LINC00958 and HOXC13-AS as key candidate biomarkers in head and neck squamous cell carcinoma by integrated bioinformatics analysis

Abstract

Background Head and neck squamous cell carcinoma (HNSCC) is a malignant tumor with a strong tendency for metastasis and recurrence. Finding effective biomarkers for the early diagnosis of HNSCC is critical for the early treatment and prognosis of patients. Methods RNA sequencing data including long non-coding RNAs (lncRNAs), messenger RNA (mRNAs) and microRNAs (miRNAs) of 141 HNSCC and 44 adjacent normal tissues were obtained from the TCGA. Differentially expressed genes were analyzed using the R package DESeq. GO terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. A competing endogenous RNAs (ceRNA) network was constructed. The most differentially expressed genes in the main ceRNA network were chosen for nasopharyngeal carcinoma (NPC) cell lines and NPEC2 Bmi-1 cell line verification. A receiver operating characteristic (ROC) curve was constructed for 141 specimens of HNSCC tissues from 44 control samples. Results In our study, 79 HNSCC-associated abnormally expressed lncRNAs , 86 abnormally expressed miRNAs and 324 abnormally expressed mRNAs were identified. The public microarray results showed that LINC00958 and HOXC13-AS expression levels were upregulated in HNSCC tissues compared with the adjacent normal tissues in this study (p < 0.0001). LINC00958 and HOXC13-AS expression levels in NPC cell lines were higher than those in the NPEC2 Bmi-1 cell line (p < 0.05). The results showed that the area under the ROC curve (AUC) of LINC00958 reached up to 0.906 at a cutoff value of 7.96, with a sensitivity and specificity of 80.85% and 90.91%, respectively. The AUC of HOXC13-AS reached up to 0.898 at a cutoff value of 0.695, with sensitivity and specificity values of 86.23% and 83.78%, respectively. Conclusion The current study indicates that LINC00958 and HOXC13-AS are new candidate diagnostic biomarkers for HNSCC patients.

MYC/MAX-Activated LINC00958 Promotes Lung Adenocarcinoma by Oncogenic Transcriptional Reprogramming Through HOXA1 Activation

“…This study reported the clinical significance, in vivo and in vitro functions, and mechanisms of LINC00958 in LUAD. Consistent with the previously reported function of LINC00958 as an oncogene in other cancer types (18,19,(33)(34)(35)(36)(37)(38)(39)(40), this study demonstrated that LINC00958 promotes lung cancer growth and metastasis and inhibits cancer cell apoptosis. This suggested that LINC00958 has a potent tumorigenesis role in cancer.…”

Human skin specific long noncoding RNA HOXC13-AS regulates epidermal differentiation by interfering with Golgi-ER retrograde transport

“…To the best of our knowledge, this is the first report showing the physiological role played by HOXC13-AS. This lncRNA has been previously identified as a cancer biomarker in cervical cancer 52 , breast cancer 53 , glioma 54 , hepatocellular carcinoma 55 , cholangiocarcinoma 56 , and head and neck squamous cell carcinoma [57][58][59] , which emphasizes the absence of HOXC13-AS expression in most normal tissues except the skin. Additionally, HOXC13-AS reportedly functions as an oncogene promoting proliferation and the epithelial-mesenchymal transition of cancer cells 57 .…”

Long Non-Coding RNA Cancer Susceptibility Candidate 9 Regulates the Malignant Biological Behavior of Nasopharyngeal Carcinoma Cells by Targeting miR-497-5p/Wnt3a/β-catenin Signaling Pathway

“…Long noncoding RNAs (LncRNAs) were considered as vital regulators in the tumorigenesis and progression of a variety of malignancies, including NPC ( 6 – 8 ). Previous studies have discovered that a few dysregulated lncRNAs are related to NPC progression via regulating cell proliferation, apoptosis, migration, invasion and drug resistance, such as AFAP1-AS, LET, LINC00958 and HOXC13-AS ( 9 – 11 ). LncRNA CASC9 was firstly reported in esophageal squamous cell carcinoma as an oncogene in 2015, and was subsequently confirmed to be associated with tumorigenesis and progression of malignant tumors including gastric cancer, hepatocellular carcinoma and breast cancer ( 12 – 14 ).…”