Identification of long non-coding RNA 00312 and 00673 in human NSCLC tissues

A Signature of 14 Long Non-Coding RNAs (lncRNAs) as a Step towards Precision Diagnosis for NSCLC

LncRNAs have arisen as new players in the world of non-coding RNA. Disrupted expression of these molecules can be tightly linked to the onset, promotion and progression of cancer. The present study estimated the usefulness of 14 lncRNAs (HAGLR, ADAMTS9-AS2, LINC00261, MCM3AP-AS1, TP53TG1, C14orf132, LINC00968, LINC00312, TP73-AS1, LOC344887, LINC00673, SOX2-OT, AFAP1-AS1, LOC730101) for early detection of non-small-cell lung cancer (NSCLC). The total RNA was isolated from paired fresh-frozen cancerous and noncancerous lung tissue from 92 NSCLC patients diagnosed with either adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC). The expression level of lncRNAs was evaluated by a quantitative real-time PCR (qPCR). Based on Ct and delta Ct values, logistic regression and gradient boosting decision tree classifiers were built. The latter is a novel, advanced machine learning algorithm with great potential in medical science. The established predictive models showed that a set of 14 lncRNAs accurately discriminates cancerous from noncancerous lung tissues (AUC value of 0.98 ± 0.01) and NSCLC subtypes (AUC value of 0.84 ± 0.09), although the expression of a few molecules was statistically insignificant (SOX2-OT, AFAP1-AS1 and LOC730101 for tumor vs. normal tissue; and TP53TG1, C14orf132, LINC00968 and LOC730101 for LUAD vs. LUSC). However for subtypes discrimination, the simplified logistic regression model based on the four variables (delta Ct AFAP1-AS1, Ct SOX2-OT, Ct LINC00261, and delta Ct LINC00673) had even stronger diagnostic potential than the original one (AUC value of 0.88 ± 0.07). Our results demonstrate that the 14 lncRNA signature can be an auxiliary tool to endorse and complement the histological diagnosis of non-small-cell lung cancer.

The Prognostic Value of LncRNA SLNCR1 in Cancers: A Meta-Analysis

Objective

This meta-analysis was performed to identify the prognostic value of SLNCR1 in multiple cancer types.

Methods

Electronic databases, including PubMed, EMBASE, and Web of Science, Cochrane Library, Medline, BioMed Central, Springer, Science Direct, and China National Knowledge Internet (CNKI), were searched for relevant studies up to August 2021, and the hazard ratios (HR) and 95% confidence intervals (95% CI) were calculated to assess the relationship between SLNCR1 expression and overall survival (OS).

Results

12 studies with a total of 1155 patients with 9 different types of cancers were included in this meta-analysis. The pooled HR indicates that high SLNCR1 expression represented poorer prognosis of cancer (HR = 2.11, 95% CI: 1.59–2.80, I² = 0%, P < 0.00001). Additionally, high SLNCR1 expression was correlated with TNM stage (odds ratio (OR): 1.72, 95% CI: 1.08–2.74, I² = 62%, P=0.02), lymph node metastasis (LNM) (OR:2.42, 95% CI: 1.61–3.64, I² = 55%, P < 0.0001), and distant metastases (DM) (OR: 2.30, 95% CI: 1.50–3.55, I² = 27%, P=0.0002). However, no evidence was found for a relationship between SLNCR1 expression and clinical features such as tumor size (OR: 1.71, 95% CI: 0.93–3.14, I² = 71%, P=0.09), age (OR: 0.86, 95% CI: 0.68–1.08, I² = 0%, P=0.19), or gender (OR: 1.07, 95% CI: 0.64–1.81, I² = 55%, P=0.79).

Conclusion

Our findings found that high SLNCR1 expression was associated with poor OS, advanced tumor stage, tumor size, LNM, and DM in multiple cancers, indicating that SLNCR1 may serve as a potential prognostic biomarker for cancer patients in China.

