Multi-omics characterization of a scoring system to quantify hypoxia patterns in patients with head and neck squamous cell carcinoma

Identification of TMEM71 as a hub NLRP3-related gene suppressing malignant behavior in nasopharyngeal carcinoma via the NLRP3/Caspase-1/GSDMD signaling pathway

OBJECTIVE

NLRP3 plays a key role in cellular pyroptosis and tumor progression. However, research on NLRP3-Related Genes (NRGs) in Nasopharyngeal Carcinoma (NPC) is limited.

METHODS

We analyzed the GSE53819 dataset to identify genes positively correlated with NLRP3 mRNA and downregulated in NPC tumors, termed NRGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to characterize their biological functions. Validation was performed using the GSE64634 and GSE102349 datasets. The GSE102349 dataset was used to evaluate the impact of NRGs on the Progression-Free Survival (PFS) and their association with immune cell infiltration. A cohort of 421 NPC patients from a local hospital underwent multivariate Cox regression to assess the prognostic significance of hub NRGs. Cellular experiments further investigated the role of hub NRGs in NPC.

RESULTS

In the GSE53819 dataset, 26 NRGs were identified, correlated with NLRP3 expression, and downregulated in tumor tissues. GO and KEGG analyses linked these 26 NRGs to the inflammasome complex. TMEM71, identified in the GSE64634 and GSE102349 datasets, was downregulated in tumor tissues and positively correlated with NLRP3 expression. It was the only NRG with prognostic value, with higher expression correlating with improved PFS. Immune cell infiltration analysis showed significant differences between high and low TMEM71 expression groups (e.g., naïve B cells). Local analysis confirmed that positive TMEM71 expression in tumor serves as an independent prognostic marker for NPC (HR = 0.53, 95% CI 0.366‒0.780). in vitro, TMEM71 activation of the NLRP3/caspase-1/GSDMD pathway suppressed malignant behaviors in NPC cell.

CONCLUSION

TMEM71 may serve as a prognostic biomarker for NPC and influence immune cell infiltration. Its overexpression could exert anticancer effects via the NLRP3/caspase-1/GSDMD pathway, highlight its potential as a therapeutic target in NPC.

Improving therapeutic strategies for Head and Neck Cancer: Insights from 3D hypoxic cell culture models in treatment response evaluation

Hypoxia in the tumor core negatively affects the outcome of patients with head and neck squamous cell carcinoma (HNSCC). Nevertheless, its role in predicting treatment response requires further exploration. Typically, reduced oxygen levels in the tumor core correlate with diminished efficacy of radiotherapy, chemotherapy, and immunotherapy, which are commonly used for HNSCC patients' treatment. Understanding the mechanistic underpinnings of these varied treatment responses in HNSCC is crucial for enhancing therapeutic outcomes and extending patients' overall survival (OS) rates. Standard monolayer cell culture conditions have major limitations in mimicking tumor physiological features and the complexity of the tumor microenvironment. Three-dimensional (3D) cell cultures enable the recreation of the in vivo tumor attributes, encompassing oxygen and nutrient gradients, cellular morphology, and intracellular connections. It is vital to use the 3D model in treatment response studies to mimic the tumor microenvironment, as evidenced by the decreased sensitivity of 3D structures to anticancer therapy. Accordingly, the aim of the study was to delineate the utility of the 3D models of hypoxic head and neck tumors in drug screening and treatment response studies.

Identification of PATL1 as a prognostic and immunotherapeutic predictive factor for nasal-type natural killer/T-cell lymphoma and head and neck squamous cell carcinoma

This research examines the function of protein associated with topoisomerase II homolog 1 (PATL1) in nasal-type natural killer/T-cell lymphoma (NKTCL) and head and neck squamous cell carcinoma (HNSCC). We analyzed bulk RNA-seq data from NKTCL, nasal polyps, and normal nasal mucosa, identifying 439 differentially expressed genes. Machine learning algorithms highlighted PATL1 as a hub gene. PATL1 exhibited significant upregulation in NKTCL and HNSCC tumor samples in comparison to normal tissues, showing high diagnostic accuracy (AUC = 1.000) for NKTCL. Further analysis of local hospital data identified PATL1 as an independent prognostic risk factor for NKTCL. Data analysis of TCGA and GEO datasets revealed that high PATL1 expression correlated with poorer prognosis in HNSCC patients (p < 0.05). We also constructed a PATL1-based nomogram, which emerged as an independent prognostic predictor for HNSCC after addressing missing values. Additionally, we found a strong correlation between PATL1 and various immune cell infiltrates (e.g., activated.CD4 T cell), and a significant association with the expression of 37 immune checkpoints genes (e.g., CTLA4, PDCD1) and 20 N6-methyladenosine-related genes (e.g., ZC3H13, METTL3) (all p < 0.05). Both TCIA and TIDE algorithms suggested that PATL1 could potentially predict immunotherapy efficacy (p < 0.05). Cellular experiments demonstrated that transfection with a silencing plasmid of PATL1 significantly inhibited the malignant behaviors of SNK6 and FaDu cell lines(p < 0.05). In conclusion, our findings suggest that PATL1 may serve as a valuable prognostic and predictive biomarker in NKTCL and HNSCC, highlighting its significant role in these cancers.

