LncRNA LINC02418 regulates proliferation and apoptosis of non-small cell lung cancer cells by regulating miR-4677-3p/SEC61G

Hsa-LINC02418/mmu-4930573I07Rik regulated by METTL3 dictates anti-PD-L1 immunotherapeutic efficacy via enhancement of Trim21-mediated PD-L1 ubiquitination

BACKGROUND

Limited response to programmed death ligand-1 (PD-L1)/programmed death 1 (PD-1) immunotherapy is a major hindrance of checkpoint immunotherapy in non-small cell lung cancer (NSCLC). The abundance of PD-L1 on the tumor cell surface is crucial for the responsiveness of PD-1/PD-L1 immunotherapy. However, the negative control of PD-L1 expression and the physiological significance of the PD-L1 inhibition in NSCLC immunotherapy remain obscure.

METHODS

Bioinformatics analysis was performed to profile and investigate the long non-coding RNAs that negatively correlated with PD-L1 expression and positively correlated with CD8+T cell infiltration in NSCLC. Immunofluorescence, in vitro PD-1 binding assay, T cell-induced apoptosis assays and in vivo syngeneic mouse models were used to investigate the functional roles of LINC02418 and mmu-4930573I07Rik in regulating anti-PD-L1 therapeutic efficacy in NSCLC. The molecular mechanism of LINC02418-enhanced PD-L1 downregulation was explored by immunoprecipitation, RNA immunoprecipitation (RIP), and ubiquitination assays. RIP, luciferase reporter, and messenger RNA degradation assays were used to investigate the m6A modification of LINC02418 or mmu-4930573I07Rik expression. Bioinformatics analysis and immunohistochemistry (IHC) verification were performed to determine the significance of LINC02418, PD-L1 expression and CD8+T cell infiltration.

RESULTS

LINC02418 is a negative regulator of PD-L1 expression that positively correlated with CD8+T cell infiltration, predicting favorable clinical outcomes for patients with NSCLC. LINC02418 downregulates PD-L1 expression by enhancing PD-L1 ubiquitination mediated by E3 ligase Trim21. Both hsa-LINC02418 and mmu-4930573I07Rik (its homologous RNA in mice) regulate PD-L1 therapeutic efficacy in NSCLC via Trim21, inducing T cell-induced apoptosis in vitro and in vivo. Furthermore, METTL3 inhibition via N6-methyladenosine (m6A) modification mediated by YTHDF2 reader upregulates hsa-LINC02418 and mmu-4930573I07Rik. In patients with NSCLC, LINC02418 expression is inversely correlated with PD-L1 expression and positively correlated with CD8+T infiltration.

CONCLUSION

LINC02418 functions as a negative regulator of PD-L1 expression in NSCLC cells by promoting the degradation of PD-L1 through the ubiquitin-proteasome pathway. The expression of LINC02418 is regulated by METTL3/YTHDF2-mediated m6A modification. This study illuminates the underlying mechanisms of PD-L1 negative regulation and presents a promising target for improving the effectiveness of anti-PD-L1 therapy in NSCLC.

Mechanism of Long Noncoding RNA HOTAIR in Nucleus Pulposus Cell Autophagy and Apoptosis in Intervertebral Disc Degeneration

Objective

Intervertebral disc degeneration (IDD) contributes to cervical and lumbar diseases. Long noncoding RNAs (lncRNAs) are implicated in IDD. This study explored the mechanism of lncRNA HOTAIR in IDD.

Methods

Normal and degenerative nucleus pulposus (NP) cells were isolated from NP tissues obtained in intervertebral disc surgery. Cell morphology was observed by immunocytochemistry staining and toluidine blue staining. NP cell markers were detected by RT-qPCR. Proliferation was detected by MTT assay. Autophagy-related proteins were detected by Western blot. Autophagosome was observed by monodansylcadaverine fluorescence staining. Apoptosis was detected by TUNEL staining and flow cytometry. si-HOTAIR and/or miR-148a inhibitor was introduced into degenerative NP cells. Binding relationships among HOTAIR, miR-148a, and PTEN were predicted and verified by dual-luciferase reporter assay and RNA pull-down. Finally, IDD rat models were established. Rat caudal intervertebral discs were assessed by HE staining. Expressions of HOTAIR, miR-148a, and PTEN were determined by RT-qPCR.

