Long noncoding RNAs in head and neck squamous cell carcinoma: biological functions and mechanisms

Unveiling NRlncRNAs as prognostic biomarkers and therapeutic targets for head-and-neck squamous cell carcinoma through machine learning

Head-and-neck squamous cell carcinoma (HNSCC) patients often exhibit insensitivity to immunotherapy, leading to treatment failure. Identifying potential biomarkers that can predict prognosis and improve the efficacy of treatment is crucial. In this study, we aimed to identify necroptosis-related long noncoding RNAs (NRlncRNAs) as potential therapeutic targets to improve the prognosis of HNSCC patients. By exploring the Genotype-Tissue Expression Project (GTEx) and the Cancer Genome Atlas (TCGA) databases, we identified NRlncRNAs and developed a risk model comprising 17 NRlncRNAs to predict the prognosis of HNSCC patients and to classify patients into two clusters based on their expression levels. We conducted various analyses, such as the Kaplan-Meier analysis, GSEA and IC50 prediction, to evaluate the differences in sensitivity to immunotherapy between the two clusters. Our findings suggest that NRlncRNAs have potential as therapeutic targets for improving the prognosis of HNSCC patients, and that individualized treatment approaches based on NRlncRNA expression levels can improve the sensitivity of immunotherapy and overall treatment outcomes. This study highlights new perspectives within clinical cancer informatics and provides insight into potential therapeutic strategies for HNSCC patients.

Stemness-related lncRNAs signature as a biologic prognostic model for head and neck squamous cell carcinoma

Cancer stem cells (CSCs) and long non-coding RNAs (lncRNAs) are particularly important for tumor cell growth and migration, and recurrence and drug resistance, including head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to explore stemness-related lncRNAs (SRlncRNAs) that could be used for prognosis of patients with HNSCC. HNSCC RNA sequencing data and matched clinical data were obtained from TCGA database, and stem cell characteristic genes related to HNSCC mRNAsi were obtained from the online database by WGCNA analysis, respectively. Further, SRlncRNAs were obtained. Then, the prognostic model was constructed to forecast patient survival through univariate Cox regression and LASSO-Cox method based on SRlncRNAs. Kaplan-Meier, ROC and AUC were used to evaluate the predictive ability of the model. Moreover, we probed the underlying biological functions, signalling pathways and immune status hidden within differences in prognosis of patients. We explored whether the model could guide personalized treatments included immunotherapy and chemotherapy for HNSCC patients. At last, RT-qPCR was performed to analyze the expressions levels of SRlncRNAs in HNSCC cell lines. A SRlncRNAs signature was identified based on 5 SRlncRNAs (AC004943.2, AL022328.1, MIR9-3HG, AC015878.1 and FOXD2-AS1) in HNSCC. Also, risk scores were correlated with the abundance of tumor-infiltrating immune cells, whereas HNSCC-nominated chemotherapy drugs were considerably different from one another. The final finding was that these SRlncRNAs were abnormally expressed in HNSCCCS according to the results of RT-qPCR. These 5 SRlncRNAs signature, as a potential prognostic biomarker, can be utilized for personalized medicine in HNSCC patients.

Potentials of lncRNA-miRNA-mRNA networks as biomarkers for laryngeal squamous cell carcinoma

