Analysis of Survival-Related lncRNA Landscape Identifies A Role for LINC01537 in Energy Metabolism and Lung Cancer Progression

A LncRNA panel within EpCAM-specific exosomes for noninvasive early diagnosing non-small cell lung cancer

BACKGROUND

Plasma tumor-associated exosomes represent a promising source for cancer biomarkers; however, the role of long non-coding RNAs (lncRNAs) within these exosomes is not well-defined in non-small cell lung cancer (NSCLC).

METHODS

We identified a panel of NSCLC-specific lncRNAs within plasma EpCAM-specific exosomes (Epexo) through a comparative analysis of lncRNA profiles between plasma Epexo and lung tissues. The panel's diagnostic value was firstly evaluated in a retrospective cohort of 210 NSCLC patients and 245 healthy controls, and validated in a prospective cohort of 192 patients with pulmonary nodules (nodule size < 3 cm in diameter). The evaluation utilized the area under the ROC curve (AUC) based on a random forest model. For precision, repeat testing was conducted with 31 randomly selected samples. Additionally, 39 paired tissue-plasma samples were employed to assess the concordance of lncRNA expression between tissue and plasma within the same individuals.

RESULTS

The panel, including linc01125, HNF1A-AS1, MIR100HG, linc01160, and ZNRF3-AS1, demonstrated superior capability in distinguishing early-stage NSCLC patients from controls, achieving AUC values of 0.805 and 0.856 in the discovery and validation set, respectively. The panel also showed potential for differentiating adenocarcinoma and squamous cell carcinoma. Repeat sample testing showed a consistency of 90.3% for this panel. The expression levels of MIR100HG and HNF1A-AS1 showed significant correlations between plasma Epexo and cancerous tissues.

CONCLUSIONS

The identified lncRNA panel, consisting of linc01125, HNF1A-AS1, MIR100HG, linc01160, and ZNRF3-AS1, presents a promising diagnostic tool for NSCLC.

CLINICAL TRIAL NUMBER

not applicable.

Nilotinib boosts the efficacy of anti-PDL1 therapy in colorectal cancer by restoring the expression of MHC-I

BACKGROUND

Although immune checkpoint inhibitors (ICIs) have revolutionized the landscape of cancer treatment, only a minority of colorectal cancer (CRC) patients respond to them. Enhancing tumor immunogenicity by increasing major histocompatibility complex I (MHC-I) surface expression is a promising strategy to boost the antitumor efficacy of ICIs.

METHODS

Dual luciferase reporter assays were performed to find drug candidates that can increase MHC-I expression. The effect of nilotinib on MHC-I expression was verified by dual luciferase reporter assays, qRT-PCR, flow cytometry and western blotting. The biological functions of nilotinib were evaluated through a series of in vitro and in vivo experiments. Using RNA-seq analysis, immunofluorescence assays, western blotting, flow cytometry, rescue experiments and microarray chip assays, the underlying molecular mechanisms were investigated.

RESULTS

Nilotinib induces MHC-I expression in CRC cells, enhances CD8+ T-cell cytotoxicity and subsequently enhances the antitumor effects of anti-PDL1 in both microsatellite instability and microsatellite stable models. Mechanistically, nilotinib promotes MHC-I mRNA expression via the cGAS-STING-NF-κB pathway and reduces MHC-I degradation by suppressing PCSK9 expression in CRC cells. PCSK9 may serve as a potential therapeutic target for CRC, with nilotinib potentially targeting PCSK9 to exert anti-CRC effects.

CONCLUSION

This study reveals a previously unknown role of nilotinib in antitumor immunity by inducing MHC-I expression in CRC cells. Our findings suggest that combining nilotinib with anti-PDL1 therapy may be an effective strategy for the treatment of CRC.

Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village

Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.

Histone acetylation-related IncRNA: Potential biomarkers for predicting prognosis and immune response in lung adenocarcinoma, and distinguishing hot and cold tumours

Background

Histone acetylation-related lncRNAs (HARlncRNAs) play significant roles in various cancers, but their impact on lung adenocarcinoma (LUAD) remains unclear. This study aimed to develop a new HARlncRNA-based prognostic model for LUAD and to explore its potential biological mechanisms.

Methods

We identified 77 histone acetylation genes based on previous studies. HARlncRNAs related to prognosis were screened by co-expression, univariate and multivariate analyses, and least absolute shrinkage selection operator regression (LASSO). Afterward, a prognostic model was established based on the screened HARlncRNAs. We analysed the relationship between the model and immune cell infiltration characteristics, immune checkpoint molecule expression, drug sensitivity, and tumour mutational burden (TMB). Finally, the entire sample was divided into three clusters to further distinguish between hot and cold tumours.

