Volume 24, Issue 8 e3441
RESEARCH ARTICLE
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SYNGR2 serves as a prognostic biomarker and correlates with immune infiltrates in esophageal squamous cell carcinoma

Bin Li

Corresponding Author

Bin Li

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

Correspondence

Bin Li, Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, 82 Cuiyingmen, Chengguan District, Lanzhou 730030, Gansu Province, China.

Email: [email protected]

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Mei-Yu Ren

Mei-Yu Ren

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

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Yu-Zhen Chen

Yu-Zhen Chen

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

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Yu-Qi Meng

Yu-Qi Meng

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

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Tie-Niu Song

Tie-Niu Song

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

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Zhi-Peng Su

Zhi-Peng Su

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

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Bo Yang

Bo Yang

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China

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First published: 15 July 2022
Citations: 1

Funding information: Science and Technology Key Research and Development Program of Gansu Province, Grant/Award Number: 20YF3FA032; Key Talent Project of Gansu Province, Grant/Award Number: Gan Zu Tong Zi (2021) 17 Hao

Abstract

Background

Synaptogyrin-2 (SYNGR2) plays an important role in regulating membrane traffic in non-neuronal cells. However, the role of SYNGR2 in esophageal squamous cell carcinoma (ESCC) remains unclear.

Methods

All original data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and integrated via R 3.5.3. SYNGR2 expression was explored in the TCGA and GEO databases. The correlations between SYNGR2 and cancer immune characteristics were analyzed via the TIMER and TISIDB databases.

Results

In general, SYNGR2 was predominantly overexpressed and had reference values in the diagnosis and prognostic estimation of ESCC. Upregulated SYNGR2 was associated with poorer overall survival, disease-specific survival and T stage in ESCC. Mechanistically, we identified hub genes that included a total of 38 SYNGR2-related genes, which were tightly associated with the protein polyubiquitination pathway in ESCC patients. SYNGR2 expression was negatively related to the infiltrating levels of T helper cells. SYNGR2 methylation was positively correlated with the expression of chemokines (CCL2 and CXCL12), chemokine receptors (CCR1 and CCR2), immunoinhibitors (CXCL12 and TNFRSF4) and immunostimulators (CSF1R and PDCD1LG2) in ESCC.

Conclusion

SYNGR2 may be used as a biomarker for determining prognosis and immune infiltration in ESCC.

Abbreviations

  • AUC
  • the area under the ROC curve
  • BP
  • biological process
  • CC
  • cellular component
  • DAVID
  • Database for Annotation, Visualization and Integrated Discover
  • ESCC
  • esophageal squamous cell carcinoma
  • GEO
  • Gene Expression Omnibus
  • GO
  • Gene Ontology
  • GSEA
  • gene set enrichment analysis
  • KEGG
  • Kyoto Encyclopedia of Genes and Genomes
  • MF
  • molecular function
  • OS
  • overall survival
  • ROC
  • receiver operating characteristic
  • SYNGR2
  • synaptogyrin-2
  • TCGA
  • The Cancer Genome Atlas
  • TILs
  • tumor-infiltrating lymphocytes
  • 1 INTRODUCTION

    Esophageal cancer is one of the most common malignancies with the highest morbidity and mortality in the world, and it consists of two histological types, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma.1-4 Among them, ESCC is the main type of esophageal cancer, ranking sixth and fourth in the morbidity and mortality of all malignant tumors in China.5, 6 Although current chemotherapy, radiotherapy and surgery have improved the overall survival of ESCC patients, the prognosis of ESCC patients is poor owing to the high recurrence probability of ESCC and limited treatment methods. In China, the 5-year survival rate of ESCC patients is only approximately 20%.7, 8 Therefore, it is necessary to explore new biomarkers for ESCC diagnosis, prognosis and treatment.

