Microarray data re-annotation reveals specific lncRNAs and their potential functions in non-small cell lung cancer subtypes

Integrative bioinformatics analysis reveals ECM and nicotine-related genes in both LUAD and LUSC, but different lung fibrosis-related genes are involved in LUAD and LUSC

There are several bioinformatics studies related to lung cancer, but most of them have mainly focused on either microarray data or RNA-Seq data alone. In this study, we have combined both types of data to identify differentially expressed genes (DEGs) specific to lung cancer subtypes. We obtained six microarray datasets from the GEO and also the expression matrix of LUSC and LUAD from TCGA, which were analyzed by GEO2R tool and GEPIA2, respectively. Enrichment analyses of DEGs were performed using the Enrichr database. Protein module identification was done by MCODE plugin in cytoscape software. We identified 30 LUAD-specific, 17 LUSC-specific, and 17 DEGs shared between LUAD and LUSC. Enrichment analyses revealed that LUSC-specific DEGs are involved in lung fibrosis. In addition, DEGs shared between LUAD and LUSC are involved in extracellular matrix (ECM), nicotine metabolism, and lung fibrosis. We identified lung fibrosis-related genes, including SPP1, MMP9, and CXCL2, involved in both LUAD and LUSC, but SERPINA1 and PLAU genes involved only in LUSC. We also found an important module separately for LUAD-specific, LUSC-specific, and shared DEGs between LUSC and LUAD. S100P, GOLM, AGR2, AK1, TMEM125, SLC2A1, COL1A1, and GHR genes were significantly associated with survival. Our findings suggest that different lung fibrosis-related genes may play roles in LUSC and LUAD. Additionally, nicotine metabolism and ECM remodeling were found to be associated with both LUSC and LUAD, regardless of subtype, emphasizing the role of smoking in the development of lung cancer and ECM in the high aggressiveness and mortality of lung cancer.

Clinical value of lncRNA SOX2-OT in pulmonary arterial hypertension and its role in pulmonary artery smooth muscle cell proliferation, migration, apoptosis, and inflammatory

BACKGROUND

Non-coding RNA is confirmed to be involved in pulmonary arterial hypertension (PAH).

OBJECTIVES

This study investigated the clinical value and potential mechanisms of the long noncoding RNA (lncRNA) SRY-box transcription factor 2 overlapping transcript (SOX2-OT) in PAH.

METHODS

SOX2-OT levels were measured by quantitative real-time polymerase chain reaction (qRT-PCR) in serum of 82 patients with PAH and 76 healthy controls. Receiver operating characteristic (ROC) analysis was performed to assess the diagnostic value of SOX2-OT. Human pulmonary arterial smooth muscle cells (hPASMCs) were treated by hypoxia to construct PAH cell models. Proliferation, migration, apoptosis, and inflammatory cytokines levels of hPASMCs were examined by CCK-8, Transwell, flow cytometry, and ELISA assay. Dual-luciferase reporter gene assays were performed to verify the target relationships between miR-455-3p and SOX2-OT, as well as small ubiquitin-related modifier 1 (SUMO1).

RESULTS

Serum SOX2-OT was highly expressed in patients with PAH (P < 0.05). And elevated SOX2-OT levels significantly differentiated PAH patients from healthy controls, confirming high diagnostic feasibility. What's more, SOX2-OT was increased in hypoxia-induced hPASMCs in a time-dependent manner. Silencing SOX2-OT could reverse hypoxia-induced proliferation, migration, anti-apoptosis, and inflammation of hPASMCs (P < 0.05). However, rescue experiments showed that this reversal effect of silencing SOX2-OT was attenuated by suppressed miR-455-3p, which was presumably achieved by SUMO1 (P < 0.05).

CONCLUSIONS

Elevated SOX2-OT is a feasible diagnostic marker for PAH, and its silencing may attenuated hypoxia-induced hPASMCs proliferation, migration, anti-apoptosis, and inflammation by modulating the miR-455-3p/SUMO1 axis, preventing vascular remodeling and PAH progression. Our research provided new insights for PAH treatment.

LncRNA LOC285758 Induced Non-Small Cell Lung Cancer Development through Up-Regulating CDK6 by Sponge Adsorption of miRNA-204

Background

Non-coding RNA played one pivotal role in NSCLC in terms of pathogenesis and progression. We aimed to determine the LncRNA, which can be one new potential target for NSCLC treatment and its possible mechanisms from Jan 2017 to Aug 2020.

