. Our model is significantly correlated with different clinicopathological features. Finally, we built a ceRNA network based on lncRNAs, which was used to display miRNAs and mRNAs related to lncRNAs. In summary, we constructed an lncRNA model to predict the survival rate of patients with hepatocellular carcinoma.

LINC00265 promotes the viability, proliferation, and migration of bladder cancer cells via the miR-4677-3p/FGF6 axis

BACKGROUND

Bladder cancer (BCa) is a common genitourinary malignancy with higher incidence in males. Long intergenic non-protein coding RNA 265 (LINC00265) is identified as an oncogene in many malignancies, while its role in BCa development remains unknown.

PURPOSE

To explore the functions and mechanism of LINC00265 in BCa.

RESEARCH DESIGN

Reverse transcription quantitative polymerase chain reaction was performed to examine LINC00265 expression in BCa cells. Cell counting kit-8 assays, colony formation assays, TdT-mediated dUTP Nick-End Labeling assays, and Transwell assays were conducted to examine BCa cell viability, proliferation, apoptosis, and migration. Luciferase reporter assays and RNA immunoprecipitation assays were carried out to explore the binding capacity between miR-4677-3p and messenger RNA fibroblast growth factor 6 (FGF6) (or LINC00265). Xenograft tumor model was established to explore the role of LINC00265 in vivo.

RESULTS

LINC00265 was highly expressed in BCa cells. LINC00265 knockdown inhibited xenograft tumor growth and BCa cell viability, proliferation and migration while enhancing cell apoptosis. Moreover, LINC00265 interacted with miR-4677-3p to upregulate the expression of FGF6. FGF6 overexpression reversed the suppressive effect of LINC00265 knockdown on malignant phenotypes of BCa cells.

CONCLUSIONS

LINC00265 promotes the viability, proliferation, and migration of BCa cells by binding with miR-4677-3p to upregulate FGF6 expression.

The Role of lncRNA PCAT6 in Cancers

Long non-coding RNA (lncRNA) PCAT6 is a member of the Prostate Cancer Associated Transcripts family of molecules. In this review, we focus on the latest studies involving PCAT6 in the diagnosis, treatment, and prognosis of malignant tumors of the digestive, respiratory, urinary, reproductive, motion, and nervous systems. PCAT6 was found to be highly expressed in gastric cancer, colon cancer, hepatocellular carcinoma, lung cancer, bladder cancer, ovarian cancer, breast cancer, cervical cancer, osteosarcoma, glioblastoma, and other tumors. PCAT6 can promote the development and progression of different types of malignant tumors through various mechanisms. Overall, these findings suggest that PCAT6 may play an increasingly vital role in the clinical assessment of these malignant tumors. It can function as an oncogene and may be used as a potential new prognostic biomarker of these tumors.

LINC00908 Promotes Diffuse Large B-Cell Lymphoma Development by Down-Regulating miR-671-5p

Introduction

Emerging evidence has revealed that long noncoding RNA (lncRNA) play important role in almost all kinds of human cancers. LINC00908 has been reported to be involved in the development of prostate cancer, colorectal cancer and gastric cancer which was functioned as an oncogene. However, the potential biology role and molecular mechanism of LINC00908 in diffuse large B-cell lymphoma are still unclear.

Methods

LINC00908 and miR-671-5p expression were evaluated in DLBCL tissues and cell lines using RT-qPCR. CCK-8 and transwell assay were used to analyze the in vitro role of LINC00908 in DLBCL progression. The xenograft model was used to explore the in vivo role of LINC00908 in DLBCL growth. The physical interaction between LINC00908 and miR-671-5p was confirmed using bioinformatics analysis and a dual luciferase assay, RIP and RNA pull down.