Results

A seven-HARlncRNA-based prognostic model was established for LUAD. The area under the curve (AUC) of the risk score was the highest among all the analysed prognostic factors, indicating the accuracy and robustness of the model. The patients in the high-risk group were predicted to be more sensitive to chemotherapeutic, targeted, and immunotherapeutic drugs. It was worth noting that clusters could effectively identify hot and cold tumours. In our study, clusters 1 and 3 were considered hot tumours that were more sensitive to immunotherapy drugs.

Conclusion

We developed a risk-scoring model based on seven prognostic HARlncRNAs that promises to be a new tool for evaluating the prognosis and efficacy of immunotherapy in patients with LUAD.

LncRNA LINC01537 Promotes Gastric Cancer Metastasis and Tumorigenesis by Stabilizing RIPK4 to Activate NF-κB Signaling

Many studies reported that long noncoding RNAs (lncRNAs) play a critical role in gastric cancer (GC) metastasis and tumorigenesis. However, the underlying mechanisms of lncRNAs in GC remain unexplored to a great extent. LINC01537 expression level was detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). Its biological roles in GC were then investigated using functional experiments. In order to investigate the underlying mechanism of LINC01537 in GC, RNA pull-down, RNA immunoprecipitation, and ubiquitination assays were performed. LINC01537 was significantly overexpressed in GC tissues and associated with a poor prognosis. Functional experimental results revealed that LINC01537 promoted the proliferation, invasion, and migration of GC cells. The animal experiments revealed that LINC01537 promoted tumorigenesis and metastasis in vivo. Mechanistically, LINC01537 stabilizes RIPK4 by reducing the binding of RIPK4 to TRIM25 and reducing its ubiquitination degradation, thereby promoting the expression of the NF-κB signaling pathway. According to our findings, the LINC01537-RIPK4-NF-κB axis promoted GC metastasis and tumorigenesis.

A universal co-expression gene network and prognostic model for hepatic-biliary-pancreatic cancers identified by integrative analyses

Hepatic, biliary and pancreatic cancers are a diverse set of malignancies with poor prognoses. It is possible that common molecular mechanisms are involved in the carcinogenesis of these cancers. Here, we identified LINC01537 and seven protein-coding genes by integrative analysis of transcriptomes of mRNAs, microRNAs and long non-coding RNAs from cholangiocarcinoma, hepatocellular carcinoma and pancreatic adenocarcinoma cohorts in TCGA. A predictive model constructed from seven biomarkers was established to successfully predict the survival rate of patients, which was then further verified in external cohorts. Additionally, patients with high-risk scores in our model were prone to epithelial-mesenchymal transition. Finally, activation of the biomarker PDE2A significantly attenuated migration and epithelial-mesenchymal transition in the HepG2 liver cancer cell line.

Construction of a Prognostic Evaluation Model for Stomach Adenocarcinoma on the Basis of Immune-Related lncRNAs

Progression, prognosis, and therapeutic strategy of stomach adenocarcinoma (STAD) have a close connection with tumor microenvironment (TME). Thus, it is pivotal to delve into the TME and immune-related genes, which may bring possibilities for improving patient's prognosis. TCGA-STAD dataset was analyzed to acquire differentially expressed lncRNAs in tumor samples, which were overlapped with the immune-related lncRNA datasets in the ImmLnc database. Twenty-six lncRNAs related to STAD immunity and patient's prognosis were acquired by univariate Cox analysis. Following lncRNA expression patterns, STAD samples could be classified into two clusters with completely different immune patterns. We performed multivariate Cox regression analysis on lncRNAs to identify 7-feature lncRNAs and constructed a corresponding prognostic model. The model validity was verified by survival analysis and ROC curve in validation and training sets. To explore connection between model and TME and tumor drug resistance, this study analyzed differences in immune cell infiltration between samples from high- and low-risk groups and then revealed immune cells follicular helper with significant differences in tumor tissue infiltration. Analysis of resistance to chemotherapeutic drugs revealed that samples in the high-risk group had resistance to cisplatin, doxorubicin, bleomycin, and gemcitabine. Through univariate and multivariate Cox analyses, we manifested that risk score could be an independent prognostic factor. Combining risk score and clinical factors, a nomogram was constructed to accurately predict patient's prognosis. This model can effectively predict prognosis, TME, and drug resistance of STAD patients, which may provide a reference for tumor development evaluation and precise treatment for clinical STAD.