Differential expression of long non-coding RNAs as diagnostic markers for lung cancer and other malignant tumors

Due to advances in chip and sequencing technology, several types and numbers of long non-coding RNAs (lncRNAs) have been identified. LncRNAs are defined as non-protein-coding RNA molecules longer than 200 nucleotides, and are now thought as a new frontier in the study of human malignant diseases including NSCLC. Diagnosis of numerous malignant tumors has been closely linked to the differential expression of certain lncRNAs. LncRNAs are involved in gene expression regulation at multiple levels of epigenetics, transcriptional regulation, and post-transcriptional regulation. Mutations, deletions, or abnormal expression levels lead to physiological abnormalities, disease occurrence and are closely associated with human tumor diseases. LncRNAs play a crucial role in cancerous processes as either oncogenes or tumor suppressor genes. The expression of lncRNAs can regulate tumor cell in the proliferation, migration, apoptosis, cycle, invasion, and metastasis. As such, lncRNAs are potential diagnostic and treatment targets for cancer. And that, tumor biomarkers need to be detectable in easily accessible body samples, should be characterized by high specificity and sufficient sensitivity. Herein, it is significant clinical importance to screen and supplement new biomarkers for early diagnosis of lung cancer. This study aimed at systematically describing lncRNAs from five aspects based on recent studies: concepts, classification, structure, molecular mechanism, signal pathway, as well as review lncRNA implications in malignant tumor.

Clinicopathological and Prognostic Significance of LINC00673 in Human Malignancy: A Review and Meta-analysis

BACKGROUND

We conducted this research to investigate the relationship between linc00673 expression and prognosis and clinicopathological parameters in human malignancies.

METHODS

The PubMed, Embase, WOS and CNKI databases were used to collect eligible research data before January 4, 2021. Meta-analysis was performed using Stata 12.0 software. Pooled ORs (odds ratios) or HRs (hazard ratios) and their 95% CIs were calculated to evaluate the association of linc00673 expression with survival outcomes and clinical parameters.

RESULTS

We finally included 17 articles and a total of 1539 cases for the meta-analysis. The results indicated that linc00673 was significantly correlated with T stage (P=0.006), tumour stage (P<0.001), lymph node metastasis (P<0.001), and distant metastasis ( P<0.001). In addition, the results suggested that elevated linc00673 expression predicted a poor overall survival time (P=0.034) and acted as an independent prognostic factor (P<0.001) for OS in patients with malignancy. Although potential evidence of publication bias was found in the studies on OS in relation to tumour stage in the multivariate analysis, the trim-and-fill analysis confirmed that the results remained stable.

CONCLUSION

Overexpression of linc00673 was significantly correlated with shorter OS time in patients with malignant tumours. Moreover, the increased expression level of linc00673 was significantly correlated with T stage, tumour stage, lymph node metastasis, and distant metastasis. The results presented in this article revealed that linc00673 might be involved in the progression and invasion of malignancy and serve as a novel prognostic biomarker and potential therapeutic target for malignancy.

A review of linc00673 as a novel lncRNA for tumor regulation

Long non-coding RNAs (LncRNAs) act as regulators and play important roles in a variety of biological processes. These regulators constitute a huge information network among genes and participate in the pathophysiological process of human diseases. Increasing evidence has demonstrated that LncRNA, as an oncogene or tumor suppressor gene, is closely related to the occurrence and development of tumors. Linc00673 is a recently discovered LncRNA molecule that is dysregulated in several solid tumors. Moreover, its genetic polymorphism is believed to affect the susceptibility of a population to the corresponding cancer species. This article summarizes the role of Linc00673 in different human cancers and its molecular mechanisms with a focus on the characteristics of Linc00673 and the existing literature on it while highlighting the future research directions for Linc00673. Linc00673 has the potential to become a feasible clinical diagnostic and prognostic marker toward providing a new molecular therapeutic target for cancer patients.

Identification of lncRNA biomarkers for lung cancer through integrative cross-platform data analyses

This study was designed to identify lncRNA biomarker candidates using lung cancer data from RNA-Seq and microarray platforms separately.