Methods

Gene LOC285758, which produced new cells in tumor cellular system, was knocked out. Its specific effects were tested in terms of cellular phenotype. LOC285758 was chosen to target for miRNA as well as downstream mRNA targeted by miRNA, which verified the combination predicted before. Specific impacts brought from miRNA on NSCLC cells were examined. At last, dynamic impacts produced through miRNA and LOC285758 on mRNA expression and NSCLC cellular phenotype were examined.

Results

LOC285758 expression was up-regulated in tissues and cells from NSCLC. Knocking out gene LOC285758 could repress cellular survival and migration of A549 and H292 cells. miRNA-204 was repressed via LOC285758 targeting. miRNA-204 over-expressing repressed invasion ability of NSCLC cells and CDK6 targeted by miRNA-204. CDK6 knocking out suppressed survival and migration of NSCLC cells. The influence brought from gene LOC285758 knocking out could be reversed through suppressing miRNA-204, causing up-regulated CDK6 as well as LOC285758 expression in NSCLC tissues. miRNA-204 was negatively correlated with CDK6 as well as LOC285758, respectively. Nonetheless, CDK6 possessed the positive relationship with LOC285758.

Conclusion

An axis of lncRNA LOC285758/miRNA-204/CDK6 can modulate NSCLC cells in terms of migration as well as survival.

Functional Peptides Encoded by Long Non-Coding RNAs in Gastrointestinal Cancer

Gastrointestinal cancer is by far the most common malignancy and the most common cause of cancer-related deaths worldwide. Recent studies have shown that long non-coding RNAs (lncRNAs) play an important role in the epigenetic regulation of cancer cells and regulate tumor progression by affecting chromatin modifications, gene transcription, translation, and sponge to miRNAs. In particular, lncRNA has recently been found to possess open reading frame (ORF), which can encode functional small peptides or proteins. These peptides interact with its targets to regulate transcription or the signal axis, thus promoting or inhibiting the occurrence and development of tumors. In this review, we summarize the involvement of lncRNAs and the function of lncRNAs encoded small peptides in gastrointestinal cancer.

Cost-Effectiveness Analysis of Nivolumab Plus Ipilimumab vs. Chemotherapy as First-Line Therapy in Advanced Non-Small Cell Lung Cancer

Background: The CheckMate 227 trial has indicated that nivolumab plus ipilimumab compared with chemotherapy significantly increases long-term survival in the first-line setting of advanced non-small-cell lung cancer (NSCLC).

Methods: A Markov model was built to estimate the cost and effectiveness of nivolumab plus ipilimumab vs. chemotherapy as the first-line therapy in patients with advanced NSCLC based on outcomes data from the CheckMate 227 trial. We calculated the cost and health outcomes at a willingness-to-pay (WTP) threshold of $150,000 per quality adjusted life year (QALY) in populations with different programmed death ligand 1 (PD-L1) expression levels (≥50, ≥1, and <1%) or a high tumor mutational burden (TMB) (≥10 mutations per megabase). Sensitivity analysis were used to test the model stability.

Results: The outcomes showed that the incremental costs and QALYs by using nivolumab plus ipilimumab were $124180.76 and 1.16, $70951.42 and 0.53, $144093.63 and 0.83 for the advanced NSCLC patients with a PD-L1 expression ≥50%, ≥1%, and <1%, which led to an incremental cost-effective ratio (ICER) of $107403.72, $133732.20, and $172589.15 per QALY, respectively. For patients with a high TMB, nivolumab plus ipilimumab contributed an extra 2.04 QALYs at a cost of $69182.50 per QALY.

Conclusion: Nivolumab plus ipilimumab as first-line therapy makes a better cost-effective strategy than chemotherapy in advanced NSCLC patients with PD-L1 expression levels ≥50% and ≥1% or a high TMB, at a willingness-to-pay threshold of $150,000 per QALY, but not in the patients with a PD-L1 expression <1%.

