Identification and validation a TGF-β-associated long non-coding RNA of head and neck squamous cell carcinoma by bioinformatics method

Crosstalk between CAFs and tumour cells in head and neck cancer

Head and neck squamous cell carcinomas (HNSCCs) are amongst the most aggressive, complex, and heterogeneous malignancies. The standard of care treatments for HNC patients include surgery, radiotherapy, chemotherapy, or their combination. However, around 50% do not benefit while suffering severe toxic side effects, costing the individuals and society. Decades have been spent to improve HNSCC treatment outcomes with only limited success. Much of the research in HNSCC treatment has focused on understanding the genetics of the HNSCC malignant cells, but it has become clear that tumour microenvironment (TME) plays an important role in the progression as well as treatment response in HNSCC. Understanding the crosstalk between cancer cells and TME is crucial for inhibiting progression and treatment resistance. Cancer-associated fibroblasts (CAFs), the predominant component of stroma in HNSCC, serve as the primary source of extra-cellular matrix (ECM) and various pro-tumoral composites in TME. The activation of CAFs in HNSCC is primarily driven by cancer cell-secreted molecules, which in turn induce phenotypic changes, elevated secretive status, and altered ECM production profile. Concurrently, CAFs play a pivotal role in modulating the cell cycle, stemness, epithelial-mesenchymal transition (EMT), and resistance to targeted and chemoradiotherapy in HNSCC cells. This modulation occurs through interactions with secreted molecules or direct contact with the ECM or CAF. Co-culture and 3D models of tumour cells and other TME cell types allows to mimic the HNSCC tumour milieu and enable modulating tumour hypoxia and reprograming cancer stem cells (CSC). This review aims to provide an update on the development of HNSCC tumour models comprising CAFs to obtain better understanding of the interaction between CAFs and tumour cells, and for providing preclinical testing platforms of current and combination with emerging therapeutics.

TTC7B is a new prognostic biomarker in head and neck squamous cell carcinoma linked to immune infiltration and ferroptosis

OBJECTIVE

To investigate the expression of TTC7B and its prognostic significance, biological roles, and impact on the immune system in patients with head and neck squamous cell carcinoma (HNSCC).

MATERIALS AND METHODS

Clinical and genomic data were obtained from TCGA (The Cancer Genome Atlas), GEO (Gene Expression Omnibus), GEPIA2 (Gene Expression Profiling Interactive Analysis 2.0), and TIMER2.0 (Tumor Immune Estimation Resource 2.0) databases. R software was utilized to process the retrieved data. qPCR and immunohistochemical assays were performed to validate the findings obtained from the databases.

RESULTS

High expression of TTC7B was observed in HNSCC, and this heightened expression is significantly associated with reduced overall survival (OS) in patients, making it an independent risk factor impacting OS. TTC7B is correlated with focal adhesions and cell migration pathways based on functional enrichment analysis. CIBERSORT analysis and TIMER2.0 show a positive link between TTC7B and multiple immune cells, particularly macrophages. Pearson's analysis reveals a significant correlation between TTC7B and ferroptosis-related genes.

CONCLUSION

In all, TTC7B could serve as a promising prognostic indicator of HNSCC, and is closely associated with focal adhesions, immune infiltration, and ferroptosis.

Tumor-Suppressive and Immunomodulating Activity of miR-30a-3p and miR-30e-3p in HNSCC Cells and Tumoroids

