Identification of Prognosis Associated microRNAs in HNSCC Subtypes Based on TCGA Dataset

The Potential microRNA Prognostic Signature in HNSCCs: A Systematic Review

Head and neck squamous cell carcinomas (HNSCCs) are often diagnosed at advanced stages, incurring significant high mortality and morbidity. Several microRNAs (miRs) have been identified as pivotal players in the onset and advancement of HNSCCs, operating as either oncogenes or tumor suppressors. Distinctive miR patterns identified in tumor samples, as well as in serum, plasma, or saliva, from patients have significant clinical potential for use in the diagnosis and prognosis of HNSCCs and as potential therapeutic targets. The aim of this study was to identify previous systematic reviews with meta-analysis data and clinical trials that showed the most promising miRs in HNSCCs, enclosing them into a biomolecular signature to test the prognostic value on a cohort of HNSCC patients according to The Cancer Genome Atlas (TCGA). Three electronic databases (PubMed, Scopus, and Science Direct) and one registry (the Cochrane Library) were investigated, and a combination of keywords such as "signature microRNA OR miR" AND "HNSCC OR LSCC OR OSCC OR oral cancer" were searched. In total, 15 systematic literature reviews and 76 prognostic clinical reports were identified for the study design and inclusion process. All survival index data were extracted, and the three miRs (miR-21, miR-155, and miR-375) most investigated and presenting the largest number of patients included in the studies were selected in a molecular biosignature. The difference between high and low tissue expression levels of miR-21, miR-155, and miR-375 for OS had an HR = 1.28, with 95% CI: [0.95, 1.72]. In conclusion, the current evidence suggests that miRNAs have potential prognostic value to serve as screening tools for clinical practice in HNSCC follow-up and treatment. Further large-scale cohort studies focusing on these miRNAs are recommended to verify the clinical utility of these markers individually and/or in combination.

Prognostic Genomic Markers of Pathological Stage in Oral Squamous Cell Carcinoma

BACKGROUND

To identify the prognostic markers of oral squamous cell carcinoma (OSCC), the genetic heterogeneity of the pathological stages was investigated.

METHODS

The data of 295 patients with primary OSCC obtained from the Cancer Genome Atlas were studied. The genetic prognostic landscape of the pathological stages was systematically analyzed by Cox regressions, Fisher's exact tests, and Gene Ontology (GO) enrichment.

RESULTS

Stage 4 patients had a poor prognosis in univariate and multivariate Cox models. Transforming growth factor-beta (TGF-β) pathway alterations were found more frequently in stage 4, whereas alterations in cell cycle pathways were significant in stages 1, 2, and 3. The differentially mutated genes were divided into three groups: risk genes of high stage, hazardless genes, and risk genes of low stage. The risk genes of low stage (RNF112, AKR7L, ZSCAN5C, and ZPBP) were independent prognostic factors with stage 4 and treatment modality in multivariate Cox regressions. Additionally, in genetic interaction analysis, NOMO1 and ZNF333 had a high co-occurrence in high stage, and WIZ had high co-occurrence in low stage. In GO enrichment, the prognostic genes were clustered at the functional term of RNA polymerase II transcription, and ZNF333 had an association with RNA transcription.

CONCLUSION

The genetic mutation type and ratio of tumor heterogeneity are different for each stage of OSCC, and stratification of OSCC patients with differential therapeutic efficacy is needed. Risk genes of both high and low stages must be identified in patients diagnosed with low-stage OSCC. Mutations in NOMO1, ZNF333, and WIZ should be considered as potential prognostic markers.

Exosomal miR-1304-3p promotes breast cancer progression in African Americans by activating cancer-associated adipocytes

Breast cancer displays disparities in mortality between African Americans and Caucasian Americans. However, the exact molecular mechanisms remain elusive. Here, we identify miR-1304-3p as the most upregulated microRNA in African American patients. Importantly, its expression significantly correlates with poor progression-free survival in African American patients. Ectopic expression of miR-1304 promotes tumor progression in vivo. Exosomal miR-1304-3p activates cancer-associated adipocytes that release lipids and enhance cancer cell growth. Moreover, we identify the anti-adipogenic gene GATA2 as the target of miR-1304-3p. Notably, a single nucleotide polymorphism (SNP) located in the miR-1304 stem-loop region shows a significant difference in frequencies of the G allele between African and Caucasian American groups, which promotes the maturation of miR-1304-3p. Therefore, our results reveal a mechanism of the disparity in breast cancer progression and suggest a potential utility of miR-1304-3p and the associated SNP as biomarkers for predicting the outcome of African American patients.

Signatures of genetic variation in human microRNAs point to processes of positive selection and population-specific disease risks

The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last 20 years. Most of them have been focused on the role of specific mutations in disease, while a minor proportion seek to analyse microRNA diversity in the genomes of human populations. We analyse the latest human microRNA annotations in the light of the most updated catalogue of genetic variation provided by the 1000 Genomes Project. By means of the in silico analysis of microRNA genetic variation we show that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or genomic location. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.