Identification of New Potential LncRNA Biomarkers in Hirschsprung Disease

Hirschsprung disease (HSCR) is a neurocristopathy defined by intestinal aganglionosis due to alterations during the development of the Enteric Nervous System (ENS). A wide spectrum of molecules involved in different signaling pathways and mechanisms have been described in HSCR onset. Among them, epigenetic mechanisms are gaining increasing relevance. In an effort to better understand the epigenetic basis of HSCR, we have performed an analysis for the identification of long non-coding RNAs (lncRNAs) by qRT-PCR in enteric precursor cells (EPCs) from controls and HSCR patients. We aimed to test the presence of a set lncRNAs among 84 lncRNAs in human EPCs, which were previously related with crucial cellular processes for ENS development, as well as to identify the possible differences between HSCR patients and controls. As a result, we have determined a set of lncRNAs with positive expression in human EPCs that were screened for mutations using the exome data from our cohort of HSCR patients to identify possible variants related to this pathology. Interestingly, we identified three lncRNAs with different levels of their transcripts (SOCS2-AS, MEG3 and NEAT1) between HSCR patients and controls. We propose such lncRNAs as possible regulatory elements implicated in the onset of HSCR as well as potential biomarkers of this pathology.

Cost-Effectiveness Analysis of Atezolizumab Plus Chemotherapy in the First-Line Treatment of Metastatic Non-Squamous Non-Small Cell Lung Cancer

INTRODUCTION

The purpose of this study was to estimate the cost-effectiveness of atezolizumab plus chemotherapy in patients with metastatic non-squamous non-small cell lung cancer (NSCLC) from the United States (US) payers' perspective in the first-line treatment.

METHODS

A mathematical Markov model was developed to estimate cost and effectiveness of atezolizumab combination therapy versus carboplatin plus nab-paclitaxel alone in the first-line therapy of metastatic non-squamous NSCLC from the data of IMpower130. Costs, quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios (ICERs) were analyzed, and model robustness was assessed by sensitivity analysis. Additional subgroup analyses were performed as well.

RESULTS

Compared to chemotherapy, treatment with atezolizumab plus chemotherapy yields an increase of 0.16 QALYs with an increase in cost of $109,809.13, resulting in an ICER of $670,309.66 per QALY. The most influential factor in this model was the cost of atezolizumab. Probabilistic sensitivity analysis showed that there was 0% probability that atezolizumab plus chemotherapy was cost-effective at willingness-to-pay (WTP) values of $150,000 per QALY. The results of subgroup analyses showed that the ICER remained greater than $150,000/QALY across the all patient subgroups.

CONCLUSION

First-line treatment with atezolizumab in combination with carboplatin plus nab-paclitaxel is not a cost-effective option in patients with metastatic non-squamous NSCLC.

Prognostic value of long non-coding RNA SNHG20 in cancer: A meta-analysis

BACKGROUND

Small nucleolar RNA host gene 20 (SNHG20) is a newly identified long non-coding RNA (lncRNA). Accumulative evidence suggest that SNHG20 is highly related to tumorigenesis. However, whether the levels of SNHG20 can be used for prognosis of patients with different cancer types was unclear. The present study aims to explore the role of SNHG20 in tumor prognosis and its clinical significance.

METHODS

Related articles published before March 14, 2019 were searched in PubMed, Excerpta Medica Database (EMBASE), ISI Web of Science, and China National Knowledge Infrastructure (CNKI). Hazard ratios (HRs) and their corresponding 95% confidence intervals (CIs) were obtained using Stata 11.0 software and used to for determination of the link between the levels of SNHG20 and overall survival (OS). Fixed or random model was chosen depending on the heterogeneity of the studies. A quality assessment of the included studies was performed according to the Newcastle-Ottawa scale. This study was approved by the Medical Ethics Committee of Xiangya Hospital of Central South University.

RESULTS

After a strict filtering process, a total of 1149 patients from 15 studies were enrolled in this study. Pooled data showed that elevated level of SNHG20 was correlated not only with poor overall survival (HR = 2.49, 95% confidence interval (CI): 2.05-2.98), but also with tumor-node-metastasis stage (TNM) (odds ratio (OR) = 3.32, 95% CI: 2.27-4.86), high histological grade (OR = 2.11, 95% CI: 1.55-2.87), tumor size (OR = 2.92, 95% CI: 2.17-3.91), and lymph node metastasis (OR = 4.48, 95% CI: 2.90-6.92). Of note, there is no significant heterogeneity difference among the studies.

CONCLUSION

Up-regulated SNHG20 predicts unfavorable prognosis for multiple kinds of cancers although further studies are in need to verify its clinical applications.