Potential of ATP5MG to Treat Metabolic Syndrome-Associated Cardiovascular Diseases

INTRODUCTION

Metabolic syndrome-associated cardiovascular disease (MetS-CVD) is a cluster of metabolism-immunity highly integrated diseases. Emerging evidence hints that mitochondrial energy metabolism may be involved in MetS-CVD development. The physiopathological role of ATP5MG, a subunit of the F0 ATPase complex, has not been fully elucidated.

METHODS

In this study, we selected ATP5MG to identify the immunity-mediated pathway and mine drugs targeting this pathway for treating MetS-CVD. Using big data from public databases, we dissected co-expressed RNA (coRNA), competing endogenous RNA (ceRNA), and interacting RNA (interRNA) genes for ATP5MG.

RESULTS

It was identified that ATP5MG may form ceRNA with COX5A through hsa-miR-142-5p and interplay with NDUFB8, SOD1, and MDH2 through RNA-RNA interaction under the immune pathway. We dug out 251 chemicals that may target this network and identified some of them as clinical drugs. We proposed five medicines for treating MetS-CVD. Interestingly, six drugs are being tested to treat COVID-19, which unexpectedly offers a new potential host-targeting antiviral strategy.

CONCLUSION

Collectively, we revealed the potential significance of the ATP5MG-centered network for developing drugs to treat MetS-CVD, which offers insights into the epigenetic regulation for metabolism-immunity highly integrated diseases.

Long Noncoding RNAs and Circular RNAs in the Metabolic Reprogramming of Lung Cancer: Functions, Mechanisms, and Clinical Potential

As key regulators of gene function, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are generally accepted to be involved in lung cancer pathogenesis and progression. Recent research has clarified the phenomenon of metabolic reprogramming in lung cancer because of its significant role in tumor proliferation, migration, invasion, metastasis, and other malignant biological behaviors. Emerging evidence has also shown a relationship between the aberrant expression of lncRNAs and circRNAs and metabolic reprogramming in lung cancer tumorigenesis. This review provides insight regarding the roles of different lncRNAs and circRNAs in lung cancer metabolic reprogramming, by how they target transporter proteins and key enzymes in glucose, lipid, and glutamine metabolic signaling pathways. The clinical potential of lncRNAs and circRNAs as early diagnostic biomarkers and components of therapeutic strategies in lung cancer is further discussed, including current challenges in their utilization from the bench to the bedside and how to adopt a proper delivery system for their therapeutic use.

Identification of Two Subtypes and Prognostic Characteristics of Lung Adenocarcinoma Based on Pentose Phosphate Metabolic Pathway-Related Long Non-coding RNAs

This study analyzed the differences in subtypes and characteristics of advanced lung adenocarcinoma (LUAD) patients based on the pentose phosphate metabolic pathway-related long non-coding RNAs (lncRNAs), along with their potential regulatory mechanisms. Using the expression profiling and corresponding clinical information of LUAD patients from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). Differential pathway scores between normal and tumor samples from TCGA were identified by rank-sum tests. Pearson correlation coefficients between pentose phosphate scores of the pentose phosphate samples and lncRNAs of the corresponding datasets were calculated. Next, the clusterProfiler software package was used for functional annotation. Clustering of pentose phosphate-related lncRNAs from LUAD samples categorized two molecular subtypes (C1, and C2). C1 was associated with a lower pentose phosphate score and a good prognosis; the C2 showed a higher pentose phosphate score and was related to poorer prognoses. The C2 was markedly associated with energy metabolic pathways. The expression of most immune cells were markedly higher in C1 subtype. Some crucial immune checkpoints, including CTLA4, CD274, and CD47, were also significantly upregulated in C1 subtype, leading to a higher score of clinical effect on the C1 subtype. Finally, one TF, BACH1, was found to be significantly upregulated in C1 subtypes; the pathways activated by this TF may be associated with tumor progression and poor prognoses. LUAD typing based on pentose phosphate metabolic pathway-related lncRNAs was confirmed. Differences in characteristics between C1 and C2 subtypes improved the current LUAD detection and treatment.

Long non-coding RNA LSAMP-1 is down-regulated in non-small cell lung cancer and predicts a poor prognosis

Background

Long noncoding RNAs (lncRNAs) are emerging as master regulators for gene expression and thus play a vital role in human tumorigenesis and progression. But the involvement of novel lncRNAs in non-small cell lung cancer (NSCLC) remains largely unelucidated.