Head and neck squamous cell carcinomas (HNSCCs) are heterogeneous tumors, well known for their frequent relapsing nature. To counter recurrence, biomarkers for early diagnosis, prognosis, or treatment response prediction are urgently needed. miRNAs can profoundly impact normal physiology and enhance oncogenesis. Among all of the miRNAs, the miR-30 family is frequently downregulated in HNSCC. Here, we determined how levels of the 3p passenger strands of miR-30a and miR-30e affect tumor behavior and clarified their functional role in LA-HNSCC. In a retrospective study, levels of miR-30a-3p and miR-30e-3p were determined in 110 patients and correlated to overall survival, locoregional relapse, and distant metastasis. miR-30a/e-3p were expressed in HNSCC cell lines and HNSCC patient-derived tumoroids (PDTs) to investigate their effect on tumor cells and their microenvironment. Both miRNAs were found to have a prognosis value since low miR-30a/e-3p expression correlates to adverse prognosis and reduces overall survival. Low expression of miR-30a/e-3p is associated with a shorter time until locoregional relapse and a shorter time until metastasis, respectively. miR-30a/e-3p expression downregulates both TGF-βR1 and BMPR2 and attenuates the survival and motility of HNSCC. Results were confirmed in PDTs. Finally, secretomes of miR-30a/e-3p-transfected HNSCC activate M1-type macrophages, which exert stronger phagocytic activities toward tumor cells. miR-30a/e-3p expression can discriminate subgroups of LA-HNSCC patients with different prognosis, making them good candidates as prognostic biomarkers. Furthermore, by targeting members of the TGF-β family and generating an immune-permissive microenvironment, they may emerge as an alternative to anti-TGF-β drugs to use in combination with immune checkpoint inhibitors.

Integrated Machine Learning and Single-Sample Gene Set Enrichment Analysis Identifies a TGF-Beta Signaling Pathway Derived Score in Headneck Squamous Cell Carcinoma

Background

The TGF-β signaling pathway is clinically predictive of pan-cancer. Nevertheless, its clinical prognosis and regulation of immune microenvironment (TME) characteristics as well as the prediction of immunotherapy efficacy need to be further elucidated in head and neck squamous cell carcinoma.

Method

At first, we summarized TGF-β related genes from previous published articles, used ssGSEA to establish the TGF-β risk score. Considering the complexity of its clinical application, we improved it with the LASSO-COX algorithm to construct the model. In addition, we explored the predictive efficacy of TGF-β risk score in the observation of TME phenotype and immunotherapy effect. Finally, the potency of TGF-β risk score in adjusting precise treatment of HNSC was evaluated.

Results

We systematically established TGF-β risk score with multi-level predictive ability. TGF-β risk score was employed to predict the tumor microenvironment status, which was negatively associated with NK cells but positively related to macrophages and fibroblasts. It reveals that patients with high TGF-β risk score predict “cold” TME status. In addition, higher risk scores indicate higher sensitivity to immunotherapy.

Conclusion

We first construct and validate TGF-β characteristics that can predict immune microenvironment phenotypes and immunotherapeutic effect in multiple datasets. Noteworthy, TGF-β risk score is helpful for individualized precise treatment of patients with the head and neck squamous cell carcinoma.

The role of long noncoding RNAs as regulators of the epithelial–Mesenchymal transition process in oral squamous cell carcinoma cells

Oral squamous cell carcinoma (OSCC) is a highly invasive and relatively prevalent cancer, accounting for around 3% of all cancers diagnosed. OSCC is associated with bad outcomes, with only 50% overall survival (OS) after five years. The ability of OSCC to invade local and distant tissues relies on the induction of the epithelial–mesenchymal transition (EMT), wherein epithelial cells shed their polarity and cell-to-cell contacts and acquire mesenchymal characteristics. Consequently, a comprehensive understanding of how tumor cell EMT induction is regulated has the potential of direct attempts to prevent tumor progression and metastasis, resulting in better patient outcomes. Several recent studies have established the significance of particular long noncoding RNAs (lncRNAs) in the context of EMT induction. Moreover, lncRNAs regulate a vast array of oncogenic pathways. With a focus on the mechanisms by which the underlined lncRNAs shape the metastatic process and a discussion of their potential utility as clinical biomarkers or targets for therapeutic intervention in patients with OSCC, the present review thus provides an overview of the EMT-related lncRNAs that are dysregulated in OSCC.