Effects of conditioned media from murine lung cancer cells and human tumor cells on cultured myotubes

Factors secreted from tumors/tumor cells are hypothesized to cause skeletal muscle wasting in cancer patients. We examined whether cancer cells secrete factors to promote atrophy by evaluating the effects of conditioned media (CM) from murine lung cancer cells and primary cultures of human lung tumor cells on cultured myotubes. We evaluated murine Lewis lung carcinoma (LLC) and KRAS^G12D cells, and primary cell lines derived from tumor biopsies from patients with lung cancer (hTCM; n = 6). In all experiments, serum content was matched across treatment groups. We hypothesized that CM from murine and human tumor cells would reduce myotube myosin content, decrease mitochondrial content, and increase mitochondrial reactive oxygen species (ROS) production. Treatment of myotubes differentiated for 7 days with CM from LLC and KRAS^G12D cells did not alter any of these variables. Effects of murine tumor cell CM were observed when myotubes differentiated for 4 days were treated with tumor cell CM and compared with undiluted differentiation media. However, these effects were not apparent if tumor cell CM treatments were compared with control cell CM or dilution controls. Finally, CM from human lung tumor primary cell lines did not modify myosin content or mitochondrial content or ROS production compared with either undiluted differentiated media, control cell CM, or dilution controls. Our results do not support the hypothesis that factors released from cultured lung cancer/tumor cells promote myotube wasting or mitochondrial abnormalities, but we cannot dismiss the possibility that these cells could secrete such factors in vivo within the native tumor microenvironment.

SOX2OT, a novel tumor-related long non-coding RNA

SOX2OT is a long non-coding RNA that is highly expressed in embryonic stem cells. The SOX2OT gene is comprised of 10 exons and more than two transcription start sites. Dysregulation of SOX2OT is observed in various tumors, including lung cancer, gastric cancer, esophageal cancer, breast cancer, hepatocellular carcinoma, ovarian cancer, pancreatic ductal adenocarcinoma, laryngeal squamous cell carcinoma, cholangiocarcinoma, osteosarcoma, nasopharyngeal carcinoma, and glioblastoma, wherein it typically functions as an oncogene and possibly as a tumor suppressor gene. The mechanisms underlying the effects of SOX2OT are complex and involve multiple factors and signaling pathways. In this review, we describe the current evidence regarding the role and potential clinical utility of SOX2OT in human cancers.

LINK-A lncRNA is upregulated in metastatic non-small cell lung cancer and is associated with poor prognosis

Long intergenic non-coding RNA for kinase activation (LINK-A) has been characterized as an oncogenic long non-coding RNA (lncRNA) in triple-negative breast cancer. However, its involvement in non-small cell lung cancer (NSCLC) remains unknown. The aim of the present study was to investigate the involvement of LINK-A in NSCLC. Expression of LINK-A lncRNA in the plasma of patients with NSCLC collected on the day of admission and the day of discharge, and in the plasma of healthy controls, was detected by reverse transcription-quantitative PCR. Diagnostic values of plasma LINK-A for metastatic NSCLC were evaluated by receiver operating characteristic curve analysis. A LINK-A lncRNA expression vector was constructed and transfected into human NSCLC cell lines, and the effects on cell migration and invasion, and Akt activation were detected by Transwell and Matrigel assays, and western blotting, respectively. Plasma levels of LINK-A were found to be significantly higher in patients with different types of metastatic NSCLC than in patients with non-metastatic NSCLC and healthy controls. Plasma levels of LINK-A were lower in patients with metastatic NSCLC on the day of discharge than on the day of admission. Patients with high plasma LINK-A had a higher mortality rate and lower progression-free survival rate within 2 years of discharge. In conclusion, LINK-A is overexpressed in metastatic NSCLC, and may promote the migration and invasion of NSCLC by activating Akt signaling.