Chemoresistance, radioresistance, and facile spreading of laryngeal squamous cell carcinoma (LSCC) make the practically clinical treatment invalid. Such dismal outcome mainly originates from the lack of effective biomarkers which are highly desirable to understand the pathogenesis of LSCC, and strives to find promising novel biomarkers to improve early screening, effective treatment, and prognosis evaluation in LSCC. Recently, long non-coding RNAs (lncRNAs), a kind of non-coding RNAs longer than 200 nucleotides, can participate in the process of tumorigenesis and progression through many regulatory modalities, such as epigenetic transcriptional regulation and post-transcriptional regulation. Meanwhile, microRNAs (miRNAs, miRs), essentially involved in the post-transcriptional regulation of gene expression, are aberrantly expressed in cancer-related genomic regions or susceptible sites. An increasing number of studies have shown that lncRNAs are important regulators of miRNAs expression in LSCC, and that miRNAs can also target to regulate the expression of lncRNAs, and they can target to regulate downstream messenger RNAs (mRNAs) transcriptionally or post-transcriptionally, thereby affecting various physiopathological processes of LSCC. Complex cross-regulatory networks existing among lncRNAs, miRNAs, and mRNAs can regulate the tumorigenesis and development of LSCC. Such networks may become promising biomarkers and potential therapeutic targets in the research field of LSCC. In this review, we mainly summarize the latest research progress on the regulatory relationships among lncRNAs, miRNAs, and downstream mRNAs, and highlight the potential applications of lncRNA-miRNA-mRNA regulatory networks as biomarkers for the early diagnosis, epithelial-mesenchymal transition (EMT) process, chemoresistance, radioresistance, and prognosis of LSCC, aiming to provide important clues for understanding the pathogenesis of LSCC and developing new diagnostic and therapeutic strategies.

Suppression of Long Noncoding RNA SNHG1 Inhibits the Development of Hypopharyngeal Squamous Cell Carcinoma via Increasing PARP6 Expression

Purpose

This study aimed to explore the function and molecular mechanism of long noncoding RNA Small Nucleolar RNA Host Gene 1 (SNHG1) in the development of hypopharyngeal squamous cell carcinoma (HSCC).

Methods

Human HSCC cell line FaDu was used in this study. Cell viability and apoptosis were detected using CCK-8 assay and flow cytometry, respectively. Cell migration and invasion were measured by Transwell assay. The expression of PARP6, XRCC6, β-catenin, and EMT-related proteins (E-cadherin and N-cadherin) were determined using western blotting. Moreover, the regulatory relationship between SNHG1 and PARP6 was investigated. Furthermore, the effects of the SNHG1/PARP6 axis on tumorigenicity were explored in vivo.

Results

Suppression of SNHG1 suppressed the viability, migration, and invasion but promoted apoptosis of FaDu cells in vitro (P < 0.01). PARP6 is a target of SNHG1, which was upregulated by SNHG1 knockdown in FaDu cells (P < 0.01). SNHG1 suppression and RARP6 overexpression inhibited FaDu cell proliferation, migration, and invasion (P < 0.05). SNHG1 suppression and RARP6 overexpression also inhibited tumorigenicity of HSCC in vivo. Furthermore, the protein expression of E-cadherin was significantly increased and that of N-cadherin, β-catenin, and XRCC6 was dramatically decreased in HSCC after SNHG1 suppression or/and RARP6 overexpression both in vitro and in vivo (P < 0.01).

Conclusions

SNHG1 silencing inhibits HSCC malignant progression via upregulating PARP6. XRCC6/β-catenin/EMT axis may be a possible downstream mechanism of the SNHG1/PARP6 axis in HSCC. SNHG1/PARP6 can be used as a promising target for the treatment of HSCC.

Local and Systemic Delivery of the BimS Gene Nano-Complex for Efficient Oral Squamous Cell Carcinoma Therapy

Purpose

Methods

Results

Conclusion

Long non-coding RNA human leucocyte antigen complex group-18 HCG18 (HCG18) promoted cell proliferation and migration in head and neck squamous cell carcinoma through cyclin D1-WNT pathway

Emerging evidence has demonstrated that long noncoding RNA (lncRNAs) play a vital role in the development of head and neck squamous cell carcinoma (HNSCC); however, the biological effects and underlying mechanisms of human leukocyte antigen complex group-18 HCG18 (HCG18) have not yet been reported in HNSCC. In this study, we detected the expression of the HCG18 in HNSCC cell lines and patient tissues. We observed that HCG18 was upregulated in HNSCC patient tissues and cell lines. Furthermore, silencing of HCG18 significantly inhibited proliferation, migration, and invasion of HNSCC cells, whereas the opposite effects were detected in the HCG18-overexpressed group. We also found that HCG18 directly binds to the functional protein cyclin D1. Upregulated cyclin D1 reversed the inhibitory effects of HCG18 in HNSCC cell lines and activated the WNT pathway-related proteins (AXIN2, survivin, c-Myc, and β-catenin) simultaneously. Knockdown of cyclin D1 could accelerate the inhibitory effects of HCG18 and decrease the expression of AXIN2, survivin, c-Myc, and β-catenin. This indicated that lncRNA HCG18 might be involved in the tumorigenesis of HNSCC via the cyclin D1-WNT pathway. These results suggest that lncRNA HCG18 could act as a promising prognostic biomarker and potential therapeutic target in HNSCC patients.

