Transcriptome profiling and pathway analysis in squamous cell carcinoma of buccal mucosa

Unraveling molecular mechanisms of Head and neck cancer

Malignancies that develop from mucosal epithelium of the upper aerodigestive tract are known as head and neck squamous cell carcinomas (HNSCC). Heterogeneity, late stage diagnosis and high recurrence rate are big hurdles in head and neck treatment regimen. Presently, the biomarkers available for diagnosis and prognosis of HNSCC are based on smoking as the major risk habit. This review shed light on the differential environment of HNSCC in smokeless tobacco consuming Indian patients. Frequent mutation in genes involved in DNA repair pathway (p53), cell proliferation (PIK3CA, HRAS) and cell death (CASP8, FADD) are common in western population. On the contrary, the genes involved in metastasis (MMPs, YAP1), lymphocyte proliferation (TNFRSF4, CD80), cell-cell adhesion (DCC, EDNRB), miRNA processing (DROSHA) and inflammatory responses (TLR9, IL-9) are mutated in Indian HNSCC patients. Gene ontology enrichment analysis highlighted that responses to chemical stimulus, immune pathways and stress pathways are highly enriched in Indian patients.

A Review of Emerging Tear Proteomics Research on the Ocular Surface in Ocular Allergy

Ocular allergy is an immunoglobulin E-mediated Type I hypersensitivity reaction localised to the ocular surface and surrounding tissues. Primary signs and symptoms of ocular allergy include itching, redness, irritation and inflammation. Eye-rubbing caused by itching has been shown to alter ocular surface protein concentrations in conditions linked to ocular allergy such as keratoconus. In keratoconus, the cornea begins to thin and sag over time, leading to progressive vision loss and blindness in severe conditions. Due to the high incidence of ocular allergy sufferers rubbing their eyes in response to symptoms of itching, the protein landscape of the ocular surface may be significantly altered. Differential protein expression caused by long-term inflammation and eye-rubbing may lead to subsequent changes in ocular surface structure and function over time. This review aims to summarise and explore the findings of current ocular allergy proteome research conducted using techniques such as gel electrophoresis, mass spectrometry and lab-on-a-chip proteomics. Proteins of interest for this review include differentially expressed immunoglobulins, mucins, functional proteins, enzymes and proteins with previously uncharacterised roles in ocular allergy. Additionally, potential applications of this research are addressed in terms of diagnostics, drug development and future research prospects.

Transcriptional Biomarkers in Oral Cancer: An Integrative Analysis and the Cancer Genome Atlas Validation

OBJECTIVE

An impervious mortality rate in oral cancer (OC) to a certain extent explains the exigencies of precise biomarkers. Therefore, the study was intended to identify OC candidate biomarkers using samples of healthy normal tissues (N=335), adjacent normal tissues (N=93) and OC tissues (N=533) from online microarray data.

METHODS

Differentially expressed genes (DEGs) were recognised through GeneSpring software (Fold change >4.0 and 'p' value.

Transcriptomic analysis of peripheral blood mononuclear cells in head and neck squamous cell carcinoma patients

OBJECTIVES

To investigate the gene expression profile of peripheral blood mononuclear cells (PBMCs) from head and neck squamous cell carcinoma (HNSCC), including oral cancer (OC) and oropharyngeal cancer (OPC) patients, and compare them with healthy controls (HC).

MATERIALS AND METHODS

Transcriptomic analysis of PBMCs was performed by RNA-sequencing. The upregulated candidate genes were selected for validation by quantitative real-time polymerase chain reaction (qPCR). In addition, related plasma protein levels were determined by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Three significantly upregulated genes, including high mobility group nucleosomal binding domain 2 (HMGN2), folate receptor gamma (FOLR3), and amphiregulin (AREG), were selected. In the first cohort, the results showed that only HMGN2 expression was significantly increased in OC patients. In the larger sample size, the overall results demonstrated that HMGN2 expression had a tendency to increase in both OC and OPC patients compared with HC. Interestingly, the plasma HMGN2 (HMG-17) protein level exhibited the same trend as that observed at the transcriptional level.

CONCLUSION

HMGN2 expression and plasma HMG-17 (HMGN2 protein) were increased in both cancer patients compared with HC. This gene may be important for further functional studies in the PBMCs of HNSCC patients.