LncRNA FOXD2-AS1 as a competitive endogenous RNA against miR-150-5p reverses resistance to sorafenib in hepatocellular carcinoma

The current study elucidated the role of a long non-coding RNA (lncRNA), FOXD2-AS1, in the pathogenesis of hepatocellular carcinoma (HCC) and the regulatory mechanism underlying FOXD2-AS1/miR-150-5p/transmembrane protein 9 (TMEM9) signalling in HCC. Microarray analysis was used for preliminary screening of candidate lncRNAs in HCC tissues. qRT-PCR and Western blot analyses were used to detect the expression of FOXD2-AS1. Cell proliferation assays, luciferase assay and RNA immunoprecipitation were performed to examine the mechanism by which FOXD2-AS1 mediates sorafenib resistance in HCC cells. FOXD2-AS1 and TMEM9 were significantly decreased and miR-150-5p was increased in SR-HepG2 and SR-HUH7 cells compared with control parental cells. Overexpression of FOXD2-AS1 increased TMEM9 expression and overcame the resistance of SR-HepG2 and SR-HUH7 cells. Conversely, knockdown of FOXD2-AS1 decreased TMEM9 expression and increased the sensitivity of HepG2 and Huh7 cells to sorafenib. Our data also demonstrated that FOXD2-AS1 functioned as a sponge for miR-150-5p to modulate TMEM9 expression. Taken together, our findings revealed that FOXD2-AS1 is an important regulator of TMEM9 and contributed to sorafenib resistance. Thus, FOXD2-AS1 may serve as a therapeutic target against sorafenib resistance in HCC.

Circulating long non-coding RNA GAS5 and SOX2OT as potential biomarkers for diagnosis and prognosis of non-small cell lung cancer

Early diagnosis of non-small cell lung cancer (NSCLC) is essential for patient treatment and prognosis. Long noncoding RNA (lncRNA) have potential roles in tumor initiation and differentiation. The objective of this study was to investigate whether the circulating lncRNA, growth arrest-specific transcript 5 (GAS5) and SOX2 overlapping transcript (SOX2OT), could be used as noninvasive biomarkers for NSCLC diagnosis. Moreover, we aimed at evaluating the association between lncRNA and the clinicopathological features of NSCLC in order to predict the cancer prognosis. The results showed significant downregulation of GAS5 expression and upregulation of SOX2OT in NSCLC patients compared with controls (P < 0.001). Furthermore, the expression level of GAS5 was declined in stage IV of NSCLC, but SOX2OT expression was increased sharply in stages III and IV. The expression levels of lncRNAs were used to distinguish NSCLC patients from control with an area under curve of 0.81 (sensitivity 82.5% and specificity 80%) for GAS5 and 0.73 (sensitivity 76.3% and specificity 78.6%) for SOX2OT. The combination of GAS5 and SOX2OT showed differentiation NSCLC patients from controls with increased sensitivity (83.8) and specificity (81.4). In conclusion, the newly developed diagnostic panel involving of circulating GAS5 and SOX2OT could be perfect biomarker for diagnosis and prognosis of NSCLC.

The prognostic value of long noncoding RNA Sox2ot expression in various cancers: A systematic review and meta-analysis

BACKGROUND

Several investigations have explored the prognostic value of long noncoding RNA Sox2 overlapping transcript (lncRNA Sox2ot) expression in human cancers, however, with inconsistent results. The aim of this study was to evaluate the prognostic role of lncRNA Sox2ot expression in various cancers.

METHODS

PubMed, Web of Science, Embase, and Cochrane Library were comprehensively searched to retrieve relevant studies. The relationships between lncRNA Sox2ot expression and prognostic parameters were detected, including overall survival (OS), tumor differentiation, clinical stage, distant metastasis, lymph node metastasis and so on.

RESULTS

A total of 10 studies involving 943 cancer patients were finally included into the study. High lncRNA Sox2ot expression was significantly related to shorter OS in cancers (HR = 2.06, 95%CI = 1.67-2.55, P < 0.01). The cancer patients with high lncRNA Sox2ot expression tended to have worse tumor differentiation (P = 0.04), advanced clinical stage (P < 0.01), earlier distant metastasis (P < 0.01), and earlier lymph node metastasis (P = 0.01) compared to those with low lncRNA Sox2ot expression. However, there was no distinct correlation between lncRNA Sox2ot expression and age (P = 0.87), gender (P = 0.48), tumor size (P = 0.08), or vascular invasion (P = 0.07).

CONCLUSION

High lncRNA Sox2ot expression was significantly associated with worse OS, advanced clinical stage, worse tumor differentiation, earlier distant metastasis, and earlier lymph node metastasis in various cancers. LncRNA Sox2ot expression might a promising prognostic factor in various cancers.