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.

Dysregulation of miR-21-5p, miR-93-5p, miR-200c-3p and miR-205-5p in Oral Squamous Cell Carcinoma: A Potential Biomarkers Panel?

Oral squamous cell carcinoma (OSCC) is considered the sixth most common cancer worldwide. To reduce the high mortality of the disease, sensitive and specific diagnostic and prognostic biomarkers are urgently needed. Non-coding RNA, microRNAs (miRNAs), which are short length non-coding transcripts, or long non-coding RNA (lncRNA) seem to be potential biomarkers, considering that they have an important role in regulation of cell fate being involved in a wide range of biological processes. Literature data emphasized the important role of these transcripts as a biomarker for diagnosis and prognosis in oral squamous cell carcinoma. Therefore, we have evaluated the expression levels of a panel of four miRNAs (miR-21-5p, miR-93-5p, miR-200c-3p and miR-205-5p) and H19, MALAT1 by quantitative real-time PCR (qRT-PCR) from 33 fresh frozen tissues and 33 normal adjacent tissues. Our date revealed miR-21-5p and miR-93-5p to be upregulated, while miR-200c-3p and miR-205-5p to be downregulated. Regarding the long non-coding RNAs, H19 and MALAT1, were also downregulated. We also investigated the expression of BCL2, which is another important gene correlated to non-coding RNAs investigated by as, and it was also under-expressed. Additional validation step at protein level was done for KI67, TP53 and BCL2. In our patient cohort no correlation with clinical stage and smoking status was observed. The results of the present study indicated the important role of miR-21-5p, miR-93-5p, miR-200c-3p, miR-205-5p and H19 in OSCC. Differential expression of these transcripts at sub-sites, may serve as a diagnostic marker with further elaboration on a larger sample size. Additional studies should be conducted to confirm the results, particularly the interconnection with coding and non-coding genes.

Robust rank aggregation and cibersort algorithm applied to the identification of key genes in head and neck squamous cell cancer

OBJECTIVE

Although multiple hub genes have been identified in head and neck squamous cell cancer (HNSCC) in recent years, because of the limited sample size and inconsistent bioinformatics analysis methods, the results are not reliable. Therefore, it is urgent to use reliable algorithms to find new prognostic markers of HNSCC.

METHOD

The Robust Rank Aggregation (RRA) method was used to integrate 8 microarray datasets of HNSCC downloaded from the Gene Expression Omnibus (GEO) database to screen differentially expressed genes (DEGs). Later, Gene Ontology (GO) functional annotation together with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was carried out to discover functions of those discovered DEGs. According to the KEGG results, those discovered DEGs showed tight association with the occurrence and development of HNSCC. Then cibersort algorithm was used to analyze the infiltration of immune cells of HNSCC and we found that the main infiltrated immune cells were B cells, dendritic cells and macrophages. A protein-protein interaction (PPI) network was established; moreover, key modules were also constructed to select 5 hub genes from the whole network using cytoHubba. 3 hub genes showed significant relationship with prognosis for TCGA-derived HNSCC patients.

RESULT

The potent DEGs along with hub genes were selected by the combined bioinformatic approach. AURKA, BIRC5 and UBE2C genes may be the potential prognostic biomarker and therapeutic targets of HNSCC.

CONCLUSIONS

The Robust Rank Aggregation method and cibersort algorithm method can accurately predict the potential prognostic biomarker and therapeutic targets of HNSCC through multiple GEO datasets.

Roles of microRNAs in Regulating Cancer Stemness in Head and Neck Cancers

Head and neck squamous cell carcinomas (HNSCCs) are epithelial malignancies with 5-year overall survival rates of approximately 40-50%. Emerging evidence indicates that a small population of cells in HNSCC patients, named cancer stem cells (CSCs), play vital roles in the processes of tumor initiation, progression, metastasis, immune evasion, chemo-/radioresistance, and recurrence. The acquisition of stem-like properties of cancer cells further provides cellular plasticity for stress adaptation and contributes to therapeutic resistance, resulting in a worse clinical outcome. Thus, targeting cancer stemness is fundamental for cancer treatment. MicroRNAs (miRNAs) are known to regulate stem cell features in the development and tissue regeneration through a miRNA-target interactive network. In HNSCCs, miRNAs act as tumor suppressors and/or oncogenes to modulate cancer stemness and therapeutic efficacy by regulating the CSC-specific tumor microenvironment (TME) and signaling pathways, such as epithelial-to-mesenchymal transition (EMT), Wnt/β-catenin signaling, and epidermal growth factor receptor (EGFR) or insulin-like growth factor 1 receptor (IGF1R) signaling pathways. Owing to a deeper understanding of disease-relevant miRNAs and advances in in vivo delivery systems, the administration of miRNA-based therapeutics is feasible and safe in humans, with encouraging efficacy results in early-phase clinical trials. In this review, we summarize the present findings to better understand the mechanical actions of miRNAs in maintaining CSCs and acquiring the stem-like features of cancer cells during HNSCC pathogenesis.