    Immunotherapy has achieved remarkable results in a variety of tumors, but the interaction between ESCC and the immune system is unclear.9, 10 Tumor-infiltrating lymphocytes (TILs) have been shown to have prognostic and predictive roles in ESCC, and TILs can be effective prognostic markers for ESCC.11, 12 TILs can affect the tumor microenvironment by triggering an inflammatory response to form an immunostimulatory, antitumor or protumor microenvironment.13 Studies have shown that the level of T helper cells is related to the prognosis of ESCC.14 Therefore, it is of great clinical significance to study the infiltration of immune cells in ESCC.

    The SYNGR2 gene is located at 17q25.3 and is a member of the synaptogyrin family. SYNGR2 has a transcript length of 1.6 kb and is highly expressed in all organs and tissues except the brain.15 Current studies have indicated that SYNGR2 plays an important role in cellular exocytosis, the storage and transport of GLUT4 at the cytoplasmic membrane, and the formation and maturation of microvesicles in neuronal cells.16 A recent study showed that SYNGR2 was significantly up-regulated during infection with severe fever with thrombocytopenia syndrome bunyavirus. Overexpression of SYNGR2 could induce the formation of synaptic vesicle-like microbubbles in neuroendocrine cells. SYNGR2 triggers the formation of vesicles or the reconstruction of existing vesicles through interaction and aggregation with virtual non-structural proteins, including membrane rearrangement or the fusion of lipid droplets on non-structural proteins, so as to reshape lipid droplets into unique formations of inclusion bodies or virus-like structures, which is conducive to the spread of bunyavirus.17, 18 A study on the cell cycle and apoptosis of lymphocytes induced by the Aggregatibacter actinomycetemcomitans cytolethal distending toxin (cdt) showed that SYNGR2 was highly expressed in human macrophages, promoted the combination of cholesterol in the lipid-rich membrane microdomain and cdtb (the active subunit B of cdt), and internalized and translocated cdtb to intracellular compartments, which played a key role in the cytotoxicity of cdt.19 At present, the achievements regarding synapsin family members in the field of tumor research are limited. Chromophobe renal cell carcinoma and renal oncocytoma are two different types of renal tumors. They have strong morphological and genetic similarities, but the current techniques for detecting the differences between them are very limited. Tan et al. found that SYNGR3 was expressed in the cytoplasm of chromophobe renal cell carcinoma, but not in the cytoplasm of renal oncocytoma. Therefore, SYNGR3 may play an important role in the differential diagnosis of chromophobe renal cell carcinoma and renal oncocytoma.20 However, the function of SYNGR2 in other diseases has been poorly studied, and there are no reports on the role of SYNGR2 in ESCC development and progression.

    To better understand the role of the SYNGR2 gene in ESCC, we comprehensively assessed the relationship between the expression level of SYNGR2 and prognosis in the The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Kaplan–Meier Plotter databases. Additionally, we validated the correlation between SYNGR2 and TILs in the TIMER and TISIDB databases. Our findings suggest that SYNGR2 can be a biomarker for predicting prognosis and immune cell infiltration in ESCC patients.

    2 MATERIAL AND METHODS

    2.1 Patient datasets

    The mRNA expression data (including 82 ESCC samples and one adjacent non-tumor sample, RNAseq, TPM) and clinical information were downloaded from the TCGA database (https://cancergenome.nih.gov).21 We also downloaded the following gene expression profiles from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)22: GSE26886 (including nine ESCC samples and 19 normal esophageal squamous epithelium samples),23 GSE45670 (including 28 ESCC samples and 10 normal esophageal epithelial samples)24 and GSE161533 (including 28 ESCC samples, 28 paired adjacent non-tumor samples and 28 normal esophageal epithelial samples).24

    2.2 Survival analysis

    Kaplan–Meier plots were generated, and the log-rank test was performed using ESCC data from the TCGA database by the R survival package to estimate the correlation between SYNGR2 expression and the survival rate of different clinical features in ESCC patients. The hazard ratio (HR) and log-rank p-value of the 95% confidence interval were also calculated.