Results

HOTAIR was highly expressed in degenerative NP cells (p < 0.05). si-HOTAIR inhibited degenerative NP cell apoptosis and autophagy (p < 0.05). HOTAIR upregulated PTEN as a sponge of miR-148a. miR-148a was poorly expressed in degenerative NP cells. miR-148a deficiency partially reversed the inhibition of si-HOTAIR on degenerative NP cell autophagy and apoptosis (all p < 0.05). In vivo assay confirmed that si-HOTAIR impeded autophagy and apoptosis in intervertebral disc tissues, thus improving pathological injury in IDD rats (all p < 0.05).

Conclusion

LncRNA HOTAIR promoted NP cell autophagy and apoptosis via promoting PTEN expression as a ceRNA of miR-148a in IDD.

Oncogenic Role of Exosomal Circular and Long Noncoding RNAs in Gastrointestinal Cancers

Circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs) are differentially expressed in gastrointestinal cancers. These noncoding RNAs (ncRNAs) regulate a variety of cellular activities by physically interacting with microRNAs and proteins and altering their activity. It has also been suggested that exosomes encapsulate circRNAs and lncRNAs in cancer cells. Exosomes are then discharged into the extracellular environment, where they are taken up by other cells. As a result, exosomal ncRNA cargo is critical for cell-cell communication within the cancer microenvironment. Exosomal ncRNAs can regulate a range of events, such as angiogenesis, metastasis, immune evasion, drug resistance, and epithelial-to-mesenchymal transition. To set the groundwork for developing novel therapeutic strategies against gastrointestinal malignancies, a thorough understanding of circRNAs and lncRNAs is required. In this review, we discuss the function and intrinsic features of oncogenic circRNAs and lncRNAs that are enriched within exosomes.

Exploring Prognosis-Associated Biomarkers of Estrogen-Independent Uterine Corpus Endometrial Carcinoma by Bioinformatics Analysis

Background

Uterine corpus endometrial carcinoma (UCEC) is one of the most common female cancers with high incidence and mortality rates. In particular, the prognosis of type II UCEC is poorer than that of type I. However, the molecular mechanism underlying type II UCEC remains unclear.

Methods

RNA-seq data and corresponding clinical information on UCEC patients were downloaded from The Cancer Genome Atlas database, which were then separated into mRNA, lncRNA, and miRNA gene expression profile matrix to perform differentially expressed gene analysis. Weighted gene co-expression network analysis (WGCNA) was used to identify key modules associated with different UCEC subtypes based on mRNA and lncRNA expression matrix. Following that, a subtype-associated competing endogenous RNA (ceRNA) regulatory network was constructed. In addition, GO functional annotation and KEGG pathway analysis were performed on subtype-related DE mRNAs, and STRING database was utilized to predict the interaction network between proteins and their biological functions. The key mRNAs were validated at the protein and gene expression levels in endometrial cancerous tissues as compared with normal tissues.

Results

In summary, we identified 4611 mRNA, 3568 lncRNAs, and 47 miRNAs as differentially expressed between endometrial cancerous tissues and normal endometrial tissues. WGCNA demonstrated that 72 mRNAs and 55 lncRNAs were correlated with pathological subtypes. In the constructed ceRNA regulatory network, LINC02418, RASGRF1, and GCNT1 were screened for their association with poor prognosis of type II UCEC. These DE mRNAs were linked to Wnt signaling pathway, and lower expression of LEF1 and NKD1 predicted advanced clinical stages and worse prognosis of UCEC patients.

Conclusion

This study revealed five prognosis-associated biomarkers that can be used to predict the worst prognosis of type II UCEC.