Lung cancer datasets were obtained from the Gene Expression Omnibus (GEO, n = 287) and The Cancer Genome Atlas (TCGA, n = 216) repositories, only common lncRNAs were used. Differentially expressed (DE) lncRNAs in tumors with respect to normal were selected from the Affymetrix and TCGA datasets. A training model consisting of the top 20 DE Affymetrix lncRNAs was used for validation in the TCGA and Agilent datasets. A second similar training model was generated using the TCGA dataset.

First, a model using the top 20 DE lncRNAs from Affymetrix for training and validated using TCGA and Agilent, achieved high prediction accuracy for both training (98.5% AUC for Affymetrix) and validation (99.2% AUC for TCGA and 92.8% AUC for Agilent). A similar model using the top 20 DE lncRNAs from TCGA for training and validated using Affymetrix and Agilent, also achieved high prediction accuracy for both training (97.7% AUC for TCGA) and validation (96.5% AUC for Affymetrix and 80.9% AUC for Agilent). Eight lncRNAs were found to be overlapped from these two lists.

Association of LINC00673 rs11655237 polymorphism with cancer susceptibility: A meta-analysis based on 23,478 subjects

BACKGROUND

Some studies on the relationship between LINC00673 polymorphism and cancer susceptibility have been inconsistent. To perform a more comprehensively quantitative assessment of LINC00673 rs11655237 and risk of overall cancer, we operated this meta-analysis for the first time.

METHODS

A comprehensive search was conducted to obtain relevant literature up to November 20, 2019. Pooled odds ratios and 95% confidence intervals were utilized to assess rs11655237 and cancer susceptibility under five different genetic models.

RESULTS

Eventually, 11 case-control studies from 9 articles were included. We found that LINC00673 rs11655237 polymorphism increased the susceptibility to overall cancer under all genetic models in the overall population. By dividing ethnicity and cancer type into subgroups, we also obtained similar positive results in subgroups of Chinese population, pancreatic cancer, cervical cancer, neuroblastoma, hepatoblastoma and gastric cancer.

CONCLUSION

Overall, this meta-analysis has demonstrated for the first time that LINC00673 rs11655237 could increase susceptibility to cancer.

RBFOX1 Regulates the Permeability of the Blood-Tumor Barrier via the LINC00673/MAFF Pathway

The blood-tumor barrier limits the delivery of therapeutic drugs to brain tumor tissues. Selectively opening the blood-tumor barrier is considered crucial for effective chemotherapy of glioma. RNA-binding proteins have emerged as crucial regulators in various biologic processes. This study found that RNA-binding Fox-1 homolog 1 (RBFOX1) was downregulated in glioma vascular endothelial cells derived from glioma tissues, and in glioma endothelial cells obtained by co-culturing endothelial cells with glioma cells. Overexpression of RBFOX1 impaired the integrity of the blood-tumor barrier and increased its permeability. Additionally, RBFOX1 overexpression decreased the expression of tight junction proteins ZO-1, occludin, and claudin-5. Subsequent analysis of the mechanism indicated that the overexpression of RBFOX1 increased musculoaponeurotic fibrosarcoma protein basic leucine zipper [bZIP] transcription factor F (MAFF) expression by downregulating LINC00673, which stabilized MAFF messenger RNA (mRNA) through Staufen1-mediated mRNA decay. Moreover, MAFF could bind to the promoter region and inhibit the promoter activities of ZO-1, occludin, and claudin-5, which reduced its expression. The combination of RBFOX1 upregulation and LINC00673 downregulation promoted doxorubicin delivery across the blood-tumor barrier, resulting in apoptosis of glioma cells. In conclusion, this study indicated that overexpression of RBFOX1 increased blood-tumor barrier permeability through the LINC00673/MAFF pathway, which might provide a new useful target for future enhancement of blood-tumor barrier permeability.