A Novel CXCR4-Targeted Diphtheria Toxin Nanoparticle Inhibits Invasion and Metastatic Dissemination in a Head and Neck Squamous Cell Carcinoma Mouse Model

Loco-regional recurrences and metastasis represent the leading causes of death in head and neck squamous cell carcinoma (HNSCC) patients, highlighting the need for novel therapies. Chemokine receptor 4 (CXCR4) has been related to loco-regional and distant recurrence and worse patient prognosis. In this regard, we developed a novel protein nanoparticle, T22-DITOX-H6, aiming to selectively deliver the diphtheria toxin cytotoxic domain to CXCR4⁺ HNSCC cells. The antimetastatic effect of T22-DITOX-H6 was evaluated in vivo in an orthotopic mouse model. IVIS imaging system was utilized to assess the metastatic dissemination in the mouse model. Immunohistochemistry and histopathological analyses were used to study the CXCR4 expression in the cancer cells, to evaluate the effect of the nanotoxin treatment, and its potential off-target toxicity. In this study, we report that CXCR4⁺ cancer cells were present in the invasive tumor front in an orthotopic mouse model. Upon repeated T22-DITOX-H6 administration, the number of CXCR4⁺ cancer cells was significantly reduced. Similarly, nanotoxin treatment effectively blocked regional and distant metastatic dissemination in the absence of systemic toxicity in the metastatic HNSCC mouse model. The repeated administration of T22-DITOX-H6 clearly abrogates tumor invasiveness and metastatic dissemination without inducing any off-target toxicity. Thus, T22-DITOX-H6 holds great promise for the treatment of CXCR4⁺ HNSCC patients presenting worse prognosis.

The role of long non-coding RNAs in the pathogenesis of head and neck squamous cell carcinoma

Head and neck cancers are a heterogeneous collection of malignancies of the upper aerodigestive tract, salivary glands, and thyroid. However, the molecular mechanisms underlying the carcinogenesis of head and neck squamous cell carcinomas (HNSCCs) remain poorly understood. Over the past decades, overwhelming evidence has demonstrated the regulatory roles of long non-coding RNAs (lncRNAs) in tumorigenesis, including HNSCC. Notably, these lncRNAs have vital roles in gene regulation and affect various aspects of cellular homeostasis, including proliferation, survival, and metastasis. They exert regulating functions by interacting with nucleic acids or proteins and affecting cancer cell signaling. LncRNAs represent a burgeoning field of cancer research, and we are only beginning to understand the importance and complicity of lncRNAs in HNSCC. In this review, we summarize the deregulation and function of lncRNAs in human HNSCC. We also review the working mechanism of lncRNAs in HNSCC pathogenesis and discuss the potential application of lncRNAs as diagnostic/prognostic tools and therapeutic targets in human HNSCC.

Exosomal hsa_circ_0125310 promotes cell proliferation and fibrosis in diabetic nephropathy via sponging miR-422a and targeting the IGF1R/p38 axis

Diabetic nephropathy (DN) is still on the rise worldwide, and millions of patients have to be treated through dialysis or transplant because of kidney failure caused by DN. Recent reports have highlighted circRNAs in the treatment of DN. Herein, we aimed to investigate the mechanism by which high glucose‐induced exo‐circ_0125310 promotes diabetic nephropathy progression. circ_0125310 is highly expressed in diabetic nephropathy and exosomes isolated from high glucose‐induced mesangial cells (MCs). High glucose‐induced exosomes promote the proliferation and fibrosis of MCs. However, results showed that the effects of exosomes on MCs can be reversed by the knockdown of circ_0125310. miR‐422a, which targets IGF1R, was the direct target of circ_0125310. circ_0125310 regulated IGF1R/p38 axis by sponging miR‐422a. Exo‐circ_0125310 increased the luciferase activity of the WT‐IGF1R reporter in the dual‐luciferase reporter gene assays and upregulated the expression level of IGF1R and p38. Finally, in vivo research indicated that the overexpression of circ_0125310 promoted the diabetic nephropathy progression. Above results demonstrated that the high glucose‐induced exo‐circ_0125310 promoted cell proliferation and fibrosis in diabetic nephropathy via sponging miR‐422a and targeting the IGF1R/p38 axis.