    2.3 Establishment and evaluation of the nomograms for ESCC survival prediction

    The receiver operating characteristic (ROC) curve of diagnosis and time-dependent curve of diagnosis were created using R packages, including the pROC and time-ROC. Independent clinicopathological prognostic variables were chosen from Cox regression analysis, and a nomogram was constructed using the R package to evaluate the 1-, 3-, and 5-year overall survival (OS) probability of ESCC patients.

    2.4 Protein–protein interaction network

    Protein–protein interaction data were extracted from the STRING database (https://string-db.org) based on protein interactions and signaling pathways to predict the protein–protein interaction network of SYNGR2 coexpressed genes.25 An interaction with a combined score >0.15 was considered statistically significant. The network was constructed using Cytoscape 3.9.1 applications.26

    2.5 Functional enrichment analysis

    To understand the biological processes and pathways that SYNGR2 may participate in, we conducted the following analysis. The first 471 genes related to SYNGR2 in ESCC and the first 913 genes related to ESCC survival were obtained from the TCGA. These genes were enriched by Gene Ontology (GO) (including biological processes, cellular components and molecular function) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using the Database for Annotation, Visualization and Integrated Discover (DAVID) and visualized by the R package ggplot2.27 A corrected p < 0.05 was determined to be statistically significant.

    2.6 Immune infiltration analysis by single-sample GSEA

    Immune infiltration analysis of ESCC samples was performed by the single-sample gene set enrichment analysis (GSEA) method using the GSVA package in R (http://www.biocondutor.org/package/release/bioc/html/GSVA.html) for 24 types of immune cells. Spearman’s correlation coefficient analysis was performed to identify relationships between ESCC and each immune cell subset.

    2.7 LinkedOmics database analysis

    The LinkedOmics database (http://www.linkedomics.org) was used to explore the expression profile of SYNGR2. We explored the GO and KEGG pathways of SYNGR2 and its coexpressed genes using GSEA in the Link Interpreter module.28

    2.8 TISIDB database analysis

    TISIDB is an integrated knowledge base portal that plays a vital role in detecting the interaction between tumors and the immune system (http://cis.hku.hk/TISIDB/).29 To further clarify the immune correlation of SYNGR2 in cancer, we used the “Immunomodulator” module of the TISIDB database to analyze and evaluate the correlation between SYNGR2 methylation levels and the levels of immune checkpoint genes. We further studied the association between SYNGR2 methylation levels and chemokine/chemokine receptor expression through the “chemokine” module.

    2.9 Statistical analysis

    Box plots were used to assess the expression level of the SYNGR2 gene in ESCC patients. The cutoff value of SYNGR2 expression was selected as the median method of gene expression. The Wilcoxon signed-rank test and logistic regression were used to investigate the relationship between clinical characteristics and SYNGR2 expression in ESCC. Forest plots were constructed using the R package “forestplot”. Univariate Cox analysis was performed to test for possible prognostic factors, and multivariate Cox analysis was utilized to confirm the influence of SYNGR2 expression on survival in conjunction with other clinical variables. R statistical software (version 3.5.3) or SPSS software was used for all statistical analyses (version 24.0). Statistical significance was defined as a p-value less than 0.05.

    3 RESULTS

    3.1 Baseline characteristics of patients

    Data from a total of 82 ESCC patients with the required clinical features were acquired from the TCGA data portal. The detailed clinical features are listed in Table 1. Among the 82 participants, 70 were male (75.4%) and 12 were female (14.6%). Among them, 63 patients (64.6%) were younger than or equal to 65 years, and 29 patients (35.4%) were older than 60 years. In terms of ESCC stage, seven patients were stage I (8.9%), 47 patients were stage II (59.5%), 22 patients were stage III (27.8%) and three patients were stage IV (3.8%). In terms of histological grade, 15 patients were grade 1 (20.8%), 38 patients were grade 2 (52.8%) and 19 patients were grade 3 (26.4%).