Methods

A total of 170 NSCLC and their adjacent non-tumor tissues were enrolled to detect the expression of Lnc-LSAMP-1 by RT-qPCR. The effects of Lnc-LSAMP-1 on cell proliferation, migration, invasion and drug-sensitivity were determined by in vitro and in vivo experiments. The proteins that interact with Lnc-LSAMP-1were confirmed by RNA pull-down assay. RNA-sequencing were used to identify the potential targets of Lnc-LSAMP-1 in NSCLC.

Results

We found that Lnc-LSAMP-1 was significantly down-regulated in 170 cases of NSCLC tissues when compared to their adjacent non-cancerous tissues. Loss expression of Lnc-LSAMP-1 was notably correlated with unfavorable prognosis of NSCLC patients. The ectopic expression of Lnc-LSAMP-1 drastically inhibited lung cancer cell proliferation, viability, invasion and migration ability, arrested cell cycle and facilitated apoptosis. Chemotherapy sensitization experiments showed that over-expressed Lnc-LSAMP-1 enhanced the inhibition of cell proliferation induced by TKI. Mechanistically, Lnc-LSAMP-1-LSAMP formed a complex which could protect the degradation of LSAMP gene, and thus exerted crucial roles in NSCLC progression and TKI targeted treatment.

Conclusions

Consequently, our findings highlight the function and prognostic value of Lnc-LSAMP-1 in NSCLC and provide potential novel therapeutic targets and prognostic biomarkers for patients with NSCLC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-022-02592-0.

Long Noncoding RNAs in Lung Cancer: From Disease Markers to Treatment Roles

There is an urgent need to identify reliable biomarkers that can be used in early diagnosis, prognostication prediction and as possible therapeutic targets for lung cancer due to its current poor prognosis. Long noncoding RNAs (lncRNAs) have recently attracted additional attention due to their potential role in carcinogenesis, invasion and metastasis. Issues involved in the biofunctions and regulatory mechanisms of oncogenic and tumor-suppressive lncRNAs in lung cancer are discussed. Some lncRNAs have shown good diagnostic value, especially in combination with conventional serum protein markers. The use of antisense oligonucleotides, small molecules and RNA interference techniques have shown promise as direct therapeutic tools for targeting lncRNAs in preclinical studies. The biomarker function of lncRNAs may also indirectly involved in tumor therapy as a reference to conventional therapy. Overall, the concept of using lncRNAs as biomarkers for prognostication and intervention in lung cancer is still in its infancy, and only with more in-depth studies could they have a significant impact.

Role of Long Noncoding RNAs in Smoking-Induced Lung Cancer: An In Silico Study

The prevalence of lung cancer induced by cigarette smoking has increased over time. Long noncoding (lnc) RNAs, regulatory factors that play a role in human diseases, are commonly dysregulated in lung cancer. Cigarette smoking is closely related to changes in lncRNA expression, which can affect lung cancer. Herein, we assess the mechanism of lung cancer initiation induced by smoking. To calculate the impact of smoking on the survival of patients with lung cancer, we extracted data from The Cancer Genome Atlas and Gene Expression Omnibus databases and identified the differentially expressed genes in the lung cancer tissue compared to the normal lung tissue. Genes positively and negatively associated with smoking were identified. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Cytoscape analyses were performed to determine the function of the genes and the effects of smoking on the immune microenvironment. lncRNAs corresponding to smoking-associated genes were identified, and a smoking-related lncRNA model was constructed using univariate and multivariate Cox analyses. This model was used to assess the survival of and potential risk in patients who smoked. During screening, 562 differentially expressed genes were identified, and we elucidated that smoking affected the survival of patients 4.5 years after the diagnosis of lung cancer. Furthermore, genes negatively associated with smoking were closely associated with immunity. Twelve immune cell types were also found to infiltrate differentially in smokers and nonsmokers. Thus, the smoking-associated lncRNA model is a good predictor of survival and risk in smokers and may be used as an independent prognostic factor for lung cancer.

Prognostic Implication of Energy Metabolism-Related Gene Signatures in Lung Adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is the major non-small-cell lung cancer pathological subtype with poor prognosis worldwide. Herein, we aimed to build an energy metabolism-associated prognostic gene signature to predict patient survival.

