Identification and validation of potential long non-coding RNA biomarkers in predicting survival of patients with head and neck squamous cell carcinoma

C10orf55, CASC2, and SFTA1P lncRNAs Are Potential Biomarkers to Assess Radiation Therapy Response in Head and Neck Cancers

Long non-coding RNAs have proven to be important molecules in carcinogenesis. Due to little knowledge about them, the molecular mechanisms of tumorigenesis are still being explored. The aim of this work was to study the effect of ionizing radiation on the expression of lncRNAs in head and neck squamous cell carcinoma (HNSCC) in patients responding and non-responding to radiotherapy. The experimental model was created using a group of patients with response (RG, n = 75) and no response (NRG, n = 75) to radiotherapy based on the cancer genome atlas (TCGA) data. Using the in silico model, statistically significant lncRNAs were defined and further validated on six HNSCC cell lines irradiated at three different doses. Based on the TCGA model, C10orf55, C3orf35, C5orf38, CASC2, MEG3, MYCNOS, SFTA1P, SNHG3, and TMEM105, with the altered expression between the RG and NRG were observed. Analysis of pathways and immune profile indicated that these lncRNAs were associated with changes in processes, such as epithelial-to-mesenchymal transition, regulation of spindle division, and the p53 pathway, and differences in immune cells score and lymphocyte infiltration signature score. However, only C10orf55, CASC2, and SFTA1P presented statistically altered expression after irradiation in the in vitro model. In conclusion, the expression of lncRNAs is affected by ionization radiation in HNSCC, and these lncRNAs are associated with pathways, which are important for radiation response and immune response. Potentially presented lncRNAs could be used as biomarkers for personalized radiotherapy in the future. However, these results need to be verified based on an in vitro experimental model to show a direct net of interactions.

A Risk-Scoring Model Based on Evaluation of Ferroptosis-Related Genes in Osteosarcoma

Background

Osteosarcoma (OS) is a bone malignancy frequently seen in pediatrics and has high mortality and incidence. Ferroptosis is an important cell death process in regulating the apoptosis and invasion of tumor cells, so constructing the risk-scoring model based on OS ferroptosis-related genes (FRGs) will benefit the evaluation of both treatment and prognosis.

Methods

The OS dataset was screened from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, and OS-related FRGs were found through the Ferroptosis Database (FerrDb) using a multivariate Cox regression model, followed by the generation of the risk scores and a risk-scoring prediction model. Further systematical exploration for immune cell infiltration and assessing the prediction of response to targeted drugs was conducted.

Results

Based on OS-related FRGs, a risk-scoring model of FRGs in OS was constructed. The six FRGs played a role in the carbon metabolism, glutathione metabolism, and pentose phosphate pathways. Results from targeted drug sensitivity analyses were concordant to pathway analyses. The response to targeted drugs statistically differed between the two groups with different risks, and the high-risk group presented a high sensitivity to targeted drugs.

Conclusions

We identified a 6-ferroptosis-gene-based prognostic signature in OS and created and verified a risk-scoring model to predict the prognosis of OS at 1, 3, and 5 years for OS patients independently.

Identification of Autophagy- and Ferroptosis-Related lncRNAs Functioned through Immune-Related Pathways in Head and Neck Squamous Carcinoma

The interplay between autophagy and ferroptosis has been highlighted as an important event to decide cancer cell fate. However, the underlying mechanisms remain largely unclear. In this study, we systematically explored the expression, prognostic value and functional roles of lncRNA in autophagy and ferroptosis. By a set of bioinformatics analyses, we identified 363 autophagy- and ferroptosis-related lncRNAs (AF-lncRNAs) and found 17 of them are dramatically related to the prognosis of head and neck squamous cell carcinoma (HNSC) patients, named as prognosis-related AF-lncRNAs (PAF-lncRNAs). Based on six key PAF-lncRNAs, a risk score model was developed and used to categorize the TCGA-retrieved HNSC patients into two groups (high-risk vs. low-risk). Functional analysis showed the differentially expressed genes (DEGs) between the two groups were mainly enriched in immune-related pathways and regulated by a PAF-lncRNA-directed ceRNA (competitive endogenous RNA) network. Combined with a variety of immune infiltration analyses, we also found a decreased landscape of immune cell infiltration in high-risk groups. Together, by revealing PAF-lncRNAs with tumor prognostic features functioned through immune-related pathways, our work would contribute to show the pathogenesis of a lncRNA-directed interplay among autophagy, ferroptosis and tumor immunity in HNSC and to develop potential prognostic biomarkers and targets for tumor immunotherapy.

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

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.