    TABLE 1. Clinical characteristics of esophageal squamous cell carcinoma patients
    Characteristic Low expression of SYNGR2 High expression of SYNGR2 p-Value
    n 41 41
    T stage, n (%) 0.114
    T1 3 (3.8%) 5 (6.3%)
    T2 10 (12.7%) 17 (21.5%)
    T3 26 (32.9%) 15 (19%)
    T4 1 (1.3%) 2 (2.5%)
    N stage, n (%) 0.246
    N0 26 (33.3%) 20 (25.6%)
    N1 12 (15.4%) 14 (17.9%)
    N2 1 (1.3%) 4 (5.1%)
    N3 0 (0%) 1 (1.3%)
    M stage, n (%) 0.615
    M0 36 (49.3%) 34 (46.6%)
    M1 1 (1.4%) 2 (2.7%)
    Pathological stage, n (%) 1.000
    Stage I 4 (5.1%) 3 (3.8%)
    Stage II 24 (30.4%) 23 (29.1%)
    Stage III 11 (13.9%) 11 (13.9%)
    Stage IV 1 (1.3%) 2 (2.5%)
    Radiation therapy, n (%) 0.857
    No 25 (32.9%) 22 (28.9%)
    Yes 14 (18.4%) 15 (19.7%)
    Primary therapy outcome, n (%) 0.217
    PD 2 (3.1%) 4 (6.2%)
    SD 2 (3.1%) 0 (0%)
    PR 0 (0%) 1 (1.6%)
    CR 33 (51.6%) 22 (34.4%)
    Gender, n (%) 0.755
    Female 7 (8.5%) 5 (6.1%)
    Male 34 (41.5%) 36 (43.9%)
    Race, n (%) 0.744
    Asian 19 (23.8%) 18 (22.5%)
    Black or African American 2 (2.5%) 4 (5%)
    White 20 (25%) 17 (21.2%)
    Age, n (%) 1.000
    ≤60 27 (32.9%) 26 (31.7%)
    >60 14 (17.1%) 15 (18.3%)
    Weight, n (%) 0.744
    ≤70 30 (37%) 33 (40.7%)
    >70 10 (12.3%) 8 (9.9%)
    Height, n (%) 0.957
    <170 14 (17.9%) 16 (20.5%)
    ≥170 24 (30.8%) 24 (30.8%)
    BMI, n (%) 0.885
    ≤25 30 (38.5%) 30 (38.5%)
    >25 8 (10.3%) 10 (12.8%)
    Histological type, n (%) 1.000
    Squamous cell carcinoma 41 (50%) 41 (50%)
    Residual tumor, n (%) 0.674
    R0 31 (43.7%) 34 (47.9%)
    R1 3 (4.2%) 1 (1.4%)
    R2 1 (1.4%) 1 (1.4%)
    Histological grade, n (%) 0.785
    G1 7 (9.7%) 8 (11.1%)
    G2 19 (26.4%) 19 (26.4%)
    G3 11 (15.3%) 8 (11.1%)
    Smoker, n (%) 1.000
    No 13 (16.5%) 14 (17.7%)
    Yes 26 (32.9%) 26 (32.9%)
    Alcohol history, n (%) 0.293
    No 12 (15%) 7 (8.8%)
    Yes 28 (35%) 33 (41.2%)
    Barrett’s esophagus, n (%) 1.000
    No 27 (46.6%) 31 (53.4%)
    Yes 0 (0%) 0 (0%)
    Reflux history, n (%) 0.482
    No 25 (37.3%) 29 (43.3%)
    Yes 4 (6%) 9 (13.4%)
    Tumor central location, n (%) 0.113
    Distal 21 (25.9%) 17 (21%)
    Mid 15 (18.5%) 22 (27.2%)
    Proximal 5 (6.2%) 1 (1.2%)
    Columnar mucosa dysplasia, n (%) 1.000
    High-grade dysplasia 2 (8.7%) 2 (8.7%)
    Low-grade dysplasia 0 (0%) 0 (0%)
    Negative/no dysplasia 7 (30.4%) 12 (52.2%)
    Columnar metaplasia, n (%) 1.000
    No 19 (44.2%) 23 (53.5%)
    Yes 0 (0%) 1 (2.3%)
    OS event, n (%) 0.009
    Alive 34 (41.5%) 22 (26.8%)
    Dead 7 (8.5%) 19 (23.2%)
    DSS event, n (%) 0.062
    Alive 36 (43.9%) 28 (34.1%)
    Dead 5 (6.1%) 13 (15.9%)
    PFI event, n (%) 0.657
    Alive 24 (29.3%) 21 (25.6%)
    Dead 17 (20.7%) 20 (24.4%)
    Age, mean ± SD 58.05 ± 10.9 58.51 ± 10.08 0.842
    • Abbreviations: BMI, body mass index; CR, complete response; DSS, disease-specific survival; PD, progressive disease; PFI, progression-free interval; PR, partial response; OS, overall survival; SD, stable disease; SYNGR2, Synaptogyrin-2.