LncRNA EPB41L4A-AS2 represses Nasopharyngeal Carcinoma Metastasis by binding to YBX1 in the Nucleus and Sponging MiR-107 in the Cytoplasm

Nasopharyngeal carcinoma (NPC) is known for its potential to progress to the lymph nodes and distant metastases at an early stage. As an important regulator in tumorigenesis biological processes, the functions of lncRNA in NPC tumor development remain largely unclear. In this research, the expression of EPB41L4A-AS2 in NPC tissues and cells was analyzed via real-time quantitative polymerase chain reaction (qRT-PCR). CCK8, colony formation, and EDU experiments were used to determine the viability of NPC cells. Transwell and wound healing assays were performed to test NPC cell migration and invasion. RNA pull-down and mass spectrometry analysis were used to identify potential binding proteins. Then, a popliteal lymph node metastasis model was established to test NPC metastasis. EPB41L4A-AS2 is repressed by transforming growth factor-beta, which is downregulated in NPC cells and tissue. It is associated with the presence of distant metastasis and adverse outcomes. The univariate and multivariate survival assays confirmed that EPB41L4A-AS2 expression was an independent predictor of progression-free survival (PFS) in patients with NPC. Biological analyses showed that overexpression of EPB41L4A-AS2 reduced the metastasis and invasion of NPC in vitro and in vivo, but had no significant effect on cell proliferation. Mechanistically, in the nucleus we identified that EPB41L4A-AS2 relies on binding to YBX1 to reduce the stability of Snail mRNA to enhance the expression of E-cadherin and reverse the progression of epithelial-to-mesenchymal transition (EMT). In the cytoplasm, we found that EPB41L4A-AS2 blocked the invasion and migration of NPC cells by promoting LATS2 expression via sponging miR-107. In a whole, the findings of this study help to further understand the metastasis mechanism of NPC and could help in the prevention and treatment of NPC metastasis.

Long noncoding RNA LINC00657 inhibits cervical cancer development by sponging miR-20a-5p and targeting RUNX3

Long noncoding RNAs act essential regulators in cervical cancer progression. Our study aimed to investigate the underlying function and molecular mechanisms of LINC00657 in cervical cancer. QRT-PCR results indicated that LINC00657 was significantly decreased in cervical cancer. Gain-and loss-of-function experiments were performed in SiHa and HeLa. Functional assays demonstrated that LINC00657 inhibited cervical cancer cell growth, migration and invasion. Moreover, miR-20a-5p was confirmed as a target of LINC00657. Furthermore, miR-20a-5p promoted the development of cervical cancer via targeting RUNX3. DR5 acts as a vital promoter in activating NK cells and is a downstream target of RUNX3. We found that LINC00657 overexpression promoted the cytotoxic activity of NK cells via regulating RUNX3/DR5 axis. Therefore, LINC00657 suppressed cervical cancer progression via inducing miR-20a-5p/RUNX3/DR5 mediated NK cell tolerance. In conclusion, LINC00657 was identified as a novel tumor-suppressor in cervical cancer and could function as a potential therapeutic target for clinical treatment.

Clinical Significance of Integrin Subunit Beta 4 in Head and Neck Squamous Cell Carcinoma

Background: The expression level and clinical significance of integrin subunit beta 4 (ITGB4) in head and neck squamous cell carcinoma (HNSCC) remain unclear. Materials and Methods: Expression of ITGB4 in HNSCC tissues were evaluated by calculating standard mean differences (SMDs) based on gene chips, RNA-seq, and immunohistochemistry data (n = 2330) from multiple sources. Receiver operating characteristic (ROC) curves were used to detect the ability of ITGB4 to distinguish HNSCC from non-HNSCC samples. The relationship between the expression level of ITGB4 and clinical parameters was evaluated by calculating SMDs. Results: Identical results of mRNA and protein levels indicated remarkable up-expression of ITGB4 in HNSCC tissues. Further ROC curves showed that ITGB4 could distinguish HNSCC from non-HNSCC samples. Genetic alteration analysis of ITGB4 in HNSCC indicated that overexpression of ITGB4 in HNSCC was likely not owing to genetic alteration of ITGB4. Moreover, ITGB4 overexpression level may be correlated with clinical T stage. Conclusion: ITGB4 likely plays an essential role in HNSCC occurrence based on our study and its potential diagnostic value is worthy of further exploration in the future.

