Identification of cancer hallmark-associated gene and lncRNA cooperative regulation pairs and dictate lncRNA roles in oral squamous cell carcinoma

Research Trends in Molecular Biological Studies on Oral Squamous Cell Carcinoma: A Bibliometric Analysis

Background: Since the discovery of PCR and ELISA, in vitro research in the realm of molecular biology pertaining to oral squamous cell carcinoma (OSCC) has witnessed significant expansion. Objective: to provide a comprehensive overview of molecular biology research on OSCC through visual mapping techniques. Methods: We conducted an analysis of publications within the "oral squamous cell carcinoma" category from Scopus' core collection. On 20 January 2023, we screened these publications using an advanced search employing the keywords "oral squamous cell cancer" and "cell line." Data analysis was performed using Microsoft Excel 2010 and VOSviewer, facilitating the examination of author contributions, journal productivity, institutional affiliations, and contributions by nations. VOSviewer was further utilized for co-occurrence and reference analysis of keywords. Results: A total of 781 papers spanning from 1992 to 2023 were collected. Notably, Japan, China, and the United States emerged as significant contributors in this field. The Osaka University Graduate School of Dentistry (Japan) ranked first with 21 publications. Chae J-I of Chonbuk National University (South Korea) emerged as the most prolific author, with 14 publications. The International Journal of Oncology and the Journal of Oral Pathology and Medicine were identified as the two most prolific journals. The central themes that emerged were epidermal growth factor receptor, invasion, epithelial-mesenchymal transition, angiogenesis, apoptosis, and metastasis. Conclusion: The rate of publications focused on the molecular biology of OSCC has seen a remarkable increase. Research priorities have shifted from topics such as "radiation, RANKL, cyclin D1, RNA interference, and matrix metalloproteinase" to encompass areas such as "chemoresistance due to cisplatin, other therapeutic agents (metformin and monoclonal antibody), autophagy, inflammation, microRNA, cancer-associated fibroblasts, and STAT3 (with roles in cell migration and tumorigenesis)." These seven significant future research areas hold promise in identifying reliable biological markers for oral cancer detection and treatment, thereby improving clinical outcomes.

U1RNP/lncRNA/Transcription Cycle Axis Promotes Tumorigenesis of Hepatocellular Carcinoma

As a component of the spliceosome, U1 small nuclear ribonucleoproteins (U1RNPs) play critical roles in RNA splicing, and recent studies have shown that U1RNPs could recruit long non-coding RNAs (lncRNAs) to chromatin which are involved in cancer development. However, the interplay of U1 snRNP, lncRNAs and downstream genes and signaling pathways are insufficiently understood in hepatocellular carcinoma (HCC). The expression of U1RNPs was found to be significantly higher in tumors than normal tissues in liver hepatocellular carcinomas of The Cancer Genome Atlas (TCGA-LIHC) dataset. LncRNAs with potential U1-binding sites (termed U1-lncRNAs) were found to be mostly located in the nucleus and their expression was higher in tumor than in normal tissues Bioinformatic analysis indicated that U1-lncRNAs worked with RNA-binding proteins and regulated the transcription cycle in HCC. A U1-lncRNA risk model was constructed using a TCGA dataset, and the AUCs of this risk model to predict 1-, 3- and 5-year overall survival were 0.82, 0.84 and 0.8, respectively. Furthermore, silencing of the small nuclear ribonucleoprotein D2 polypeptide (SNRPD2) resulted in impaired proliferation, G1/M cell cycle arrest and downregulation of transcription-cycle-related genes in HCC cell lines. Taken together, these results indicate that U1RNPs interact with lncRNAs and promote the transcription cycle process in HCC, which suggests that these could be novel biomarkers in the clinical management of HCC.

miR-653 Induces Bone Marrow Mesenchymal Stem Cells Proliferation via Activating Epithelial-Mesenchymal Transition in Oral Squamous Cell Carcinoma

This study intends to assess miR-653’s expression in MSCs and OSCC and discuss molecular biological mechanism of changes of EMT in MSCs through activating miR-653 in OSCC. miR-653 expression in MSCs and OSCC was detected. si-miR-653 was transfected into MSCs followed by analysis of cell proliferation by CCK-8 and clone formation assay, cell apoptosis and cycle by FCM, and the changes of transcription factor as ZEB1 and Snail by qRT-PCR. miR-653 expression in OSCC cell was up-regulated significantly from the result of q-RT-PCR detection. The proliferation of MSCs induced by miR-653 was restrained and apoptotic rate was increased after treatment with si-miR-653 along with stagnated cycle of G1/G0 staging cell. The expression of transcription factor of EMT type as ZEB1 and Snail was elevated significantly after intervention using si-miR-653. In conclusion, the proliferation of OSCC could be induced by MSCs through activation with miR-653 which might be through regulation of EMT process.