    3.2 SYNGR2 is highly expressed in ESCC

    To explore the expression level of SYNGR2 in normal and tumor tissues, we downloaded and analyzed the expression levels of SYNGR2 mRNA in different tumors and normal tissues from the TCGA using the R package. The results showed that SYNGR2 expression was significantly higher in tumor tissues such as esophageal carcinoma, bladder urothelial carcinoma, breast cancer, colon adenocarcinoma, head and neck squamous cell carcinoma, glioblastoma multiforme, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, pheochromocytoma and paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma, stomach adenocarcinoma, thyroid carcinoma and uterine corpus endometrial carcinoma than in normal tissues. In addition, lower expression was observed in kidney chromophobe (Figure 1A). We used the TCGA database to evaluate the mRNA expression levels of SYNGR2 in ESCC patients and compared these with the expression levels in adjacent tissues. The results showed that the expression level of SYNGR2 in ESCC was significantly higher than that in paracarcinoma tissues (p < 0.001; Figure 1B). The results were verified in ESCC and paired paracarcinoma tissues (Figure 1C). Next, we used logistic analysis to analyze the relationship between different clinical parameters and the prognosis of patients, and we found that the T stage was associated with OS (Table 2). To analyze the correlation between the SYNGR2 expression and clinical characteristics in ESCC patients, we analyzed the mRNA expression levels of SYNGR2 in different clinical categories in the TCGA database. The association identified between SYNGR2 expression and clinical features in patients with ESCC is summarized in Table 3. The results showed that high expression of SYNGR2 was significantly related to T stage (p < 0.05) and OS (p < 0.05) (Figure 1D and Table 3). These data suggest that SYNGR2 is significantly upregulated in ESCC.