Type I conventional dendritic cells and CD8+ T cells predict favorable clinical outcome of head and neck squamous cell carcinoma patients

Head and neck squamous cell carcinoma (HNSCC) is one of the most common tumor entities worldwide, with human papillomavirus (HPV) infection contributing to cancer development. Conventional therapies achieve only limited efficiency, especially in recurrent or metastatic HNSCC. As the immune landscape decisively impacts the survival of patients and treatment efficacy, this study comprehensively investigated the immunological tumor microenvironment (TME) and its association with patient outcome, with special focus on several dendritic cell (DC) and T lymphocyte subpopulations. Therefore, formalin-fixed paraffin-embedded tumor samples of 56 HNSCC patients, who have undergone resection and adjuvant radiotherapy, were analyzed by multiplex immunohistochemistry focusing on the detailed phenotypic characterization and spatial distribution of DCs, CD8+ T cells, and T-helper cell subsets in different tumor compartments. Immune cell densities and proportions were correlated with clinical characteristics of the whole HNSCC cohort and different HPV- or hypoxia-associated subcohorts. Tumor stroma was highly infiltrated by plasmacytoid DCs and T lymphocytes. Among the T-helper cells and CD8+ T cells, stromal regulatory T cells and intraepithelial exhausted CD8+ T cells expressing programmed cell death protein-1 (PD-1+) and/or lymphocyte-activation gene-3 (LAG-3+) were the predominant phenotypes, indicating an immunosuppressive TME. HPV-associated tumors showed significantly higher infiltration of type I and type II conventional DCs (cDC1, cDC2) as well as several CD8+ T cell phenotypes including exhausted, activated, and proliferating T cells. On the contrary, tumors with hypoxia-associated gene signatures exhibited reduced infiltration for these immune cells. By multivariate Cox regression, immune-related prognostic factors were identified. Patient clusters defined by high infiltration of DCs and T lymphocytes combined with HPV positivity or low hypoxia showed significantly prolonged survival. Thereby, cDC1 and CD8+ T cells emerged as independent prognostic factors for local and distant recurrence. These results might contribute to the implementation of an immune cell infiltration score predicting HNSCC patients' survival and such patient stratification might improve the design of future individualized radiochemo-(immuno)therapies.

GAPDH: unveiling its impact as a key hypoxia-related player in head and neck squamous cell carcinoma tumor progression, prognosis, and therapeutic potential

Head and neck squamous cell carcinoma (HNSCC), characterized by hypoxia patterns, ranks as the sixth most prevalent malignant tumor worldwide. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays a role in oncogenesis under hypoxic conditions in various cancers. However, its precise function in HNSCC, especially under varied hypoxic conditions, including at high altitudes, remains unclear. Elevated GAPDH mRNA and protein levels in HNSCC relative to normal tissues have been demonstrated through data from The Cancer Genome Atlas (TCGA), GSE29330, and the Human Protein Atlas (P<0.05). This elevation was further confirmed through in vitro experiments utilizing two HNSCC cell lines and a normal oral mucosal epithelial cell line. Additionally, data from TCGA and GSE41613 reveal a correlation between elevated GAPDH expression and diminished overall and progression-free survival in patients (P<0.05). Subsequent analysis identifies GAPDH as an independent risk factor for HNSCC (P<0.05). Using the ESTIMATE and single-sample gene set enrichment analysis (ssGSEA) algorithms, high GAPDH expression was found to be associated with reduced immune scores and diminished anti-tumor cell infiltration, such as CD8+ T cells, in TCGA and GSE41613 datasets (P<0.05). Analysis of single-cell RNA sequencing data from GSE139324 suggests that elevated GAPDH expression hinders communication between plasmacytoid dendritic cells and mast cells (P<0.05). Furthermore, in the TCGA and GSE41613 datasets, GAPDH's biological function is closely tied to hypoxia through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Variation Analysis (GSVA) analyses. Moreover, its expression is linked to one cuproptosis-related gene, five N6-methyladenosine-related genes, six immune checkpoint genes, and pivotal pathways such as MYC and E2F (P<0.05). GAPDH showed excellent predictive value in estimating the efficacy of immunotherapy and 11 anti-tumor drugs (e.g., cisplatin) (P<0.05), using TIDE and pRRophetic algorithms on the TCGA and GSE41613 datasets. Under 1% O2 in vitro, HNSCC cells show elevated GAPDH expression, leading to decreased apoptosis and increased migration, clonogenicity, invasiveness, and resistance to cisplatin (P<0.05). At 5% O2, these effects persisted, albeit less pronouncedly. Inhibiting GAPDH reversed these effects under all oxygen concentrations (P<0.05). Overall, our findings reveal GAPDH as a key hypoxia-related player influencing tumor progression, prognosis, and therapeutic potential in HNSCC.