Identification of Novel Biomarkers for Predicting Prognosis and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma Based on ceRNA Network and Immune Infiltration Analysis

Objectives

Patients with head and neck squamous cell carcinoma (HNSCC) have poor prognosis and show poor responses to immune checkpoint (IC) inhibitor (ICI) therapy. Competing endogenous RNA (ceRNA) networks, tumor-infiltrating immune cells (TIICs), and ICIs may influence tumor prognosis and response rates to ICI therapy. This study is aimed at identifying prognostic and IC-related biomarkers and key TIIC signatures to improve prognosis and ICI therapy response in HNSCC patients.

Methods and Results

Ninety-five long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and 1746 mRNAs were identified using three independent methods. We constructed a ceRNA network and estimated the proportions of 22 immune cell subtypes. Ten ceRNAs were related to prognosis according to Kaplan–Meier analysis. Two risk signatures based, respectively, on nine ceRNAs (ANLN, CFL2, ITGA5, KDELC1, KIF23, NFIA, PTX3, RELT, and TMC7) and three immune cell types (naïve B cells, neutrophils, and regulatory T cells) via univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analyses could accurately and independently predict the prognosis of HNSCC patients. Key mRNAs in the ceRNA network were significantly correlated with naïve B cells and regulatory T cells and with stage, grade, and immune and molecular subtype. Eight IC genes exhibited higher expression in tumor tissues and were correlated with eight key mRNAs in the ceRNA network in HNSCC patients with different HPV statuses according to coexpression and TIMER 2.0 analyses. Most drugs were effective in association with expression of these key signatures (ANLN, CFL2, ITGA5, KIF23, NFIA, PTX3, RELT, and TMC7) based on GSCALite analysis. The prognostic value of key biomarkers and associations between key ceRNAs and IC genes were validated using online databases. Eight key ceRNAs were confirmed to predict response to ICI in other cancers based on TIDE analysis.

Conclusions

We constructed two risk signatures to accurately predict prognosis in HNSCC. Key IC-related signatures may be associated with response to ICI therapy. Combinations of ICIs with inhibitors of eight key mRNAs may improve survival outcomes of HNSCC patients.

YKT6, as a potential predictor of prognosis and immunotherapy response for oral squamous cell carcinoma, is related to cell invasion, metastasis, and CD8+ T cell infiltration

Metastasis and immune suppression account for the poor prognosis of oral squamous cell carcinoma (OSCC). YKT6 is a member of the soluble NSF attachment protein receptor (SNARE) family, and the effect of YKT6 in OSCC remains elusive. The purpose of this study was to explore promising prognostic and immune therapeutic candidate biomarkers for OSCC and to understand the expression pattern, prognostic value, immune effects, and biological functions of YKT6. Genes correlated with tumor metastasis and CD8 + T cell levels were identified by weighted gene coexpression network analysis (WGCNA). Next, YKT6 was analyzed through differential expression, prognostic and machine learning analyses. The molecular and immune characteristics of YKT6 were analyzed in independent cohorts, clinical specimens, and in vitro. In addition, we investigated the role of YKT6 at the pan-cancer level. The results suggested that the red module in WGCNA, as a hub module, was associated with lymph node (LN) metastasis and CD8 + T cell infiltration. Upregulation of YKT6 was found in OSCC and linked to adverse prognosis. A nomogram model containing YKT6 expression and tumor stage was constructed for clinical practice. The aggressive and immune-inhibitory phenotypes showed YKT6 overexpression, and the effect of YKT6 on OSCC cell invasion and metastasis in vitro was observed. Moreover, the low expression of YKT6 was correlated with high CD8 + T cell levels and potential immunotherapy response in OSCC. Similar results were found at the pan-cancer level. In total, YKT6 is a promising candidate biomarker for prognosis, molecular, and immune characteristics in OSCC.

lincRNA-RP11400K9.4 Regulates Cell Survival and Migration of Breast Cancer Cells

BACKGROUND/AIM

Several works in the past decades pointed out the key role of long intergenic non-coding RNA (lincRNA) in breast cancer development. Here in we report for first time the importance of deregulation of lincRNA RP11-400K9.4 in breast cancer cells which played a role in cell survival and migration.

MATERIALS AND METHODS

After RP11-400K9.4 silencing by short hairpin RNAs or overexpression by GeneBlocks, real-time quantitative polymerase chain reaction (RT-PCR), microarray, migration, proliferation and viability assay were performed.

RESULTS

RP11-400K9.4 expression was mainly in the cytoplasmic fraction in 2D culture. Overexpression of RP11-400K9.4 led to a reduction of migration by MCF-7 and MDA-MB-368 cells and an increase in cellular survival after UV-C radiation. Bioinformatic analyses highlighted irradiation-induced DNA damage, DNA repair and cell-cycle pathways as the mainly affected by RP11-400K9.4. Furthermore RT-PCR assay demonstrated the overexpression of baculoviral IAP repeat containing 3 (BIRC3) a known oncogene that promotes radiotherapy resistance through the nuclear factor kappa B (NFĸB) pathway.

CONCLUSION

RP11-400K9.4 participates in the modulation of migration and survival processes probably via the BIRC3/NFĸB pathway.