    Details are in the caption following the image
    The expression level of Synaptogyrin-2 (SYNGR2) in different human cancers. (A) Increased or decreased SYNGR2 expression in datasets of different cancers compared with normal tissues in the The Cancer Genome Atlas (TCGA) database. (B–E) Expression level of SYNGR2 in normal tissues and paired adjacent tissues [unmatched tissues (B) and matched tissues (C)] and tumor tissues from patients with different clinical characteristics in TCGA [T stage (D) and overall survival event (E)]. *p < 0.05, **p < 0.01, ***p < 0.001.
    TABLE 2. Logistic analysis of the association between SYNGR2 expression and clinical characteristics
    Characteristics Total (N) Odds ratio p-Value
    T stage (T3 and T4 vs. T1 and T2) 79 0.372 (0.146–0.917) 0.034
    N stage (N1, N2 and N3 vs. N0) 78 1.900 (0.767–4.826) 0.169
    M stage (M1 vs. M0) 73 2.118 (0.194–46.801) 0.548
    Pathological stage (stages III and IV vs. stages I and II) 79 1.167 (0.450–3.043) 0.750
    Histological grade (G2 and G3 vs. G1) 72 0.787 (0.245–2.477) 0.681
    Age (>60 vs. ≤60) 82 1.113 (0.449–2.773) 0.817
    Gender (male vs. female) 82 1.482 (0.432–5.432) 0.534
    BMI (>25 vs. ≤25) 78 1.250 (0.434–3.693) 0.679
    Smoker (yes vs. no) 79 0.929 (0.363–2.362) 0.876
    Alcohol history (yes vs. no) 80 2.020 (0.713–6.090) 0.193
    Radiation therapy (yes vs. no) 76 1.218 (0.481–3.101) 0.677
    Residual tumor (R1 and R2 vs. R0) 71 0.456 (0.060–2.505) 0.383
    Race (Black or African American and White vs. Asian) 80 1.008 (0.417–2.437) 0.987
    Weight (>70 vs. ≤70) 81 0.727 (0.247–2.082) 0.553
    Height (≥170 vs. <170) 78 0.875 (0.348–2.184) 0.775
    Reflux history (yes vs. no) 67 1.940 (0.558–7.868) 0.315
    Tumor central location (mid and proximal vs. distal) 81 1.421 (0.593–3.445) 0.432
    Columnar mucosa dysplasia (high-grade dysplasia vs. negative/no dysplasia) 23 0.583 (0.058–5.759) 0.626
    TABLE 3. Univariate and multivariate cox regression analyses of clinical characteristics associated with overall survival
    Characteristics Total (N) Univariate analysis Multivariate analysis
    Hazard ratio (95% CI) p-Value Hazard ratio (95% CI) p-Value
    T stage 79
    T1 and T2 35 Reference
    T3 and T4 44 0.942 (0.414–2.142) 0.887
    N stage 78
    N0 46 Reference
    N1, N2 and N3 32 2.337 (1.007–5.425) 0.048 0.983 (0.287–3.367) 0.979
    M stage 73
    M0 70 Reference
    M1 3 3.197 (0.909–11.238) 0.070 1.028 (0.247–4.275) 0.970
    Pathological stage 79
    Stages I and II 54 Reference
    Stages III and IV 25 2.178 (0.958–4.952) 0.063 1.748 (0.563–5.430) 0.334
    Histological grade 72
    G1 15 Reference
    G2 and G3 57 1.293 (0.434–3.851) 0.645
    Smoker 79
    No 27 Reference
    Yes 52 1.661 (0.620–4.447) 0.313
    Age 82
    ≤60 53 Reference
    >60 29 1.592 (0.676–3.749) 0.288
    Gender 82
    Male 70 Reference
    Female 12 0.100 (0.013–0.756) 0.026 0.000 (0.000-Inf) 0.998
    BMI 78
    ≤25 60 Reference
    >25 18 1.066 (0.434–2.619) 0.889
    Residual tumor 71
    R0 65 Reference
    R1 and R2 6 2.454 (0.804–7.489) 0.115
    Reflux history 67
    No 54 Reference
    Yes 13 1.348 (0.524–3.469) 0.536
    Alcohol history 80
    No 19 Reference
    Yes 61 3.087 (0.722–13.204) 0.128
    SYNGR2 82
    Low 41 Reference
    High 41 3.756 (1.546–9.128) 0.003 3.309 (1.116–9.812) 0.031
    • Note: Values with p-value < 0.05 are in bold.