Long non‑coding RNA LINC00312 regulates breast cancer progression through the miR‑9/CDH1 axis

Long non‑coding RNAs (lncRNAs) are important mediators of the initiation and progression of tumors, including breast cancer (BC). The exact role of long intergenic non‑coding RNA 00312 (LINC00312) in BC and its mechanism of action have not been reported to date. In the present study, LINC00312 was found to be downregulated in human BC tissues and cell lines by RT‑qPCR. The findings of a functional study indicated that overexpression of LINC00312 suppressed the proliferation, colony forming ability, migration and invasiveness of BC cell lines. Mechanistically, LINC00312 was found to induce suppression of cell migration and invasion by directly binding to miR‑9. Overexpression of LINC00312 increased the expression of cadherin 1 (CDH1), a direct target of miR‑9, and decreased the expression of vimentin (VIM), a major cytoskeletal component of mesenchymal cells as determined by western blot analysis. miR‑9 partly abrogated the upregulation of CDH1 and downregulation of VIM induced by LINC00312. Taken together, the results of the present study indicate a role for the LINC00312/miR‑9/CDH1 axis in the progression of BC, and suggest a novel lncRNA‑based diagnostic biomarker or therapeutic target for BC.

Long non-coding RNA in lung cancer

Lung cancer is the leading cause of cancer-related death worldwide. Owing to the difficulty in early diagnosis and the lack of effective treatment strategies, the 5-year survival rates for lung cancer remain very low. With the development of whole genome and transcriptome sequencing technology, long non-coding RNA (lncRNA) has attracted increasing attention. LncRNAs regulate gene expression at the epigenetic, transcriptional and post-transcriptional levels and are widely involved in a variety of diseases, including tumorigenesis. In lung cancer studies, multiple differentially expressed lncRNAs have been identified; several lncRNAs were identified as oncogenic lncRNAs with tumor-driving effects, while other lncRNAs play a role in tumor inhibition and are called tumor-suppressive lncRNAs. These tumor-suppressive lncRNAs are involved in multiple physiological processes such as cell proliferation, apoptosis, and metastasis and thus participate in tumor progression. In this review, we discussed the oncogenic and tumor-suppressive lncRNAs in lung cancer, as well as their biological functions and regulatory mechanisms. Furthermore, we found the potential significance of lncRNAs in clinical diagnosis and treatment.

Investigation of association between LINC00673 rs11655237 C>T and Wilms tumor susceptibility

BACKGROUND

Wilms tumor (WT) is the most common pediatric renal malignancy. Previous genome-wide association studies have identified that the LINC00673 rs11655237 C>T polymorphism is associated with the risk of several types of cancer. However, few studies have investigated the association between LINC00673 rs11655237 C>T and WT susceptibility.

METHOD

We genotyped LINC00673 rs11655237 C>T in 145 patients with WT and 531 cancer-free controls recruited from southern Chinese children. The strength of association was estimated by odds ratios (ORs) and 95% confidence intervals (CIs).

RESULTS

Our study indicated that there was no significant association between LINC00673 rs11655237 C>T polymorphism and WT risk under all the tested genetic models (CT vs CC: adjusted OR = 0.94, 95% CI = 0.63-1.40; TT vs CC: adjusted OR = 0.60, 95% CI = 0.22-1.59; TT/CT vs CC: adjusted OR = 0.89, 95% CI = 0.61-1.31; and TT vs CC/CT: adjusted OR = 0.61, 95% CI = 0.23-1.61). Further stratified analysis detected no significant association, either.

CONCLUSION

In conclusion, we failed to find any association between the LINC00673 rs11655237 C>T polymorphism and WT risk. This finding needs to be verified in larger studies and other populations.

Exosome-mediated transfer of lncRNA‑SNHG14 promotes trastuzumab chemoresistance in breast cancer