Long noncoding RNA PTCSC1 drives esophageal squamous cell carcinoma progression through activating Akt signaling

Long noncoding RNAs (lncRNAs) have critical roles in various malignancies. However, the specific expression and roles of lncRNA PTCSC1 in esophageal squamous cell carcinoma (ESCC) are still unknown. Here, we identified that lncRNA PTCSC1 was elevated in ESCC tissues and cell lines compared with adjacent noncancerous tissues and normal esophageal epithelial cell line, respectively. Enhanced expression of PTCSC1 facilitated ESCC cells proliferation and migration in vitro and ESCC xenograft growth in vivo. Conversely, deficiency of PTCSC1 suppressed ESCC cells proliferation and migration in vitro and ESCC tumor growth in vivo. Furthermore, PTCSC1 was found to activate Akt signaling in ESCC cells. Blocking Akt signaling with MK-2206 abolished the pro-proliferative and pro-migratory roles of PTCSC1. In summary, our findings demonstrated PTCSC1 as an oncogenic lncRNA in ESCC via activating Akt signaling and suggested that targeting PTCSC1 represents a promising therapeutic strategy against ESCC.

Comprehensive Analysis of Long Non-coding RNA-Associated Competing Endogenous RNA Network in Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is one of the most severe neuromuscular disorders. Long non-coding RNAs (lncRNAs) are a group of non-coding transcripts, which could regulate messenger RNA (mRNA) by binding the mutual miRNAs, thus acting as competing endogenous RNAs (ceRNAs). So far, the role of lncRNA in DMD pathogenesis remains unclear. In the current study, expression profile from a total of 33 DMD patients and 12 healthy people were downloaded from Gene Expression Omnibus (GEO) database (GSE38417 and GSE109178). Differentially expressed (DE) lncRNAs were discovered and targeted mRNAs were predicted. The ceRNA network of lncRNAs-miRNAs-mRNAs was then constructed. Genome Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the putative mRNAs in the ceRNA network were performed through Database for Annotation, Visualization and Integration Discovery (DAVID) website. Topological property of the network was analyzed using Cytoscape to disclose the hub lncRNAs. According to our assessments, 19 common DElncRNAs and 846 common DEmRNAs were identified in DMD compared to controls. The created ceRNA network contained 6 lncRNA nodes, 69 mRNA nodes, 27 miRNA nodes and 102 edges, while four hub lncRNAs (XIST, AL132709, LINC00310, ALDH1L1-AS2) were uncovered. In conclusion, our latest bioinformatic analysis demonstrated that lncRNA is likely involved in DMD. This work highlights the importance of lncRNA and provides new insights for exploring the molecular mechanism of DMD. The created ceRNA network contained 6 lncRNA nodes, 69 mRNA nodes, 27 miRNA nodes and 102 edges, while four hub lncRNAs (XIST, AL132709, LINC00310, ALDH1L1-AS2) were uncovered. Remarkably, KEGG analysis indicated that targeted mRNAs in the network were mainly enriched in "microRNAs in cancer" and "proteoglycans in cancer". Our study may offer novel perspectives on the pathogenesis of DMD from the point of lncRNAs. This work might be also conducive for exploring the molecular mechanism of increased incidence of tumorigenesis reported in DMD patients and experimental models.

Development of Prognostic Indicator Based on Autophagy-Related lncRNA Analysis in Colon Adenocarcinoma

There were no systematic researches about autophagy-related long noncoding RNA (lncRNA) signatures to predict the survival of patients with colon adenocarcinoma. It was necessary to set up corresponding autophagy-related lncRNA signatures. The expression profiles of lncRNAs which contained 480 colon adenocarcinoma samples were obtained from The Cancer Genome Atlas (TCGA) database. The coexpression network of lncRNAs and autophagy-related genes was utilized to select autophagy-related lncRNAs. The lncRNAs were further screened using univariate Cox regression. In addition, Lasso regression and multivariate Cox regression were used to develop an autophagy-related lncRNA signature. A risk score based on the signature was established, and Cox regression was used to test whether it was an independent prognostic factor. The functional enrichment of autophagy-related lncRNAs was visualized using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Ten prognostic autophagy-related lncRNAs (AC027307.2, AC068580.3, AL138756.1, CD27-AS1, EIF3J-DT, LINC01011, LINC01063, LINC02381, AC073896.3, and SNHG16) were identified to be significantly different, which made up an autophagy-related lncRNA signature. The signature divided patients with colon adenocarcinoma into the low-risk group and the high-risk group. A risk score based on the signature was a significantly independent factor for the patients with colon adenocarcinoma (HR = 1.088, 95%CI = 1.057 - 1.120; P < 0.001). Additionally, the ten lncRNAs were significantly enriched in autophagy process, metabolism, and tumor classical pathways. In conclusion, the ten autophagy-related lncRNAs and their signature might be molecular biomarkers and therapeutic targets for the patients with colon adenocarcinoma.