We found 13 FAM-related genes differentially expressed in HNSCC and then classified HNSCC patients into three groups with considerably different survival outcomes based on their expression levels in three clusters. Further analysis revealed significant differences between clusters in immune cell infiltration, immune score, stromal score, ESTIMATE score, and tumor purity among these 3 clusters. Next, a 9-gene signature predictive risk model was developed. Using the algorithm, risk scores were then calculated, and median risk scores classified the HNSCC patients in TCGA into high- and low-risk groups. Our study confirmed that the risk score was an independent prognostic factor for HNSCC and had favourable predictive power for OS. Finally, we investigated the correlation between the risk score, immune infiltration, clinicopathological features, and chemotherapeutic treatment responses.
Our study finally identified 9 genes (PLAU, VEGFC, MT2A, TNFRSF12A, CXCL17, ST6GALNAC1, FAM83E, JCHAIN, and SPINK6) that were associated with HNSCC prognosis to construct a gene signature. Of these 9 genes, PLAU, VEGFC, MT2A, and TNFRSF12A were risk genes, expressed at elevated levels in the high-risk group and associated with a poor prognosis. CXCL17, ST6GALNAC1, FAM83E, JCHAIN, and SPINK6 were protective genes. Our study showed that the levels of CXCL17, ST6GALNAC1, FAM83E, JCHAIN, and SPINK6 were higher in the low-risk group and were correlated with a better prognosis. Several studies have proven the significance of the genes above in HNSCC. For instance, PLAU was shown to have a crucial role in tissue remodeling and migration during tumor growth [17, 18]. In HNSCC, PLAU was upregulated, closely correlated with poor survival [19], and was even a key immune-related marker for predicting outcomes [20]. VEGF-C has been characterized as a lymphangiogenic and angiogenic growth, and it has been demonstrated to have a high expression in HNSCC and correlates with a poor prognosis and a positive lymph node status [21]. MT2A was downregulated in HNSCC, reducing cell proliferation, migration, and invasion [22]. TNFRSF12A expression was associated with adverse mortality in patients with HNSCC [23, 24], and it can be used as a target for anticancer drugs [23]. In our study, the levels of CXCL17, ST6GALNAC1, and FAM83E were higher in the low-risk group and were correlated with a good prognosis. In our study, CXCL17, ST6GALNAC1, and FAM83E were higher in the low-risk group and were related to a good prognosis. In malignant tumors, CXCL17 can promote angiogenesis, metastasis, and cell proliferation [25]. In HNSCC, CXCL17 expression is lower than in normal tissue, and higher levels of CXCL17 mRNA are positively correlated with relapse-free survival and OS [26]. ST6GALNAC1 was upregulated in the blood and tissues of oral cancer patients and was related to the advancement of oral cancer [27, 28]. In some malignancies, FAM83E is highly expressed, and its level of expression correlates with the stage of the tumor [29, 30]. Nevertheless, no previous research has revealed a relationship between FAM83E and HNSCC.
JCHAIN (also known as IGJ) encodes the immunoglobulin J chain, the unit that connects IgA and IgM monomers, and it has decreased expression in HNSCC and is related to a better prognosis [31]. JCHAIN is also a new B-cell prognostic biomarker that can predict OS in HNSCC [32, 33]. Many studies have shown a relationship between B-cell immunity and a good prognosis for patients with HNSCC [32–34]. We found that JCHAIN was a highly expressed protective gene in the low-risk group. Additionally, the single-cell dataset analysis revealed that JCHAIN was highly expressed in B cells. Our results suggested that JCHAIN gene expression was related to B cells, and there may be an association between its high expression and a good prognosis.
A study has shown that SPINK6 activates the EGFR pathway to promote NPC metastasis, and higher SPINK6 expression in primary NPC is independently associated with poor prognosis [35]. Our study showed that low-risk patients with high SPINK6 expression had a better prognosis. Furthermore, analysis of single-cell datasets revealed that SPINK6 is highly differentially expressed in cancer cells. Thus, we suggest that SPINK6 may be a prognostic biomarker for HNSCC.