Currently, resistance to trastuzumab, a human epidermal growth factor receptor 2 (HER2) inhibitor, has become an important obstacle to improving the clinical outcome of patients with advanced HER2⁺ breast cancer. While cell behavior may be modulated by long non-coding RNAs (lncRNAs), the contributions of lncRNAs within extracellular vesicles (exosomes) are largely unknown. To this end, the involvement and regulatory functions of potential lncRNAs contained within exosomes during the formation of chemoresistance in human breast cancer were investigated. Trastuzumab-resistant cell lines were established by continuously grafting HER2⁺ SKBR-3 and BT474 cells into trastuzumab-containing culture medium. An lncRNA micro-array assay followed by reverse transcription-quantitative polymerase chain reaction analysis identified that lncRNA-small nucleolar RNA host gene 14 (SNHG14) was upregulated in trastuzumab-resistant cells when compared with parental breast cancer cells. Functional experimentation demonstrated that knockdown of lncRNA-SNHG14 potently promoted trastuzumab-induced cytotoxicity. Furthermore, extracellular lncRNA-SNHG14 was able to be incorporated into exosomes and transmitted to sensitive cells, thus disseminating trastuzumab resistance. Treatment of sensitive cells with exosomes highly expressing lncRNA-SNHG14 induced trastuzumab resistance, while knockdown of lncRNA-SNHG14 abrogated this effect. The Signal Transduction Reporter Array indicated that lncRNA-SNHG14 may promote the effect of trastuzumab by targeting the apoptosis regulator Bcl-2 (Bcl-2)/apoptosis regulator BAX (Bax) signaling pathway. Furthermore, the expression level of serum exosomal lncRNA-SNHG14 was upregulated in patients who exhibited resistance to trastuzumab, compared with patients exhibiting a response. Therefore, lncRNA-SNHG14 may be a promising therapeutic target for patients with HER2⁺ breast cancer.

Long non-coding RNA Linc00312 modulates the sensitivity of ovarian cancer to cisplatin via the Bcl-2/Caspase-3 signaling pathway

Chemotherapy is one of the main treatments for ovarian cancer (OC). Cisplatin combined with paclitaxel is a commonly used chemotherapy regimen. However, effective cancer therapy is hindered by a patient's resistance to cisplatin. The mechanism that potentially leads to that resistance is unclear. The current study examined the mechanism by which Linc00312 is involved in resistance to cisplatin in OC. Quantitative real-time PCR (RT-qPCR) was used to test for expression of Linc00312 in freshly frozen tissue samples of OC and in SKOV3 and SKOV3/DDP cells. In situ hybridization was performed to examine the distribution of Linc00312 expression in paraffin-embedded histological sections that were sensitive or resistant to cisplatin. The cell counting kit-8 assay was used to detect cell viability. Flow cytometry was used to measure cell apoptosis. RT-qPCR was performed to confirm changes in expression of MDR1, MRP1, Bcl-2, Bax, Caspase-3, and Caspase-9 mRNA. Levels of MDR1, Bcl-2, Bax, Caspase-3, and Caspase-9 protein were detected with Western blotting. Experiments indicated that the expression of Linc00312 decreased significantly in SKOV3/DDP cells compared to that in SKOV3 cells. Upregulation of Linc00312 can considerably increase the sensitivity of SKOV3/DDP cells to cisplatin, while down-regulation of Linc00312 has the exact opposite effect in SKOV3 cells. Linc00312 enhanced the sensitivity of SKOV3/DDP cells to cisplatin by promoting cell apoptosis via the Bcl-2/Caspase-3 signaling pathway. These findings suggest that Linc00312 may be a promising clinical strategy for the treatment of drug-resistant OC.

Exosome-mediated transfer of lncRNA RP11‑838N2.4 promotes erlotinib resistance in non-small cell lung cancer