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

Head and neck squamous cell carcinoma (HNSCC) is the primary malignant tumor of the oral cavity, larynx, nasopharynx, esophagus and tongue. Although several novel therapeutic methods for HNSCC have been developed, the final therapeutic effect on the patient is still not satisfactory. Thus, it is imperative that scientists identify novel distinguishable markers with specific molecular characteristics that can be used in therapeutic and prognostic evaluation. Previous reports have shown that long noncoding RNAs (lncRNAs) are important regulators of gene expression in many cancers, including head and neck squamous cell carcinomas. Translational studies of lncRNAs in HNSCC are urgently required before their application as a treatment can be realized. We aimed to address the most relevant findings on lncRNAs as biomarkers or treatment targets in head and neck squamous cell carcinoma and to summarize their discovered pathways and mechanisms of action to reveal the possible future applications of these novel biomarkers in clinical translational research.

Long non-coding RNAs and TGF-β signaling in cancer

Cancer is driven by genetic mutations in oncogenes and tumor suppressor genes and by cellular events that develop a misregulated molecular microenvironment in the growing tumor tissue. The tumor microenvironment is guided by the excessive action of specific cytokines including transforming growth factor-β (TGF-β), which normally controls embryonic development and the homeostasis of young or adult tissues. As a consequence of the genetic alterations generating a given tumor, TGF-β can preserve its homeostatic function and attempt to limit neoplastic expansion, whereas, once the tumor has progressed to an aggressive stage, TGF-β can synergize with various oncogenic stimuli to facilitate tumor invasiveness and metastasis. TGF-β signaling mechanisms via Smad proteins, various ubiquitin ligases, and protein kinases are relatively well understood. Such mechanisms regulate the expression of genes encoding proteins or non-coding RNAs. Among non-coding RNAs, much has been understood regarding the regulation and function of microRNAs, whereas the role of long non-coding RNAs is still emerging. This article emphasizes TGF-β signaling mechanisms leading to the regulation of non-coding genes, the function of such non-coding RNAs as regulators of TGF-β signaling, and the contribution of these mechanisms in specific hallmarks of cancer.

Increased levels of long noncoding RNA LINC00691 correlate with poor prognosis in non-small-cell lung cancer patients

Background

Although long intergenic non‐protein coding RNA 691 (LINC00691) has been functionally identified in several tumors, the association between LINC00691 and non–small‐cell lung cancer (NSCLC) has not been reported. The objective of our study was to explore the clinical significance of LINC00691 in NSCLC.

Methods

RT‐PCR was performed to detect LINC00691 levels in 177 pairs of human NSCLC tissues and matched normal lung specimens. A chi‐squared test was used to analyze the possible influence of LINC00691 on the clinical progress of NSCLC. Kaplan‐Meier methods were used to determine differences in patient survival. The prognostic value of survival variables was evaluated using univariate and multivariate analyses.

Results

We found that LINC00691 levels were increased in tumor specimens compared with matched normal lung tissues (P < .01). Increased LINC00691 levels correlated with lymph node metastasis (P = .025) and advanced TNM stage (P = .002) in NSCLC patients. Moreover, clinical investigations revealed that NSCLC patients with high LINC00691 expression had a shorter overall survival than those with low LINC00691 expression (P = .0042). Finally, Cox regression assays confirmed LINC00691 as an independent prognostic factor for NSCLC patients.

Conclusions

The aberrant expression of LINC00691 may function as a reliable marker for the progression and prognosis of NSCLC in patients.

Circular RNA circ_0001368 inhibited growth and invasion in renal cell carcinoma by sponging miR-492 and targeting LATS2