    3.3 Validation using independent external databases and clinical specimens

    To further verify the expression level of SYNGR2 in ESCC, we selected another three independent external GEO datasets (validation cohort) to analyze the SYNGR2 transcription levels of cancer tissues and adjacent tissues in SYNGR2, including GSE26886, GSE45670 and GSE161533. The results showed that the transcription level of SYNGR2 in ESCC was significantly higher than that in non-cancerous adjacent tissues from ESCC datasets (GSE26886, GSE45670 and GSE161533, p < 0.001; Figure 2A–C). The results of this comparison were also verified in ESCC tissues and accurately matched non-cancerous tissues (GSE161533, p < 0.001; Figure 2D). These data verify that SYNGR2 is highly expressed in ESCC.

    Details are in the caption following the image
    Validation of the high expression of SYNGR2 in esophageal squamous cell carcinoma (ESCC) using independent external databases. (A–C) Expression of SYNGR2 in tumor and unpaired paracarcinoma tissues in the GSE26886, GSE45670 and GSE161533 datasets in the Gene Expression Omnibus (GEO) database. (D) Expression level of SYNGR2 in tumor and paired adjacent tissues in the GSE161533 datasets of the GEO database. *p < 0.05, ***p < 0.001.

    3.4 High expression of SYNGR2 is an independent prognostic factor for the overall survival of ESCC

    To identify whether SYNGR2 expression affects patient survival, we classified ESCC patients in the TCGA database into a high SYNGR2 expression group (the top 50% of samples with the highest expression) and a low SYNGR2 expression group (the remaining 50% of the samples) to perform survival analysis according to the mean expression value of SYNGR2. The Kaplan–Meier survival analysis showed that the high expression of SYNGR2 was related to the overall survival (HR = 4.34, p = 0.002) and disease-specific survival (HR = 3.64, p = 0.015) of ESCC patients (Figure 3A and B). Subgroup analysis showed that high SYNGR2 expression was significantly correlated with poor prognosis in ESCC in the following cases: T1, T2 and T3 stages, HR = 4.23, p = 0.006; T2 and T3 stages, HR = 3.67, p = 0.015; T3 and T4 stages, HR = 4.58, p = 0.025; N0 stage, HR = 5.20, p = 0.044; pathological stages I and II, HR = 4.91, p = 0.023; pathological stages II and III, HR = 5.10, p = 0.005; histological grades 1 and 2, HR = 4.31, p = 0.023; histological grades 2 and 3, HR = 3.53, p = 0.029; male sex, HR = 3.37, p = 0.008; and age ≤60 years old, HR = 3.66, p = 0.024. These data are shown in Figure 3C–L. Univariate Cox analysis demonstrated that high SYNGR2 expression was significantly correlated with poor OS (HR = 3.309, 95% CI = 1.126–9.812, p = 0.031; Figure 4, Table 3). These data suggest that high expression of SYNGR2 is an independent prognostic factor for the OS of ESCC patients.

    Details are in the caption following the image
    Kaplan–Meier survival curve analysis of the prognostic significance of high and low expression of SYNGR2 in ESCC using TCGA. (A) Kaplan–Meier estimates of the overall survival probability of TCGA patients in all ESCC patients. (B) Kaplan–Meier estimates of the disease-free survival probability of TCGA patients in all ESCC patients. (C–L) Subgroup analysis for T1 and T2 and T3 (C), T2 and T3 (D), T3 and T4 (E), stage N0 (F), pathological stages I and II (G), pathological stages II and III (H), histological stages G1 and G2(I), histological stages G2 and G3 (J), male sex (K) and age lower than 60 years (L).
    Details are in the caption following the image
    Forest plot of the multivariate Cox regression analysis in ESCC.

    3.5 Diagnostic value of SYNGR2 expression in ESCC

    To analyze the diagnostic value of SYNGR2 expression in ESCC, we drew the ROC curve and performed nomogram analyses on the SYNGR2 gene expression data from the TCGA database to evaluate the diagnostic value of the gene. The area under the ROC curve (AUC) was 0.881, suggesting a higher diagnostic value, as shown in Figure 5A. A time-dependent survival ROC curve of SYNGR2 was created to predict the 1, 3 and 5 year survival rates. All of these AUC values were >0.55, which is considered suitable for prediction (Figure 5B). Then, we combined the expression level of SYNGR2 with the clinical variables to construct a nomogram to predict the survival probability of patients at 1, 3 and 5 years. The nomogram indicated that the prognostic prediction of the expression level of SYNGR2 was better than that of the traditional clinical features of age, T stage, M stage and histological grade (Figure 5C).

