Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas

Abstract

Identification of novel prognostic biomarkers typically requires a large dataset which provides sufficient statistical power for discovery research. To this end, we took advantage of the high‐throughput data from The Cancer Genome Atlas (TCGA) to identify a set of prognostic biomarkers in head and neck squamous cell carcinomas (HNSCC) including oropharyngeal squamous cell carcinoma (OPSCC) and other subtypes. In this study, we analyzed miRNA‐seq data obtained from TCGA patients to identify prognostic biomarkers for OPSCC. The identified miRNAs were further tested with an independent cohort. miRNA‐seq data from TCGA was also analyzed to identify prognostic miRNAs in oral cavity squamous cell carcinoma (OSCC) and laryngeal squamous cell carcinoma (LSCC). Our study identified that miR‐193b‐3p and miR‐455‐5p were positively associated with survival, and miR‐92a‐3p and miR‐497‐5p were negatively associated with survival in OPSCC. A combined expression signature of these four miRNAs was prognostic of overall survival in OPSCC, and more importantly, this signature was validated in an independent OPSCC cohort. Furthermore, we identified four miRNAs each in OSCC and LSCC that were prognostic of survival, and combined signatures were specific for subtypes of HNSCC. A robust 4‐miRNA prognostic signature in OPSCC, as well as prognostic signatures in other subtypes of HNSCC, was developed using sequencing data from TCGA as the primary source. This demonstrates the power of using TCGA as a potential resource to develop prognostic tools for improving individualized patient care.

Improving accuracy of RNA-based diagnosis and prognosis of oral cancer by using noninvasive methods

“…This is not to say that these miRNAs are not involved in tumor aggressiveness, but that the difference is not useful diagnostically. Recently, using large datasets, two groups have established prognostic RNA-based classifiers for OSCC using 4 miRNAs and for HNSCC using 6 miRNAs [84, 86]. We note that of the excess of 25 miRNAs reported in earlier studies to be relevant to HNSCC and OSCC prognosis prediction only one, mir-218-5p, is in the newly identified OSCC classifier and one, miR-125b-2, in the new HNSCC classifier.…”

“…We note that of the excess of 25 miRNAs reported in earlier studies to be relevant to HNSCC and OSCC prognosis prediction only one, mir-218-5p, is in the newly identified OSCC classifier and one, miR-125b-2, in the new HNSCC classifier. Of greater concern is that in the study where the information is provided, the changes in miRNA marker levels between the high risk (short overall survival) versus low risk (long overall survival) are slight, 19% to 43% [86]. Thus usage of the measurement of levels of these markers to predict prognosis would require extreme accuracy in miRNA measurement for usage in the clinic.…”

Molecular features of adenoid cystic carcinoma with an emphasis on microRNAexpression

“…12). These two mutual miRNAs (hsamiR-455-5p and hsa-miR-181d-5p) have been repeatedly found to be overexpressed in other malignancies (219)(220)(221). Interestingly, there was no difference in miRNA expression between breast ACC and normal breast tissue.…”

Four microRNAs Signature for Survival Prognosis in Colon Cancer using TCGA Data

“…Several diagnostic and predicted miRNAs signature have revealed by scientists worldwide. It was reported that several miRNAs markers were identified for cancer prediction and prognosis, such as head and neck squamous cell carcinomas7, bile duct cancer prediction8, and glioma9. However, up to date, the miRNAs expression patterns in the survival prognosis of colon cancer have not been investigated systematically.…”

“…It was reported that several miRNAs markers were identified in caners, such as head and neck squamous cell carcinomas7, six-miRNAs signature in bile duct cancer prediction8, and 5-miRNAs prognosis in glioma9. However, as to the smaller patient number or limited miRNAs number, or different miRNAs-chip platform in colon cancer study, studies lacked a normalized standard.…”