Results

The expression of LINC00908 was markedly up-regulated in diffuse large B-cell lymphoma tissues and cell lines, and the decreased expression of LINC00908 significantly inhibited diffuse large B-cell lymphoma cell proliferation and invasion. Then, we revealed that LINC00908 directly interacted with miR-671-5p, which was down-regulated in diffuse large B-cell lymphoma cells and highly expressed with LINC00908 knockdown. Moreover, luciferase reporter assays and RNA immunoprecipitation (RIP) assay further proved that miR-671-5p is a direct target of LINC00908 in diffuse large B-cell lymphoma cells. Rescue experiments were also performed, and we confirmed that LINC00908 acts as an oncogene role in diffuse large B-cell lymphoma through miR-671-5p. Finally, the influence of LINC00908 silence significantly inhibited diffuse large B-cell lymphoma growth in vivo.

Conclusion

LINC00908 promotes malignancy of diffuse large B-cell lymphoma through regulating miR-671-5p.

The Genome Stability Maintenance DNA Helicase DDX11 and Its Role in Cancer

DDX11/ChlR1 is a super-family two iron–sulfur cluster containing DNA helicase with roles in DNA replication and sister chromatid cohesion establishment, and general chromosome architecture. Bi-allelic mutations of the DDX11 gene cause a rare hereditary disease, named Warsaw breakage syndrome, characterized by a complex spectrum of clinical manifestations (pre- and post-natal growth defects, microcephaly, intellectual disability, heart anomalies and sister chromatid cohesion loss at cellular level) in accordance with the multifaceted, not yet fully understood, physiological functions of this DNA helicase. In the last few years, a possible role of DDX11 in the onset and progression of many cancers is emerging. Herein we summarize the results of recent studies, carried out either in tumoral cell lines or in xenograft cancer mouse models, suggesting that DDX11 may have an oncogenic role. The potential of DDX11 DNA helicase as a pharmacological target for novel anti-cancer therapeutic interventions, as inferred from these latest developments, is also discussed.

Identification novel prognostic signatures for Head and Neck Squamous Cell Carcinoma based on ceRNA network construction and immune infiltration analysis

Background: Head and neck squamous cell carcinoma (HNSCC) is a common malignancy with high mortality and morbidity worldwide, but the underlying biological mechanisms of molecules and tumor infiltrating-immune cells (TIICs) are still unknown. Methods and Results: We obtained mRNAs, lncRNAs, and miRNAs expression profiles of 546 HNSCC from The Cancer Genome Atlas (TCGA) database to develop a ceRNA network. CIBERSORT was employed to estimate the fraction of 22 types of TIICs in HNSCC. Univariate and multivariate Cox regression and lasso regression analyses were used to develop prognostic signatures. Then, two novel risk signatures were constructed respectively based on six ceRNAs (ANLN, KIT, PRKAA2, NFIA, PTX3 and has-miR-148a-3p) and three immune cells (naïve B cells, regulatory T cells and Neutrophils). Kaplan-Meier (K-M) analysis and Cox regression analysis further proved that these two signatures were significant prognostic factors independent of multiple clinicopathological characteristics. Two nomograms were built based on ceRNAs-riskScore and TIICs-riskScore that could be used to predict the prognosis of HNSCC. Co-expression analysis showed significant correlations between miR-148a-3p and naive B cells, naive B cells and plasmas cells. Conclusion: Through construction of the ceRNA network and estimation of TIICs, we established two risk signatures and their nomograms with excellent utility, which indicated the potential molecular and cellular mechanisms, and predicted the prognosis of HNSCC.

A novel three-long noncoding RNA risk score system for the prognostic prediction of triple-negative breast cancer

Background: Triple-negative breast cancer (TNBC) is characterized by fast tumor increase, rapid recurrence and natural metastasis. We aimed to identify a genetic signature for predicting the prognosis of TNBC. Materials & methods: We conducted a weighted correlation network analysis of datasets from the Gene Expression Omnibus. Multivariate Cox regression was used to construct a risk score model. Results: The multi-factor risk scoring model was meaningfully associated with the prognosis of patients with TBNC. The predictive power of the model was demonstrated by the time-dependent receiver operating characteristic curve and Kaplan-Meier curve, and verified using a validation set. Conclusion: We established a long noncoding RNA-based model for the prognostic prediction of TNBC.