Circular RNAs (circRNAs) act as essential regulators in the tumorigenesis of renal cell carcinoma. Our study aims to investigate the underlying function and the molecular mechanisms of circ_0001368 in renal cell carcinoma. The qRT-PCR results indicate that the circ_0001368 expression level was downregulated in the carcinoma cells and tissues of the renal cell. circ_0001368 weakened cell proliferation and invasion in the ACHN and 786-O cells. The luciferase reporter assay showed that circ_0001368 functioned as an endogenous sponge for miR-492. The transwell and CCK8 assays showed that circ_0001368 suppressed cell proliferation and invasion in the ACHN and 786-O cells. Large tumor suppressor kinase 2 (LATS2) was confirmed by Targetscan as a target gene of miR-492. The overexpression of LATS2 repressed the growth and invasion of ACHN and 786-O cells. circ_0001368 upregulated the LATS2 expression and suppressed ACHN and 786-O cell growth and invasion by sponging miR-492. circ_0001368 suppressed the proliferation ability of 786-O in vivo. In conclusion, circ_0001368 was identified in this study as a novel anti-tumor RNA in renal cell carcinoma and can function as a potential therapeutic target for renal cell carcinoma treatment.

Clinical prognostic implications of EPB41L4A expression in multiple myeloma

Background: Multiple myeloma (MM) is one of the most common incurable malignancies in malignant plasma cell disease. EPB41L4A is a target gene for the Wnt/β-catenin pathway, which is closely related to the survival of multiple myeloma cells. However, there is currently no research report on the prognostic significance of the EPB41L4A gene in MM. Methods: We studied the biological significance and prognostic significance of EPB41L4A expression in MM by integrating 1956 MM samples from 7 datasets, and explored the relationship between EPB41L4A expression and MM ISS stage, molecular type, therapeutic response and survival. Results: We found that the expression level of EPB41L4A is inversely proportional to the copy number of 1q21 (P = 3.4e-13). EPB41L4A was low expressed in MAF, MMSET and proliferating molecular typing patients (P <= 0.001). High expression of EPB41L4A can predict good survival in MM (EFS: P < 0.0001; OS: P < 0.0001). We found that patients with relapsed MM had lower expression levels of EPB41L4A than those without recurrence (P = 0.0039). We also found that EPB41L4A can predict the prognosis of MM patients may be related to DNA replication. These results indicate that the initial expression level of EPB41L4A can predict the prognosis of MM patients. Conclusions: We found that the high expression of EPB41L4A predicts good survival level in MM.

Long non-coding RNA EPB41L4A-AS2 suppresses progression of ovarian cancer by sequestering microRNA-103a to upregulate transcription factor RUNX1T1

NEW FINDINGS

What is the central question of this study? What is the specific mechanism by which EPB41L4A-AS2 exerts a regulatory role in ovarian cancer? What is the main finding and its importance? Overexpressed EPB41L4A-AS2 inhibited cell proliferation, migration and invasion in ovarian cancer by upregulating RUNX1T1 through downregulation of miR-103a. This study provides new insight into the role of EPB41L4A-AS2 in ovarian cancer.

ABSTRACT

Ovarian cancer (OC) is a malignant tumour with a poor prognosis. Emerging evidence has shown that long non-coding RNAs (lncRNAs) are regulators that can be used for prognosis, diagnosis and targeted therapy of cancers. Therefore, our purpose was to investigate the possible regulatory role of the lncRNA EPB41L4A-AS2 in the progression of OC. Initially, EPB41L4A-AS2 expression was determined in OC tissues and matched paracancerous tissues. Then the RNA crosstalk among EPB41L4A-AS2, miR-103a and RUNX1T1 was determined. Subsequently, the expression of EPB41L4A-AS2, miR-103a and RUNX1T1 was up- or downregulated by exogenous transfection in SK-OV-3 cells to investigate their roles in the proliferation, migration, colony formation and invasion of OC cells. Further, the tumour formation ability of nude mice was tested in vivo. EPB41L4A-AS2 was poorly expressed in OC tissues and cells, and microarray data revealed upregulation of miR-103a and downregulation of RUNX1T1 in OC. RUNX1T1 was a target gene of miR-103a and EPB41L4A-AS2 bound to miR-103a. Moreover, EPB41L4A-AS2 increased RUNX1T1 expression by decreasing miR-103a expression. EPB41L4A-AS2-overexpressing SK-OV-3 cells exhibited inhibited proliferation, migration, colony formation and invasion, which was rescued by overexpression of miR-103a or silencing of RUNX1T1. Besides, overexpressed EPB41L4A-AS2 repressed tumour formation in vivo. Altogether, the current study demonstrates that overexpressed EPB41L4A-AS2 can potentially bind to miR-103a to promote the expression of RUNX1T1, thereby inhibiting OC, highlighting the potential of EPB41L4A-AS2 as a target for OC.