Methods

The gene expression profiles of patients with LUAD were downloaded from the TCGA and GEO databases, and energy metabolism (EM)-related genes were downloaded from the GeneCards database. Univariate Cox and LASSO analyses were performed to identify the prognostic EM-associated gene signatures. Kaplan–Meier and receiver operating characteristic (ROC) curves were plotted to validate the predictive effect of the prognostic signatures. A CIBERSORT analysis was used to evaluate the correlation between the risk model and immune cells. A nomogram was used to predict the survival probability of LUAD based on a risk model.

Results

We constructed a prognostic signature comprising 13 EM-related genes (AGER, AHSG, ALDH2, CIDEC, CYP17A1, FBP1, GNB3, GZMB, IGFBP1, SORD, SOX2, TRH and TYMS). The Kaplan–Meier curves validated the good predictive ability of the prognostic signature in TCGA AND two GEO datasets (p<0.0001, p=0.00021, and p=0.0034, respectively). The area under the curve (AUC) of the ROC curves also validated the predictive accuracy of the risk model. We built a nomogram to predict the survival probability of LUAD, and the calibration curves showed good predictive ability. Finally, a functional analysis also unveiled the different immune statuses between the two different risk groups.

Conclusion

Our study constructed and verified a novel EM-related prognostic gene signature that could improve the individualized prediction of survival probability in LUAD.

Integrative Analyses of Circulating mRNA and lncRNA Expression Profile in Plasma of Lung Cancer Patients

Circulating-free RNAs (cfRNAs) have been regarded as potential biomarkers for "liquid biopsy" in cancers. However, the circulating messenger RNA (mRNA) and long noncoding RNA (lncRNA) profiles of lung cancer have not been fully characterized. In this study, we profiled circulating mRNA and lncRNA profiles of 16 lung cancer patients and 4 patients with benign pulmonary nodules. Compared with benign pulmonary nodules, 806 mRNAs and 1,762 lncRNAs were differentially expressed in plasma of lung adenocarcinoma patients. For lung squamous cell carcinomas, 256 mRNAs and 946 lncRNAs were differentially expressed. A total of 231 mRNAs and 298 lncRNAs were differentially expressed in small cell lung cancer. Eleven mRNAs, 51 lncRNAs, and 207 canonical pathways were differentially expressed in lung cancer in total. Forty-five blood samples were collected to verify our findings via performing qPCR. There are plenty of meaningful mRNAs and lncRNAs that were found. MYC, a transcription regulator associated with the stemness of cancer cells, is overexpressed in lung adenocarcinoma. Transforming growth factor beta (TGFB1), which plays pleiotropic roles in cancer progression, was found to be upregulated in lung squamous carcinoma. MALAT1, a well-known oncogenic lncRNA, was also found to be upregulated in lung squamous carcinoma. Thus, this study provided a systematic resource of mRNA and lncRNA expression profiles in lung cancer plasma.

Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs

Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.

Novel long non‐coding RNA CYB561‐5 promotes aerobic glycolysis and tumorigenesis by interacting with basigin in non‐small cell lung cancer

Abnormally expressed long non‐coding RNAs (lncRNAs) have been recognized as potential diagnostic biomarkers or therapeutic targets in non‐small cell lung cancer (NSCLC). The role of the novel lnc‐CYB561‐5 in NSCLC and its specific biological activity remain unknown. In this study, lncRNAs highly expressed in NSCLC tissue samples compared with paired adjacent normal tissue samples and atypical adenomatous hyperplasia were identified by RNA‐seq analysis. Lnc‐CYB561‐5 is highly expressed in human NSCLC and is associated with a poor prognosis in lung adenocarcinoma. In vivo, downregulation of lnc‐CYB561‐5 significantly decreases tumour growth and metastasis. In vitro, lnc‐CYB561‐5 knockdown treatment inhibits cell migration, invasion and proliferation ability, as well as glycolysis rates. In addition, RNA pulldown and RNA immunoprecipitation (RIP) assays show that basigin (Bsg) protein interacts with lnc‐CYB561‐5. Overall, this study demonstrates that lnc‐CYB561‐5 is an oncogene in NSCLC, which is involved in the regulation of cell proliferation and metastasis. Lnc‐CYB561‐5 interacts with Bsg to promote the expression of Hk2 and Pfk1 and further lead to metabolic reprogramming of NSCLC cells.