Identification and in vitro validation of prognostic lncRNA signature in head and neck squamous cell carcinoma

Long non-coding RNAs (lncRNAs) are promising cancer prognostic markers. However, the clinical significance of lncRNA signatures in evaluating overall survival (OS) outcomes of head and neck squamous cell carcinoma (HNSCC) has not been explored. This study aimed to assess the significance of lncRNA in HNSCC and to develop a lncRNA signature related to OS in HNSCC. LncRNA expression matrices were retrieved from the Cancer Genome Atlas (TCGA) data. Least Absolute Shrinkage and Selection of the Operator (LASSO), univariate and multivariate Cox regression were used for establishing a prognostic model. In vitro experiments were carried out to demonstrate the biological role of lncRNA. A prognosis model based on 7 DElncRNAs was finally established.The patients were then divided into high-risk and low-risk groups. Relative to the low-risk group, overall survival times for patients in the high-risk group were significantly low (P=2.466e−07). Risk score remained an independent prognostic factor in univariate (HR=1.329, 95%CI=1.239−1.425, p < 0.001) and multivariate (HR=1.279, 95%CI=1.184−1.382, p < 0.001) Cox regression analyses. The area under the curve (AUC) of the signature was as high as 0.78. Expressions of FOXD2-AS1  in tumor tissues were elevated, and significantly correlated with OS (P=0.008). FOXD2-AS1 silencing then significantly reduced HNSCC cell proliferation, invasion, and migration. In conclusion, a lncRNA signature was established for HNSCC prognostic prediction and FOXD2-AS1 was identified as an HNSCC oncogene.

Telomeric-Like Repeats Flanked by Sequences Retrotranscribed from the Telomerase RNA Inserted at DNA Double-Strand Break Sites during Vertebrate Genome Evolution

Interstitial telomeric sequences (ITSs) are stretches of telomeric-like repeats located at internal chromosomal sites. We previously demonstrated that ITSs have been inserted during the repair of DNA double-strand breaks in the course of evolution and that some rodent ITSs, called TERC-ITSs, are flanked by fragments retrotranscribed from the telomerase RNA component (TERC). In this work, we carried out an extensive search of TERC-ITSs in 30 vertebrate genomes and identified 41 such loci in 22 species, including in humans and other primates. The fragment retrotranscribed from the TERC RNA varies in different lineages and its sequence seems to be related to the organization of TERC. Through comparative analysis of TERC-ITSs with orthologous empty loci, we demonstrated that, at each locus, the TERC-like sequence and the ITS have been inserted in one step in the course of evolution. Our findings suggest that telomerase participated in a peculiar pathway of DNA double-strand break repair involving retrotranscription of its RNA component and that this mechanism may be active in all vertebrate species. These results add new evidence to the hypothesis that RNA-templated DNA repair mechanisms are active in vertebrate cells.

The Role and Mechanism of MALAT1 Long Non-Coding RNA in the Diagnosis and Treatment of Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most common malignant tumor of the head and neck. HNSCC mainly affects the oral cavity and the laryngeal, laryngopharyngeal, and oropharyngeal tracts. The high incidence, hidden onset, low survival rate, and unsatisfactory effects of treatment effect underscore the importance of identify the mechanisms of HNSCC occurrence and development. Although there is a very urgent need for early diagnosis and treatment, there are currently no reliable early HNSCC diagnosis biomarkers or effective treatment targets. Long non-coding RNA (lncRNA) is widely involved in biological processes, especially as a key regulator of tumorigenesis and development. Lung adenocarcinoma metastasis-associated transcript 1 (MALAT1) is an important member of the lncRNA family that can regulate the occurrence and development of a variety of malignant tumors and is anticipated to be an ideal marker for early tumor diagnosis and an effective therapeutic target. Here, we review the research progress into the role of MALAT1 in the diagnosis and treatment of HNSCC and its regulatory mechanism.