The Impact of lncRNAs and miRNAs on Apoptosis in Lung Cancer

Apoptosis is a coordinated cellular process that occurs in several physiological situations. Dysregulation of apoptosis has been documented in numerous pathological situations, particularly cancer. Non-coding RNAs regulate apoptosis via different mechanisms. Lung cancer is among neoplastic conditions in which the role of non-coding RNAs in the regulation of apoptosis has been investigated. Non-coding RNAs that regulate apoptosis in lung cancer have functional interactions with PI3K/Akt, PTEN, GSK-3β, NF-κB, Bcl-2, Bax, p53, mTOR and other important cancer-related pathways. Globally, over-expression of apoptosis-blocking non-coding RNAs has been associated with poor prognosis of patients, while apoptosis-promoting ones have the opposite effect. In the current paper, we describe the impact of lncRNAs and miRNAs on cell apoptosis in lung cancer.

SEC61G identified as a prognostic biomarker of head and neck squamous cell carcinoma

Purpose

It is of obvious interest to identify clinical prognosis-related oncogenes in HNSCC (head and neck squamous cell carcinoma).

Methods

Based on the available datasets within the TCGA (The Cancer Genome Atlas) and the GEO (Gene Expression Omnibus) databases, the potential mechanism of action of the SEC61G (SEC61 translocon subunit gamma) gene in HNSCC tumorigenesis was explored by several bioinformatics approaches.

Results

There was a higher expression level of SEC61G in primary HNSCC tumor tissues than in normal tissues. Moreover, highly expressed SEC61G was statistically associated with the poor survival prognosis of HNSCC patients. When HPV (human papilloma virus) was considered, we also observed a relatively lower proportion of “arm-level gain” and “high amplification” types of CNA (copy-number alteration) in the HNSCC-HPV (+) group than in the HNSCC-HPV (−) group. Additionally, we identified SEC61G CAN-correlated genes, such as CCT6A (chaperonin-containing TCP1 subunit 6A) and HUS1 (HUS1 checkpoint clamp component), and found a correlation between SEC61G copy-number segments and prognosis related to overall and progression-free survival intervals of HNSCC patients. Moreover, the molecular regulation mechanisms of the spliceosome, ribosome, proteasome degradation, cell adhesion, and immune infiltration of B and CD8⁺ T cells may contribute to the involvement of SEC61G in the pathogenesis of HNSCC.

Conclusions

The SEC61G gene was identified for the first time as a prognostic biomarker of HNSCC. The detailed underlying mechanism merits further research.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00405-021-06955-7.

A Combined RNA Signature Predicts Recurrence Risk of Stage I-IIIA Lung Squamous Cell Carcinoma

Objective

Recurrence remains the main cause of the poor prognosis in stage I-IIIA lung squamous cell carcinoma (LUSC) after surgical resection. In the present study, we aimed to identify the long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) related to the recurrence of stage I-IIIA LUSC. Moreover, we constructed a risk assessment model to predict the recurrence of LUSC patients.

Methods

RNA sequencing data (including miRNAs, lncRNAs, and mRNAs) and relevant clinical information were obtained from The Cancer Genome Atlas (TCGA) database. The differentially expressed lncRNAs, miRNAs, and mRNAs were identified using the “DESeq2” package of the R language. Univariate Cox proportional hazards regression analysis and Kaplan-Meier curve were used to identify recurrence-related genes. Stepwise multivariate Cox regression analysis was carried out to establish a risk model for predicting recurrence in the training cohort. Moreover, Kaplan-Meier curves and receiver operating characteristic (ROC) curves were adopted to examine the predictive performance of the signature in the training cohort, validation cohort, and entire cohort.