Analysis of differentially expressed long non‑coding RNAs revealed a pro‑tumor role of MIR205HG in cervical cancer

Cervical cancer is the fourth most common female malignancy for both incidence and mortality worldwide and is one of the major threats to women's health. The role of long non‑coding RNAs (lncRNAs) in cervical cancer remains largely unknown. In the present study, the differentially expressed lncRNAs in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tissues were retrieved form The Cancer Genome Atlas (TCGA) and were analyzed. The expression analysis of related genes was performed with GEPIA. The proliferation and migratory and invasive abilities of MIR205HG knockdown CESC cells were analyzed using Cell Counting Kit‑8 and transwell assays. The expression of Ki‑67 and p16 was detected by immunofluorescence. A total of 203 differentially expressed lncRNAs were identified. The results demonstrated that MIR205HG was overexpressed in CESC tissues. Furthermore, the genes related to MIR205HG were enriched in cancer‑related pathways. MIR205HG knockdown significantly decreased the proliferation and migratory and invasive abilities of CESC cells. In addition, silencing of MIR205HG significantly decreased the expression of p16 in C‑33 A cells. The expression of fibroblast growth factor receptor 3, thymidine phosphorylase and GTPase HRas was downregulated in MIR205HG knockdown CESC cells. These findings revealed some potential lncRNA candidates for cervical cancer research and suggested that MIR205HG may have a pro‑tumor role in CESC.

The Emerging Roles of Long Noncoding RNAs as Hallmarks of Lung Cancer

Noncoding ribonucleic acids (ncRNAs) are closely associated with tumor initiation, growth, and progress in lung cancer. Long ncRNAs (lncRNAs), as one of the three subclasses of ncRNAs, play important roles in chromatin modification, transcription, and post-transcriptional processing. Various lncRNAs have recently been reported to be dysfunctional or dysregulated in cancers and have pro- or anti-tumor potential. Importantly, as a new class of cancer biomarkers, studies have demonstrated the plausibility of using certain subsets of lncRNAs as promising diagnostic, therapeutic, or prognostic strategies to manage cancers. This review focuses on lncRNAs associated with hallmarks of lung cancer, especially those discovered in the last five years. The expression levels of these lncRNAs in tumor samples are discussed, alongside their mechanisms of action, drug resistance, and potential as diagnostic and prognostic markers for lung cancer.

Integrated Analysis of lncRNA-Associated ceRNA Network Identifies Two lncRNA Signatures as a Prognostic Biomarker in Gastric Cancer

Background

Gastric cancer (GC) is a malignant tumour that originates in the gastric mucosal epithelium and is associated with high mortality rates worldwide. Long noncoding RNAs (lncRNAs) have been identified to play an important role in the development of various tumours, including GC. Yet, lncRNA biomarkers in a competing endogenous RNA network (ceRNA network) that are used to predict survival prognosis remain lacking. The aim of this study was to construct a ceRNA network and identify the lncRNA signature as prognostic factors for survival prediction.

Methods

The lncRNAs with overall survival significance were used to construct the ceRNA network. Function enrichment, protein-protein interaction, and cluster analysis were performed for dysregulated mRNAs. Multivariate Cox proportional hazards regression was performed to screen the potential prognostic lncRNAs. RT-qPCR was used to measure the relative expression levels of lncRNAs in cell lines. CCK8 assay was used to assess the proliferation of GC cells transfected with sh-lncRNAs.

Results

Differentially expressed genes were identified including 585 lncRNAs, 144 miRNAs, and 2794 mRNAs. The ceRNA network was constructed using 35 DElncRNAs associated with overall survival of GC patients. Functional analysis revealed that these dysregulated mRNAs were enriched in cancer-related pathways, including TGF-beta, Rap 1, calcium, and the cGMP-PKG signalling pathway. A multivariate Cox regression analysis and cumulative risk score suggested that two of those lncRNAs (LINC01644 and LINC01697) had significant prognostic value. Furthermore, the results indicate that LINC01644 and LINC01697 were upregulated in GC cells. Knockdown of LINC01644 or LINC01697 suppressed the proliferation of GC cells.

Conclusions

The authors identified 2-lncRNA signature in ceRNA regulatory network as prognostic biomarkers for the prediction of GC patient survival and revealed that silencing LINC01644 or LINC01697 inhibited the proliferation of GC cells.

Clinical significance of PDE2A in prognosis and immune infiltration in gastrointestinal cancer based on bioinformatics analysis

BACKGROUND

Gastrointestinal cancer is one of the most common malignant cancers, but its prognosis is still poor. Exploring potential biomarkers is an important aspect of cancer research. We intended to explore potential biomarkers for gastrointestinal cancer using bioinformatics methods.