Long noncoding RNA SLC9A3‑AS1 increases E2F6 expression by sponging microRNA‑486‑5p and thus facilitates the oncogenesis of nasopharyngeal carcinoma

Long noncoding RNA SLC9A3 antisense RNA 1 (SLC9A3-AS1) plays a central role in lung cancer; yet, its functions in nasopharyngeal carcinoma (NPC) have not been elucidated. The present study revealed the roles of SLC9A3-AS1 in NPC and dissected the mechanisms downstream of SLC9A3-AS1. SLC9A3-AS1 levels in NPC were assessed by applying RT-qPCR. The modulatory role of SLC9A3-AS1 interference on NPC cells was examined using numerous functional experiments. High expression of SLC9A3-AS1 was observed in NPC samples. Patients with NPC with a high level of SLC9A3-AS1 experienced a shorter overall survival than those with a low SLC9A3-AS1 level. Loss of SLC9A3-AS1 reduced NPC cell proliferation, colony formation, migration, and invasion but induced cell apoptosis in vitro. Animal experiments further revealed that the depletion of SLC9A3-AS1 hindered NPC tumour growth in vivo. As a competitive endogenous RNA, SLC9A3-AS1 sponged microRNA-486-5p (miR-486-5p), consequently upregulating E2F transcription factor 6 (E2F6). Finally, the effects of SLC9A3-AS1 silencing on NPC cells were reversed by inhibiting miR-486-5p or overexpressing E2F6. In summary, SLC9A3-AS1 exerted carcinogenic effects on NPC cells by adjusting the miR-486-5p/E2F6 axis. Accordingly, the newly identified SLC9A3-AS1/miR-486-5p/E2F6 pathway may offer attractive therapeutic targets for future development.

Long Non-Coding RNA UBA6-AS1 Promotes the Malignant Properties of Glioblastoma by Competitively Binding to microRNA-760 and Enhancing Homeobox A2 Expression

Background

The dysregulation of long non-coding RNAs is a frequent finding in glioblastoma (GBM) and is considered as a crucial mechanism contributing to GBM oncogenesis and progression. The biological roles and underlying mechanisms of action of UBA6 antisense RNA 1 (UBA6-AS1) in GBM have been rarely investigated. Therefore, the aim of the present study was to investigate in detail the role of UBA6-AS1 in the modulation of the malignant properties of GBM and explore the possible underlying mechanism(s).

Methods

The expression of UBA6-AS1 in GBM was determined via reverse transcription-quantitative PCR. Cell Counting Kit-8 assay, flow cytometric analysis, Transwell migration and invasion assays, and in vivo tumorigenicity assay were applied to elucidate the biological effects of UBA6-AS1 on GBM cells. The possible biological events associated with UBA6-AS1 were investigated by luciferase reporter, RNA immunoprecipitation (RIP) and rescue assays.

Results

UBA6-AS1 was overexpressed in GBM, which was consistent with the data from The Cancer Genome Atlas database. In the case of UBA6-AS1 depletion, GBM cell proliferation, migration and invasion were notably decreased and cell apoptosis was enhanced in vitro. Additionally, knockdown of UBA6-AS1 suppressed the proliferation of GBM cells in vivo. Mechanistically, UBA6-AS1 functioned as a competing endogenous RNA by adsorbing miR-760 and, consequently, upregulating homeobox A2 (HOXA2) expression. Rescue experiments demonstrated that the UBA6-AS1 silencing-mediated regulatory effects on GBM cells were reversed by the decrease of miR-760 or restoration of HOXA2 expression.

Conclusion

Therefore, the results of the present study revealed that UBA6-AS1 promoted the malignant progression of GBM via targeting the miR-760/HOXA2 axis, thereby representing a promising effective target for the treatment of GBM.