Currently, resistance to tyrosine kinase inhibitors, such as erlotinib, has become a major obstacle for improving the clinical outcome of patients with metastatic and advanced-stage non-small cell lung cancer (NSCLC). While cell behavior can be modulated by long non-coding RNAs (lncRNAs), the roles of lncRNAs within extracellular vesicles (exosomes) are largely unknown. To this end, in this study, the involvement and regulatory functions of potential lncRNAs wrapped by exosomes during the development of chemoresistance in human NSCLC were investigated. Erlotinib-resistant cell lines were established by grafting HCC827 and HCC4006 cells into mice and which were treated with erlotinib. After one treatment course, xenografted NSCLC cells were isolated and transplanted into nude mice again followed by erlotinib treatment. This process was repeated until 4th generation xenografts were isolated and confirmed to be erlotinib-resistant NSCLC cells. lncRNA microarray assays followed by RT-qPCR were then performed which identified that lncRNA RP11-838N2.4 was upregulated in erlotinib-resistant cells when compared to normal NSCLC cells. Furthermore, bioinformatics analysis and chromatin immunoprecipitation revealed that forkhead box protein O1 (FOXO1) could bind to the promoter region of lncRNA RP11-838N2.4, resulting in its silencing through the recruitment of histone deacetylase. Functional experiments demonstrated that the knockdown of lncRNA RP11-838N2.4 potently promoted erlotinib-induced cytotoxicity. Furthermore, extracellular lncRNA RP11-838N2.4 could be incorporated into exosomes and transmitted to sensitive cells, thus disseminating erlotinib resistance. Treatment-sensitive cells with exosomes containing lncRNA RP11-838N2.4 induced erlotinib resistance, while the knockdown of lncRNA RP11-838N2.4 abrogated this effect. In addition, the serum expression levels of exosomal lncRNA RP11-838N2.4 were upregulated in patients exhibiting resistance to erlotinib treatment. On the whole, exosomal lncRNA RP11-838N2.4 may serve as a therapeutic target for patients with NSCLC.

LINC00673 rs11655237 C>T confers neuroblastoma susceptibility in Chinese population

Neuroblastoma, which accounts for approximately 10% of all pediatric cancer-related deaths, has become a therapeutic challenge and global burden attributed to poor outcomes and mortality rates of its high-risk form. Previous genome-wide association studies (GWASs) identified the LINC00673 rs11655237 C>T polymorphism to be associated with the susceptibility of several malignant tumors. However, the association between this polymorphism and neuroblastoma susceptibility is not clear. We genotyped LINC00673 rs11655237 C>T in 393 neuroblastoma patients in comparison with 812 age-, gender-, and ethnicity-matched healthy controls. We found a significant association between the LINC00673 rs11655237 C>T polymorphism and neuroblastoma risk (TT compared with CC: adjusted odds ratio (OR) =1.80, 95% confidence interval (CI) =1.06-3.06, P=0.029; TT/CT compared with CC: adjusted OR =1.31, 95% CI =1.02-1.67, P=0.033; and T compared with C: adjusted OR =1.29, 95% CI =1.06-1.58, P=0.013). Furthermore, stratified analysis indicated that the rs11655237 T allele carriers were associated with increased neuroblastoma risk for patients with tumor originating from the adrenal gland (adjusted OR =1.51, 95% CI =1.06-2.14, P=0.021) and International Neuroblastoma Staging System (INSS) stage IV disease (adjusted OR =1.60, 95% CI =1.12-2.30, P=0.011). In conclusion, we verified that the LINC00673 rs11655237 C>T polymorphism might be associated with neuroblastoma susceptibility. Prospective studies with a large sample size and different ethnicities are needed to validate our findings.

Long non-coding RNA 00312 downregulates cyclin B1 and inhibits hepatocellular carcinoma cell proliferation in vitro and in vivo

Long non-coding RNAs are dysregulated in human hepatocellular carcinoma (HCC). We tested the potential effect of long non-coding RNA 00312 ("Lnc00312") on human HCC cell behavior in vitro and in vivo. Forced-expression of Lnc00312 by a lentiviral vector induced proliferation inhibition and apoptosis in HepG2 cells and primary human HCC cells. Lnc00312 downregulated cyclin B1 and induced G2-M cell cycle arrest in HCC cells. Restoring cyclin B1 expression by a cyclin B1 cDNA construct inhibited Lnc00312-induced cytotoxicity against HCC cells. Conversely, siRNA-mediated knockdown of Lnc00312 increased cyclin B1 expression and promoted HepG2 cell proliferation. In vivo, the growth of HepG2 xenograft tumors in severe combined immunodeficient (SCID) mice was largely inhibited after expression of Lnc00312. Significantly, Lnc00312 is downregulated in human HCC tissues, which is negatively correlated with the tumor grade. Overall, Lnc00312 inhibits human HCC cell proliferation in vitro and in vivo. Cyclin B1 could be a key target protein of Lnc00312 in human HCC cells.