A recent review summarized that HPV impacts cells' ability to reprogram their metabolism by boosting glucose intake, activating glycolysis and the pentose phosphate pathway, and elevating lactate dehydrogenase levels in the cervical epithelium [36]. In a recent investigation of RNA sequencing data, fatty acid synthesis, lipid synthesis, and nucleotide biosynthesis pathways were more abundant in HPV-negative tumors [37]. Human papillomavirus (HPV) status is also a distinct clinical phenotype in HNSCC. Fleming et al. found that HPV-positive and HPV-negative genes differ in the expression of glycolysis, oxidative phosphorylation, and carbohydrate metabolism in HNSCC [38]. Our data showed unique HPV status among subtypes with different fatty acid metabolism landscapes. However, the association between HPV status and fatty acid metabolism remains unclear and how HPV affects fatty acid metabolism encourages us to develop further research in this field.
The TME is a complex environment with a critical function in tumorigenesis, progression, and metastasis. It consists of stromal cells, fibroblasts, endothelial cells, innate immune cells, and adaptive immune cells [39, 40]. Tumor-infiltrating lymphocytes (TILs), which contain T cells, B cells, and NK cells, are representative components of the host's antitumor immune response and have been associated with several cancer prognoses [41–44]. It has been demonstrated in several studies that TILs are related to a better prognosis in HNSCC and can be used as a prognostic marker [45–49]. Additionally, higher CD8 expression in the tumor stroma was associated with no regional lymph node metastasis and was an independent predictor of survival for patients [50]. We analyzed the immune cell infiltration among three clusters of HNSCC patients with different OS based on FAM-related genes and found that most of the immune cells, such as central memory CD4 T cells, effector memory CD8 T cells, MDSCs, memory B cells, monocytes, NK cells, NK T cells, and neutrophils were significantly different in the three clusters. Furthermore, we found higher levels of immune cell infiltration in the low-risk group, especially B and T cells. Since the low-risk group was associated with a better prognosis, we hypothesized that the risk score might be able to estimate the immune status of patients with HNSCC. Higher levels of immune-activated cell infiltration were associated with a better immune response to cancer cells, which may explain the better outcome in low-risk patients.
More than 65% of patients previously treated with HNSCC will develop local recurrences or distant metastases [3]. Treating unresectable patients with local recurrence, recurrent, or metastatic HNSCC has been extremely challenging for physicians. Several studies have demonstrated the effectiveness of immunotherapy in patients with relapsed/metastatic HNSCC and have clinical implications in terms of prolonging OS and a favourable safety profile [51–53]. In the group with the low-risk score, the expression of the majority of immunological checkpoints was elevated. When we investigated the relationship between risk score and chemotherapy, we found that patients in the high-risk group responded more effectively to cisplatin and docetaxel. In addition, analysis of whether risk scores predicted immunotherapy response showed that although neither group had a significant immune response to anti-PD-L1, shorter survival times were observed in patients with high-risk scores for immunotherapy, according to Kaplan‒Meier analysis. Overall, patients with low-risk scores would be more likely to benefit from immunotherapy, while patients with high scores were more likely to benefit from the related chemotherapy drugs. In addition, risk score characteristics may be predictive of OS after immunotherapy in patients with HNSCC.
To predict the survival of patients with HNSCC, we developed a risk score signature that can serve as an independent and reliable prognostic biomarker. It can be used to assess HNSCC patients' clinicopathological features, including HPV infection status, tumor stage, and margin status. In addition, it may be applied to stratify patients with HNSCC and identify the features of their TME cell infiltration to guide more effective clinical practice. Furthermore, the risk score signature can be a predictor of chemotherapy efficacy and overall survival for patients receiving anti-PD-L1 immunotherapy. Our study may help to promote comprehensive treatment, develop novel immunotherapeutic drugs, and provide new ideas for future personalized cancer immunotherapy in HNSCC.