AIM

To explore the correlation between the expression of PDE2A and immune infiltration in gastrointestinal cancer, and to investigate the prognostic value of PDE2A in gastrointestinal cancer.

METHODS

The mRNA and protein expression of PDE2A in different gastrointestinal cancers was analyzed based on the HPA, TIMER, and UALCAN databases. GEPIA database was used to investigate the effect of PDE2A on prognosis of patients with different gastrointestinal cancers. The relationship between PDE2A expression and immune infiltration was analyzed using the TIMER database. Frequencies of PDE2A mutations were analyzed using cBioPortal database. Protein-protein interaction network analysis of PDE2A was based on the STRING database.

RESULTS

The mRNA and protein expression of PDE2A in liver hepatocellular carcinoma (LIHC), stomach adenocarcinoma (STAD), pancreatic adenocarcinoma (PAAD), colon adenocarcinoma (COAD), and esophageal carcinoma (ESCA) was lower than that in normal adjacent tissues. Patients with LIHC and PAAD with high PDE2A expression had a better prognosis. The expression of PDE2A was positively or negatively correlated with different immune cells such as CD4+ T cells, CD8+ T cells, B cells, macrophages, and neutrophils in LIHC, STAD, PAAD, COAD, and ESCA. Finally, there were missense mutations in PDE2A gene in STAD, PAAD, COAD, and ESCA.

CONCLUSION

The expression of PDE2A is related to immune infiltration in gastrointestinal cancer. Patients with LIHC and PAAD with high PDE2A expression have a better prognosis. PDE2A may be a potential immunotherapy target and prognostic marker for gastrointestinal cancer.

Revisiting Lung Cancer Metastasis: Insight From the Functions of Long Non-coding RNAs

Globally, lung cancer is the most common cause of cancer-related deaths. After diagnosis at all stages, <7% of patients survive for 10 years. Thus, diagnosis at later stages and the lack of effective and personalized drugs reflect a significant need to better understand the mechanisms underpinning lung cancer progression. Metastasis should be responsible for the high lethality and recurrence rates seen in lung cancer. Metastasis depends on multiple crucial steps, including epithelial–mesenchymal transition, vascular remodeling, and colonization. Therefore, in-depth investigations of metastatic molecular mechanisms can provide valuable insights for lung cancer treatment. Recently, long noncoding RNAs (lncRNAs) have attracted considerable attention owing to their complex roles in cancer progression. In lung cancer, multiple lncRNAs have been reported to regulate metastasis. In this review, we highlight the major molecular mechanisms underlying lncRNA-mediated regulation of lung cancer metastasis, including (1) lncRNAs acting as competing endogenous RNAs, (2) lncRNAs regulating the transduction of several signal pathways, and (3) lncRNA coordination with enhancer of zeste homolog 2. Thus, lncRNAs appear to execute their functions on lung cancer metastasis by regulating angiogenesis, autophagy, aerobic glycolysis, and immune escape. However, more comprehensive studies are required to characterize these lncRNA regulatory networks in lung cancer metastasis, which can provide promising and innovative novel therapeutic strategies to combat this disease.

RNA sequencing: new technologies and applications in cancer research

Over the past few decades, RNA sequencing has significantly progressed, becoming a paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing to single-molecular, single-cell and spatial transcriptome approaches has enabled increasingly accurate, individual cell resolution incorporated with spatial information. Cancer, a major malignant and heterogeneous lethal disease, remains an enormous challenge in medical research and clinical treatment. As a vital tool, RNA sequencing has been utilized in many aspects of cancer research and therapy, including biomarker discovery and characterization of cancer heterogeneity and evolution, drug resistance, cancer immune microenvironment and immunotherapy, cancer neoantigens and so on. In this review, the latest studies on RNA sequencing technology and their applications in cancer are summarized, and future challenges and opportunities for RNA sequencing technology in cancer applications are discussed.

