m7G-related genes—NCBP2 and EIF4E3 determine immune contexture in head and neck squamous cell carcinoma by regulating CCL4/CCL5 expression
Xuhui Xu
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorYue Zhao
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorYukang Ying
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorHaoran Zhu
Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
Search for more papers by this authorJun Luo
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorTingchen Mou
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorCorresponding Author
Zhenxing Zhang
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Correspondence Zhenxing Zhang, Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), No. 999, Donghai Avenue, Taizhou, 318000 Zhejiang, China.
Email: [email protected]
Search for more papers by this authorXuhui Xu
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorYue Zhao
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorYukang Ying
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorHaoran Zhu
Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
Search for more papers by this authorJun Luo
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorTingchen Mou
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Search for more papers by this authorCorresponding Author
Zhenxing Zhang
Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
Correspondence Zhenxing Zhang, Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), No. 999, Donghai Avenue, Taizhou, 318000 Zhejiang, China.
Email: [email protected]
Search for more papers by this authorXuhui Xu and Yue Zhao contributed equally to this work.
Abstract
Aberrant N7-methylguanosine (m7G) levels closely correlate with tumor genesis and progression. NCBP2 and EIF4E3 are two important m7G-related cap-binding genes. This study aimed to identify the relationship between the EIF4E3/NCBP2 function and immunological characteristics of head and neck squamous cell carcinoma (HNSCC). Hierarchical clustering was employed in classifying HNSCC patients into two groups based on the expressions of NCBP2 and EIF4E3. The differentially expressed genes were identified between the two groups, and GO functional enrichment was subsequently performed. Weighted gene co-expression network analysis was conducted to identify the hub genes related to EIF4E3/NCBP2 expression and immunity. The differential infiltration of immune cells and the response to immunotherapy were compared between the two groups. Single-cell sequence and trajectory analyses were performed to predict cell differentiation and display the expression of EIF4E3/NCBP2 in each state. In addition, quantitative real-time PCR, spatial transcriptome analysis, transwell assay, and western blotting were conducted to verify the biological function of EIF4E3/NCBP2. Here, group A showed a higher EIF4E3 expression and a lower NCBP2 expression, which had higher immune scores, proportion of most immune cells, immune activities, expression of immunomodulatory targets, and a better response to cancer immunotherapy. Besides, 56 hub molecules with notable immune regulation significance were identified. A risk model containing 17 hub genes and a prognostic nomogram was successfully established. Moreover, HNSCC tissues had a lower EIF4E3 expression and a higher NCBP2 expression than normal tissues. NCBP2 and EIF4E3 played a vital role in the differentiation of monocytes. Furthermore, the expression of CCL4/CCL5 can be regulated via EIF4E3 overexpression and NCBP2 knockdown. Collectively, NCBP2 and EIF4E3 can affect downstream gene expression, as well as immune contexture and response to immunotherapy, which could induce “cold-to-hot” tumor transformation in HNSCC patients.
Open Research
DATA AVAILABILITY STATEMENT
The data that support the findings of this study are available from the corresponding author upon reasonable request. The original contributions presented in the study are included in the article. Further inquiries can be directed to the corresponding authors.
Supporting Information
| Filename | Description |
|---|---|
| mc23548-sup-0001-Figure_S1.tif18.3 MB | FIGURE S1 Different expression of 24 m7G-regulators. |
| mc23548-sup-0002-Figure_S2.tif13.5 MB | FIGURE S2 Four factors affecting immune response. Patients were classified according to gender (A), HPV infection (B), smoking history (C), and anatomical location (D). |
| mc23548-sup-0003-Figure_S3.tif19.7 MB | FIGURE S3 Comparison of mutational landscapes between two clusters. (A) TMB value. (B) Mutational landscape of Group A and Group B. (C) Difference in gene mutation between two groups. ***P < 0.01 and ***P < 0.001. |
| mc23548-sup-0004-Figure_S4.tif20.8 MB | FIGURE S4 GSE65858 validation of immune contexture in the two groups. (A) Classification of patients into two groups according to NCBP2 and EIF4E3 expressions. (B) Negative correlation between the EIF4E3 and NCBP2 expression. (C) Comparison of ESTIMATE results between the two groups. Comparison of immunotherapeutic targets (D) and immune cell proportions (E) between the two groups. (F) The relationship between the expressions of EIF4E3/NCBP2 and four chemokines was obtained from the GEPIA database. *P < 0.05,**P < 0.01, ***P < 0.001 and ****P < 0.0001. |
| mc23548-sup-0005-Table_S1.doc15 KB | Supporting information. |
| mc23548-sup-0006-Table_S2.doc16.5 KB | Supporting information. |
| mc23548-sup-0007-Table_S3.doc36 KB | Supporting information. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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