Results

Based on the TCGA database, we analyzed the differentially expressed genes (DEGs) among 27 patients with recurrent stage I-IIIA LUSC and 134 patients with non-recurrent stage I-IIIA LUSC, and identified 431 lncRNAs, 36 miRNAs, and 746 mRNAs with different expression levels. Out of these DEGs, the optimal combination of DEGs was finally determined, and a nine-joint RNA molecular signature was constructed for clinical prediction of recurrence, including LINC02683, AC244517.5, LINC02418, LINC01322, AC011468.3, hsa-mir-6825, AC020637.1, AC027117.2, and SERPINB12. The ROC curve proved that the model had good predictive performance in predicting recurrence. The area under the curve (AUC) of the prognostic model for recurrence-free survival (RFS) was 0.989 at 3 years and 0.958 at 5 years (in the training set). The combined RNA signature also revealed good predictive performance in predicting the recurrence in the validation cohort and entire cohort.

Conclusions

In the present study, we constructed a nine-joint RNA molecular signature for recurrence prediction of stage I-IIIA LUSC. Collectively, our findings provided new and valuable clinical evidence for predicting the recurrence and targeted treatment of stage I-IIIA LUSC.

SEC61G promotes breast cancer development and metastasis via modulating glycolysis and is transcriptionally regulated by E2F1

Breast cancer is the most common cancer in women and its incidence rates are rapidly increasing in China. Understanding the molecular mechanisms of breast cancer tumorigenesis enables the development of novel therapeutic strategies. SEC61G is a subunit of the endoplasmic reticulum translocon that plays critical roles in various tumors. We aimed to investigate the expression and function of SEC61G in breast cancer. By analyzing The Cancer Genome Atlas breast cancer cohort, we found that SEC61G was highly expressed in breast cancer and predicted poor prognosis of breast cancer patients. Overexpression of SEC61G and its prognostic role was also confirmed in the Nanjing Medical University (NMU) breast cancer cohort. Functionally, we demonstrated that knockdown of SEC61G suppressed breast cancer cell proliferation, migration, invasion, and promoted breast cancer cell apoptosis in vitro. Xenograft breast tumor model revealed that knockdown of SEC61G inhibited breast tumor development in vivo. Furthermore, we demonstrated that SEC61G positively regulated glycolysis in breast cancer cells. Mechanistically, we showed that transcription factor E2F1 directly bound to the promoter of SEC61G and regulated its expression in breast cancer cells. SEC61G overexpression antagonized the effect of E2F1 knockdown in regulating breast cancer cell proliferation, invasion, and apoptosis. Finally, we demonstrated that the E2F1/SEC61G axis regulated glycolysis and chemo-sensitivity of Herceptin in breast cancer cells. Taken together, these results of in vitro and in vivo studies demonstrate that SEC61G promotes breast cancer development and metastasis via modulating glycolysis and is transcriptionally regulated by E2F1, which might be utilized as a promising therapeutic target of breast cancer treatment.

High SEC61G expression predicts poor prognosis in patients with Head and Neck Squamous Cell Carcinomas

Background: Overexpression of the membrane protein SEC61 translocon gamma subunit (SEC61G) has been observed in a variety of cancers; however, its role in head and neck squamous cell carcinomas (HNSCC) is unknown. This study aimed to elucidate the relationship between SEC61G and HNSCC based on data from The Cancer Genome Atlas (TCGA) database. Methods: Data for HNSCC patients were collected from TCGA and the expression level of SEC61G was compared between paired HNSCC and normal tissues using the Wilcoxon rank-sum test. The relationship between clinicopathologic features and SEC61G expression was also analyzed using the Wilcoxon rank-sum test and logistic regression. Receiver operating characteristic (ROC) curves were generated to evaluate the value of SEC61G as a binary classifier using the area under the curve (AUC value). The association of clinicopathologic characteristics with prognosis in HNSCC patients was assessed using Cox regression and the Kaplan-Meier methods. A nomogram, based on Cox multivariate analysis, was used to predict the impact of SEC61G on prognosis. Functional enrichment analysis was performed to determine the hallmark pathways associated with differentially expressed genes in HNSCC patients exhibiting high and low SEC61G expression. Results: The expression of SEC61G was significantly elevated in HNSCC tissues compared to normal tissues (P < 0.001). The high expression of SEC61G was significantly correlated with the T stage, M stage, clinical stage, TP53 mutation status, PIK3CA mutation status, primary therapy outcome, and cervical lymph node dissection (all P < 0.05). Meanwhile, ROC curves suggested the significant diagnostic ability of SEC61G for HNSCC (AUC = 0.923). Kaplan-Meier survival analysis showed that patients with HNSCC characterized by high SEC61G expression had a poorer prognosis than patients with low SEC61G expression (hazard ratio = 1.95, 95% confidence interval 1.48-2.56, P < 0.001). Univariate and multivariate analyses revealed that SEC61G was independently associated with overall survival (P = 0.027). Functional annotations indicated that SEC61G is involved in pathways related to translation and regulation of SLITs/ROBOs expression, SRP-dependent co-translational protein targeting to the membrane, nonsense-mediated decay, oxidative phosphorylation, and Parkinson's disease. Conclusion: SEC61G plays a vital role in HNSCC progression and prognosis; it may, therefore, serve as an effective biomarker for the prediction of patient survival.

Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: A Feature Selection Approach

Prostate cancer is one of the most common malignancies in men. It is characterized by a high molecular genomic heterogeneity and, thus, molecular subtypes, that, to date, have not been used in clinical practice. In the present paper, we aimed to better stratify prostate cancer patients through the selection of robust long non-coding RNAs. To fulfill the purpose of the study, a bioinformatic approach focused on feature selection applied to a TCGA dataset was used. In such a way, LINC00668 and long non-coding(lnc)-SAYSD1-1, able to discriminate ERG/not-ERG subtypes, were demonstrated to be positive prognostic biomarkers in ERG-positive patients. Furthermore, we performed a comparison between mutated prostate cancer, identified as "classified", and a group of patients with no peculiar genomic alteration, named "not-classified". Moreover, LINC00920 lncRNA overexpression has been linked to a better outcome of the hormone regimen. Through the feature selection approach, it was found that the overexpression of lnc-ZMAT3-3 is related to low-grade patients, and three lncRNAs: lnc-SNX10-87, lnc-AP1S2-2, and ADPGK-AS1 showed, through a co-expression analysis, significant correlation values with potentially druggable pathways. In conclusion, the data mining of publicly available data and robust bioinformatic analyses are able to explore the unknown biology of malignancies.

LncRNA LINC02418 affects proliferation, migration, invasion, and apoptosis of hepatocellular carcinoma cells by regulating miR-940 expression

BACKGROUND

The long noncoding RNA (lncRNA) LINC02418 is up-regulated in non-small cell lung cancer, lung adenocarcinoma, colorectal cancer, and other tumors, and promotes the development of tumors. However, the role and mechanism of LINC02418 in the occurrence and development of liver cancer are unknown. Target gene prediction with LncBase Predicted v.2 shows that LINC02418 may target miR-940. This study hypothesized that LINC02418 can target and regulate miR-940 to affect the proliferation, migration, invasion, and apoptosis of liver cancer cells, thereby affecting the development of liver cancer.

AIM

To investigate the effect of lncRNA LINC02418 on the proliferation, migration, invasion, and apoptosis of hepatocellular carcinoma cells and the underlying mechanism.

METHODS

RT-qPCR was used to detect the expression levels of LINC02418 and miR-940 in hepatocellular carcinoma cancer tissues and adjacent tissues. After LINC02418 small interfering RNA or miR-940 mimic was transfected into liver cancer HCCLM3 cells, RT-qPCR was used to detect the transfection efficiency, and CCK-8 assay, Transwell assay, flow cytometry, and Western blot were used to detect the effects of LINC02418 down-regulation or miR-940 up-regulation on HCCLM3 cell viability, migration, invasion, and apoptosis, as well as the protein expression levels of CyclinD1, p21, MMP-2, MMP-9, Bcl-2, and Bax. The regulatory relationship between miR-940 and LINC02418 was verified by double luciferase reporter gene assay.