Large-scale analyses identify a cluster of novel long noncoding RNAs as potential competitive endogenous RNAs in progression of hepatocellular carcinoma

The abnormal expression of noncoding RNAs has attracted increasing interest in the field of hepatocellular carcinoma progression. However, the underlying molecular mechanisms mediated by noncoding RNAs in these processes are unclear. Here, we obtained the expression profiles of long noncoding RNAs, microRNAs, and mRNAs from the Gene Expression Omnibus database and identified hepatocarcinogenesis-specific differentially expressed transcripts. Next, we identified significant Gene Ontology and pathway terms that the differentially expressed transcripts involved in. Using functional analysis and target prediction, we constructed a hepatocellular carcinoma-associated deregulated competitive endogenous RNA network to reveal the potential mechanisms underlying tumor progression. By analyzing The Cancer Genome Atlas dataset, six key long noncoding RNAs showed significant association with overall survival as well as strong correlation with some microRNAs and mRNAs in the competitive endogenous RNA network. We further validated the above results and determined their diagnostic and prognostic value in clinical samples. Importantly, by large-scale analyses, we identified a cluster of long noncoding RNAs, GBAP1, MCM3AP-AS1, SLC16A1-AS1, C3P1, DIO3OS, and HNF4A-AS1 as candidate biomarkers for the diagnosis and prognosis of hepatocellular carcinoma, which will improve our understanding of competitive endogenous RNA-mediated regulatory mechanisms underlying hepatocellular carcinoma development and will provide novel therapeutic targets in the future.

LINC00355 Promotes Tumor Progression in HNSCC by Hindering MicroRNA-195-Mediated Suppression of HOXA10 Expression

Emerging evidence suggests that long non-coding RNAs (lncRNAs) are involved in the progression of head and neck squamous cell carcinoma (HNSCC). However, the specific role of LINC00355 in HNSCC remains elusive. Here, we identify the relationship between LINC00355 and the development of HNSCC through the interaction of LINC00355 with microRNA-195 (miR-195), which in turn targets homeoboxA10 (HOXA10). First, we identified differentially expressed lncRNAs and genes related to HNSCC. Next, the interaction among LINC00355, miR-195, and HOXA10 was identified. Subsequently, the expression of LINC00355 and miR-195 was altered to evaluate their effects on viability, invasion, migration, epithelial mesenchymal transition (EMT), and apoptosis of cancer stem cells (CSCs) in HNSCC. Finally, we assessed the ability of LINC00355 to alter tumor growth after HNSCC CSCs were injected into nude mice. Our findings indicate that LINC00355 and HOXA10 were highly expressed in HNSCC, while miR-195 was poorly expressed. CSCs with upregulated aldehyde dehydrogenase 1 (ALDH-1) were sorted. Silencing LINC00355 in these cells led to increased miR-195 expression and a reduction in HOXA10 expression, which inhibited viability, invasion, migration, and EMT and promoted apoptosis of CSCs. Silencing LINC00355 in vivo also led to decreased tumor growth. Our study provides evidence that LINC00355 acts as a miR-195 sponge to promote viability, invasion, migration, and EMT and inhibit apoptosis of CSCs by upregulating HOXA10, suggesting that LINC00355 represents a potential therapeutic target in the treatment of HNSCC.

Modulation of cancer cell signaling by long noncoding RNAs

Cellular signaling pathways play a very important role in almost all molecular processes in the cell, and are generally composed of a complex set of cascades in which enzymes and proteins play a key role. These signaling pathways include different types of cellular signaling classified based on their receptors and effector proteins such as enzyme-linked receptors, cytokine receptors, and G-protein-coupled receptors each of which is subdivided into different classes. Signaling pathways are tightly controlled by different mechanisms mostly thorough inhibiting/activating their receptors or effector proteins. In the last two decades, our knowledge of molecular biology has changed dramatically and today we know that more than 85% of the human genome expresses noncoding RNAs most of which are crucial in the cellular and molecular mechanisms of cells. One of these noncoding RNAs are long noncoding RNAs (lncRNA) containing more than 200 nucleotides. LncRNAs participate in the progression of cancer growth through several mechanism including signaling pathways. In this review, we summarize some of the most important of lncRNAs and their effect on important signaling pathways.