Transcriptomic heterogeneity of driver gene mutations reveals novel mutual exclusivity and improves exploration of functional associations

Background

Lung adenocarcinoma (LUAD), as the most common subtype of lung cancer, is the leading cause of cancer deaths in the world. The accumulation of driver gene mutations enables cancer cells to gradually acquire growth advantage. Therefore, it is important to understand the functions and interactions of driver gene mutations in cancer progression.

Methods

We obtained gene mutation data and gene expression profile of 506 LUAD tumors from The Cancer Genome Atlas (TCGA). The subtypes of tumors with driver gene mutations were identified by consensus cluster analysis.

Results

We found 21 significantly mutually exclusive pairs consisting of 20 genes among 506 LUAD patients. Because of the increased transcriptomic heterogeneity of mutations, we identified subtypes among tumors with non‐silent mutations in driver genes. There were 494 mutually exclusive pairs found among driver gene mutations within different subtypes. Furthermore, we identified functions of mutually exclusive pairs based on the hypothesis of functional redundancy of mutual exclusivity. These mutually exclusive pairs were significantly enriched in nuclear division and humoral immune response, which played crucial roles in cancer initiation and progression. We also found 79 mutually exclusive triples among subtypes of tumors with driver gene mutations, which were key roles in cell motility and cellular chemical homeostasis. In addition, two mutually exclusive triples and one mutually exclusive triple were associated with the overall survival and disease‐specific survival of LUAD patients, respectively.

Conclusions

We revealed novel mutual exclusivity and generated a comprehensive functional landscape of driver gene mutations, which could offer a new perspective to understand the mechanisms of cancer development and identify potential biomarkers for LUAD therapy.

Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning

DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. clinical end-points resulted in 11,176 to 27,786 differentially methylated genes (DMGs). Innovative automated machine learning (AutoML) was employed to construct signatures with translational value. Three highly performing and low-feature-number signatures were built: (1) A 5-gene signature discriminating BrCa patients from healthy individuals (area under the curve (AUC): 0.994 (0.982-1.000)). (2) A 3-gene signature identifying BrCa metastatic disease (AUC: 0.986 (0.921-1.000)). (3) Six equivalent 5-gene signatures diagnosing early disease (AUC: 0.973 (0.920-1.000)). Validation in independent patient groups verified performance. Bioinformatic tools for functional analysis and protein interaction prediction were also employed. All protein encoding features included in the signatures were associated with BrCa-related pathways. Functional analysis of DMGs highlighted the regulation of transcription as the main biological process, the nucleus as the main cellular component and transcription factor activity and sequence-specific DNA binding as the main molecular functions. Overall, three high-performance diagnostic/prognostic signatures were built and are readily available for improving BrCa precision management upon prospective clinical validation. Revisiting archived methylomes through novel bioinformatic approaches revealed significant clarifying knowledge for the contribution of gene methylation events in breast carcinogenesis.

Exosomal cargoes in OSCC: current findings and potential functions

Oral squamous cell carcinoma (OSCC) is the most prevalent malignancy in head and neck cancer, with high recurrence and mortality. Early diagnosis and efficient therapeutic strategies are vital for the treatment of OSCC patients. Exosomes can be isolated from a broad range of different cell types, implicating them as important factors in the regulation of human physiological and pathological processes. Due to their abundant cargo including proteins, lipids, and nucleic acids, exosomes have played a valuable diagnostic and therapeutic role across multiple diseases, including cancer. In this review, we summarize recent findings concerning the content within and participation of exosomes relating to OSCC and their roles in tumorigenesis, proliferation, migration, invasion, metastasis, and chemoresistance. We conclude this review by looking ahead to their potential utility in providing new methods for treating OSCC to inspire further research in this field.

Identification of cancer hallmark-associated gene and lncRNA cooperative regulation pairs and dictate lncRNA roles in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is the most common malignant tumour in the oral and maxillofacial region. Numerous cancers share ten common traits ("hallmarks") that govern the transformation of normal cells into cancer cells. Long non-coding RNAs (lncRNAs) are important factors that contribute to tumorigenesis. However, very little is known about the cooperative relationships between lncRNAs and cancer hallmark-associated genes in OSCC. Through integrative analysis of cancer hallmarks, somatic mutations, copy number variants (CNVs) and expression, some OSCC-specific cancer hallmark-associated genes and lncRNAs are identified. A computational framework to identify gene and lncRNA cooperative regulation pairs (GLCRPs) associated with different cancer hallmarks is developed based on the co-expression and co-occurrence of mutations. The distinct and common features of ten cancer hallmarks based on GLCRPs are characterized in OSCC. Cancer hallmark insensitivity to antigrowth signals and self-sufficiency in growth signals are shared by most GLCRPs in OSCC. Some key GLCRPs participate in many cancer hallmarks in OSCC. Cancer hallmark-associated GLCRP networks have complex patterns and specific functions in OSCC. Specially, some key GLCRPs are associated with the prognosis of OSCC patients. In summary, we generate a comprehensive landscape of cancer hallmark-associated GLCRPs that can act as a starting point for future functional explorations, the identification of biomarkers and lncRNA-based targeted therapy in OSCC.