Background: Head and Neck Squamous Cell Carcinoma (HNSCC) remain a significant global cancer burden, with limited improvement in outcomes due to late diagnosis and biological heterogeneity. Advances in Next-Generation Sequencing (NGS) have enabled unbiased, high-resolution profiling of the cancer transcriptome, revealing extensive dysregulation of non-coding RNAs (ncRNAs). Long non-coding RNAs (lncRNAs) represent an emerging and underexplored class of regulatory molecules with critical roles in transcriptional control, RNA stability, and oncogenic signaling in HNSCC. The discovery of dysregulated lncRNA panels through NGS provides a robust framework for identifying early molecular alterations associated with malignant transformation, offering innovative opportunities for HNSCC diagnosis, therapy, and ultimately, cancer prevention research.
 

Objective: Using NGS–based transcriptomic profile, this study aimed to identify candidate lncRNA(s) from the Differentially Expressed Gene panel in HNSCC. Furthermore, the biological relevance of the candidate lncRNA–mRNA-cellular interaction network was delineated through integrative in silico analyses, ex vivo validation in an independent cohort of HNSCC patient samples, and functional approaches. 

 

Methods: High-throughput RNA sequencing was performed on a subset of HNSCC tissues (N = 5) to identify differentially expressed lncRNAs and mRNAs, which were analyzed using DESeq2 and edgeR. Integrative bioinformatic analyses were applied to construct lncRNA–mRNA interaction networks and to prioritize candidate regulatory targets. The lead lncRNA, SNHG3, was subsequently validated in an independent cohort of HNSCC tissues (N = 100) and in a representative oral cancer cell line (FaDu). RNA immunoprecipitation (RIP) followed by qRT-PCR was used to assess interactions between SNHG3 and its predicted target transcripts. Functional relevance was evaluated through siRNA-mediated knockdown of SNHG3 in FaDu cells, with assessments of cell viability, morphological changes, and apoptosis.
 

Results: The NGS transcriptome profile revealed SNHG3 as a significantly (Log2FC = 2.23; p = 0.0003) dysregulated lncRNA candidate. Validation in clinical samples demonstrated markedly higher SNHG3 expression in HNSCC tissues (N=100) compared with matched normal tissues (93/100; p < 0.0001). Corroborating with ex vivo data, SNHG3 showed significant upregulation (p = 0.0001) in FaDu cells compared to normal HaCaT cells. Predicted targets of SNHG3, c-MYC, and β-catenin exhibited concordant upregulation at both mRNA and protein levels. In silico analyses indicated a high probability (score = 0.9) of an SNHG3–c-MYC interaction, which in turn enhances the stabilization of BMI1 mRNA; this was subsequently confirmed by RIP and qRT-PCR. Functional knockdown of SNHG3 significantly (p < 0.01) reduced viability, induced pronounced morphological changes, and promoted apoptotic cell death in FaDu cells, suggesting a plausible oncogenic role for SNHG3 in HNSCC. Interestingly, plasma from HNSCC patients showed upregulation of SNHG3 expression (41/50, p = 0.0001), indicating its overall clinical significance in disease theragnosis, which warrants further functional approaches. 

Conclusion: This integrative transcriptomic and functional study identifies SNHG3 as a key oncogenic lncRNA that is consistently dysregulated in HNSCC.  In vitro, SNHG3 could contribute to carcinogenesis through stabilization of BMI1-mRNA upon binding to the c-MYC protein or by regulating c-MYC expression. Thus, SNHG3/c-MYC/BMI1 axis poses a novel therapeutic target for HNSCC.