RESULTS

Compared with adjacent tissues, the expression of LINC02418 in hepatocellular carcinoma tissues increased (P < 0.05), while the expression of miR-940 decreased (P < 0.05). Down-regulating LINC02418 or up-regulating miR-940 reduced HCCLM3 cell viability, the number of migrating and invading cells, and the protein expression of CyclinD1, MMP-2, MMP-9, and Bcl-2 (P < 0.05), but increased apoptosis and the protein expression of p21 and Bax (P < 0.05). LINC02418 negatively regulated the expression of miR-940. Down-regulating miR-940 reversed the effects of down-regulating LINC02418 on the proliferation, migration, invasion, and apoptosis of HCCLM3 cells.

CONCLUSION

The expression of LINC02418 is elevated in liver cancer tissues, and down-regulating its expression may inhibit the malignant biological behavior of hepatocellular carcinoma cells by up-regulating miR-940, which could be used as a molecular target for liver cancer treatment.

SEC61G plays an oncogenic role in hepatocellular carcinoma cells

Hepatocellular carcinoma (HCC) is one of the most aggressive malignant diseases and requires more effective prevention and treatment strategies. Mutations or overexpression of endoplasmic reticulum (ER) proteins have been frequently identified in a solid tumor, suggesting that ER proteins play an important role in tumor development. SEC61G, a component of Sec61 complex located in the membrane of the human ER, has been revealed a potential relevance in glioblastoma multiforme. Analyses from TCGA database showed that SEC61G was overexpressed in HCC. Additionally, the expression of SEC61G mRNA was associated with the survival time of HCC patients. We verified that the higher expression of SEC61G in HCC tissues than paracancerous tissues. Moreover, knockdown of SEC61G inhibited cell proliferation and induced cell apoptosis in vitro. Besides, SEC61G was required for cell migration and invasion, conferring a potential role for SEC61G in tumor transfer. Taken together, our results revealed the role of SEC61G in HCC cells. Further detailed understanding of the signaling networks underlying SEC61G involvement in HCC cells would make SEC61G as a viable therapeutic target for pharmaceutical intervention of HCC.

Circ_0001421 facilitates glycolysis and lung cancer development by regulating miR-4677-3p/CDCA3

BACKGROUND

Lung cancer (LC) is a malignant tumor originating in the bronchial mucosa or gland of the lung. Circular RNAs (circRNAs) are proved to be key regulators of tumor progression. However, the regulatory effect of circ_0001421 on lung cancer tumorigenesis remains unclear.

METHODS

The expression levels of circ_0001421, microRNA-4677-3p (miR-4677-3p) and cell division cycle associated 3 (CDCA3) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Methyl thiazolyl tetrazolium (MTT), Transwell and Tumor formation assays were performed to explore the role of circ_0001421 in LC. Glucose consumption and lactate production were examined by a Glucose assay kit and a Lactic Acid assay kit. Western blot was utilized to examine the protein levels of Hexokinase 2 (HK2) and CDCA3. The interaction between miR-4677-3p and circ_0001421 or CDCA3 was confirmed by dual-luciferase reporter assay.

RESULTS

Circ_0001421 was increased in LC tissues and cells, and knockdown of circ_0001421 repressed cell proliferation, migration, invasion and glycolysis in vitro. Meanwhile, circ_0001421 knockdown inhibited LC tumor growth in vivo. Mechanistically, circ_0001421 could bind to miR-4677-3p, and CDCA3 was a target of miR-4677-3p. Rescue assays manifested that silencing miR-4677-3p or CDCA3 overexpression reversed circ_0001421 knockdown-mediated suppression on cell proliferation, migration, invasion and glycolysis in LC cells.

CONCLUSION

Circ_0001421 promoted cell proliferation, migration, invasion and glycolysis in LC by regulating the miR-4677-3p/CDCA3 axis, which providing a new mechanism for LC tumor progression.