The Role of Long Non-coding RNAs in Cancer Metabolism: A Concise Review

Dysregulation of metabolic pathways in cancer cells is regarded as a hallmark of cancer. Identification of these abnormalities in cancer cells dates back to more than six decades, far before discovery of oncogenes and tumor suppressor genes. Based on the importance of these pathways, several researchers have aimed at modulation of these functions to intervene with the pathogenic course of cancer. Numerous genes have been shown to participate in the regulation of metabolic pathways, thus aberrant expression of these genes can be involved in the pathogenesis of cancer. The recent decade has experienced a significant attention toward the role of long non-coding RNAs (lncRNAs) in the biological functions. These transcripts regulate expression of genes at several levels, therefore influencing the activity of cancer-related pathways. Among the most affected pathways are those modulating glucose homeostasis, as well as amino acid and lipid metabolism. Moreover, critical roles of lncRNAs in regulation of mitochondrial function potentiate these transcripts as novel targets for cancer treatment. In the current review, we summarize the most recent literature regarding the role of lncRNAs in the cancer metabolism and their significance in the design of therapeutic modalities.

Long non-coding RNA FAM133B-2 represses the radio-resistance of nasopharyngeal cancer cells by targeting miR-34a-5p/CDK6 axis

Long non-coding RNAs (lncRNAs) were found to play roles in various cancers, including nasopharyngeal carcinoma. In this study, we focused on the biological function of the lncRNA FAM133B-2 in the radio-resistance of nasopharyngeal carcinoma. The RNA-seq and qRT-PCR analysis showed that FAM133B-2 is highly expressed in the radio-resistant nasopharyngeal carcinoma cells. The following biochemical assays showed that FAM133B-2 represses the nasopharyngeal carcinoma radio-resistance and also affects the apoptosis and proliferation of nasopharyngeal carcinoma cells. Further investigations suggested that miR-34a-5p targets FAM133B-2 and also regulates the cyclin-dependent kinase 6 (CDK6). All these results suggested that the lncRNA FAM133B-2 might function as a competitive endogenous RNA (ceRNA) for miR-34a-5p in nasopharyngeal carcinoma radio-resistance, thus it may be regarded as a novel prognostic biomarker and therapeutic target in nasopharyngeal carcinoma diagnosis and treatment.

Resibufogenin suppresses tumor growth and Warburg effect through regulating miR-143-3p/HK2 axis in breast cancer

Increasing evidence confirmed that the Warburg effect plays an important role involved in the progression of malignant tumors. Resibufogenin (RES) has been proved to have a therapeutic effect in multiple malignant tumors. However, the mechanism of whether RES exerted an antitumor effect on breast cancer through regulating the Warburg effect is largely unknown. The effect of RES on glycolysis was determined by glucose consumption, lactate production, ATP generation, extracellular acidification rate and oxygen consumption rate in breast cancer cells. The total RNA and protein levels were respectively measured by RT-qPCR and western blot. Cell proliferation and apoptosis were examined using the CCK-8 assay, colony formation assay, and flow cytometry, respectively. The interaction between miR-143-3p and HK2 was verified by dual-luciferase reporter gene assay. We also evaluated the influence of RES on the tumor growth and Warburg effect in vivo. RES treatment significantly decreased glycolysis, cell proliferation and induced apoptosis of both MDA-MB-453 and MCF-7 cells. Simultaneously, the expression of HK2 was decreased in breast cancer cells treated with RES, which was positively associated with tumor size and glycolysis. Moreover, HK2 was a direct target gene of miR-143-3p. Mechanistically, upregulation of miR-143-3p by RES treatment inhibited tumor growth by downregulating HK2-mediated Warburg effect in breast cancer. Our findings suggested that RES exerted anti-tumorigenesis and anti-glycolysis activities in breast cancer through upregulating the inhibitory effect of miR-143-3p on HK2 expression, which provided a new potential strategy for breast cancer clinical treatment.

Non-coding RNA profile in lung cancer

Lung cancer is the most frequently diagnosed malignancy and the leading source of cancer-associated mortality. This kind of cancer has heterogeneous nature and is divided into two broad classes of small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). In addition to aberrant expression of several signaling pathways and oncogenes, lung cancer is associated with dysregulation of expression of non-coding RNAs including both long non-coding RNAs (lncRNAs) and miRNAs. These aberrantly expressed transcripts are putative therapeutic targets and diagnostic/ prognostic markers. Integrative assessment of expression of lncRNAs, miRNAs and mRNAs has led to construction of competing endogenous RNA networks in which several lncRNAs act as molecular sponges to inhibit regulatory function of miRNAs on mRNAs. Notably, some of these networks seem to have subtype-specific functions in lung cancer. In this review, we summarize recent findings about the importance of these networks in the pathogenesis of lung cancer and provide a list of onco-miRNAs, tumor suppressor miRNAs, oncogenic lncRNAs and tumor suppressor lncRNAs based on their roles in the carcinogenic process in lung cancer.