Long noncoding RNA EPB41L4A-AS2 inhibits hepatocellular carcinoma development by sponging miR-301a-5p and targeting FOXL1

BACKGROUND

Hepatocellular carcinoma (HCC) is the major histological type of liver cancer with high morbidity and mortality worldwide. Long noncoding RNAs (lncRNA) has been proved to be associated with various cancer types, while its regulation in HCC is largely unknown.

METHODS

To figure out the specific role of lncRNA EPB41L4A-AS2 in HCC. Fluorescence in situ hybridization (FISH) was first used to determine the cellular sublocalization of EPB41L4A-AS2 to determine its primary mode of action. QRT-PCR, Western blot and hematoxylin-eosin staining were then used to measure the expression of genes in cells and tissues. Cell proliferation and invasion assays were performed to determine the effects of EPB41L4A-AS2, miR-301a-5p and FOXL1 on the malignant phenotype of tumor cells. With luciferase reporter assay, the direct interaction between target genes were further confirmed for research on molecular mechanism. Finally, the mice hepatocarcinoma model was also established to disclose the tumor suppressor effects of EPB41L4A-AS2 in vivo.

RESULTS

Here, we have identified a novel lncRNA EPB41L4A-AS2, which is significantly downregulated both in HCC cells and tissues, and plays a negative regulatory role in HCC proliferation and invasion. Mechanistically, cytoplasmic lncRNA EPB41L4A-AS2 functions as an efficient miR-301a-5p sponge, thereby release the expression inhibition of forkhead box L1 (FOXL1). Indeed, lncRNA EPB41L4A-AS2 inhibits proliferation and migration by upregulating FOXL1 expression and FOXL1 was confirmed as a direct target of miR-301a-5p. MiR-301a-5p shows an inverse correlation with EPB41L4A-AS2 expression and was verified as a direct target of EPB41L4A-AS2 as well. Correspondingly, FOXL1 and miR-301a-5p show opposite biological effects in cell proliferation and migration. Moreover, miR-301a-5p overexpression rescued the EPB41L4A-AS2 upregulation induced depression in proliferation, migration and invasion of HCC cells, as well as promotion effect on FOXL1 expression. Also, in vivo experiments proved that EPB41L4A-AS2 suppress tumor growth and extrahepatic metastasis (lung) via the miR-301a-5p-FOXL1 axis.

CONCLUSIONS

Taken together, this research revealed a concrete mechanism of lncRNA EPB41L4A-AS2 in HCC, which may serve as a potential biomarkers and novel therapeutic targets for further clinical application.

Long non-coding RNA LOC541471: A novel prognostic biomarker for head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer. Early detection and management of HNSCC may prevent progression of the disease. Long non-coding RNAs (lncRNAs) may serve as prognostic biomarkers for various cancer types. The current study downloaded an RNA-Seq dataset containing 43 tumor-normal pairs. An independent t-test identified that the expression level of lncRNA LOC541471 was significantly increased in tumor tissues compared with healthy tissues. Additionally, the current study demonstrated that high lncRNA LOC541471 expression was significantly associated with increasing lymph node metastasis classification and perineural invasion. A multivariate Cox regression analysis revealed that high lncRNA LOC541471 expression levels were an independent predictor for reduced overall survival (n=487) and relapse-free survival (n=355). According to the anatomic neoplasm subdivision, HNSCC samples were classified as oropharyngeal carcinoma (n=297), oral carcinoma (n=80), laryngeal carcinoma and hypopharyngeal carcinoma (n=123). A negative association was revealed between lncRNA LOC541471 expression and overall survival in all subtypes of HNSCC. Therefore, lncRNA LOC541471 is significantly negatively associated with overall survival and relapse-free survival of patients with HNSCC and may be considered a potential prognostic factor for HNSCC.