    Details are in the caption following the image
    Diagnostic value of SYNGR2 expression in ESCC. (A) Receiver operating characteristic (ROC) curve analysis for SYNGR2 expression in ESCC and adjacent tissue. (B) Time-dependent survival ROC analysis for SYNGR2 expression in ESCC and adjacent tissue to predict 1, 3 and 5 year survival rates. (C) Nomogram survival prediction chart for predicting the 1, 3 and 5 year overall survival rates.

    3.6 Functional enrichment and analyses of SYNGR2-related genes in ESCC

    To understand the biological function of SYNGR2 in ESCC, we used the LinkFinder module of the LinkedOmics website to detect the coexpression pattern of SYNGR2 in ESCC in the TCGA database. The red dot indicates the top 25 genes that were positively correlated with SYNGR2, and the green dot represents the bottom 25 genes that were negatively correlated with SYNGR2 (Figure 6A). We used DAVID Functional Annotation Bioinformatics Microarray Analysis to identify the enriched GO functional enrichment and KEGG pathways among the SYNGR2-related genes (top 600) and found that the steroid metabolic process, small molecule catabolic process and steroid biosynthetic process were enriched among these genes (Figure 6B and Table 4). To identify genes with the same regulatory direction in high SYNGR2 and non-survival patients, we crossed the 471 genes (the absolute value of correlation coefficient ≥0.3) with the highest SYNGR2 correlation with the 913 survival-related upregulated genes (p Cox < 0.05) in ESCC and detected 38 genes at the intersection that were related to SYNGR2 and ESCC survival (Figure 6C). These 38 protein-coding genes may be potential genetic biomarkers for ESCC patients. GO functional enrichment and KEGG pathway analysis were performed for these 38 genes, and the results showed that differentially expressed genes were significantly enriched in retinal cone cell differentiation, retinal cone cell development and protein polyubiquitination (Figure 6D and Table 5). After discovering significantly different pathways, protein–protein interactions and correlated analysis were used to identify the interactions between these 38 proteins. We found that there was a stronger enrichment network among these proteins than in random proteins (Figure 6E). Gene coexpression correlation analysis showed that most of the proteins in the network had a strong positive correlation with each other (Figure 6F). Therefore, these SYNGR2-associated established genes have a strong intertwined interaction and can be used as multigene biomarkers to predict the survival of ESCC patients.

    Details are in the caption following the image
    SYNGR2 functional clustering and interaction network analysis of SYNGR2-related genes. (A) Heatmap showing the top 50 genes in ESCC that were positively and negatively related to SYNGR2. Red represents positively related genes and blue represents negatively related genes. (B) Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of SYNGR2-related genes in ESCC. (C) Venn diagram of SYNGR2-related genes and survival-related and upregulated genes in ESCC. (D) GO term and KEGG pathway analyses of SYNGR2-related genes and ESCC survival-related genes in ESCC. (E) SYNGR2-related gene interaction network. (F) Gene coexpression matrix.
    TABLE 4. Gene sets enriched in the SYNGR2-related genes (top 600)
    Ontology ID Description Gene ratio Bg ratio p-Value p-Adjust q-Value
    BP GO:0008202 Steroid metabolic process 26/528 331/18670 2.91 × 10−6 0.012 0.011
    BP GO:0044282 Small molecule catabolic process 30/528 445/18670 1.11 × 10−5 0.017 0.016
    BP GO:0006694 Steroid biosynthetic process 18/528 196/18670 1.22 × 10−5 0.017 0.016
    BP GO:0010498 Proteasomal protein catabolic process 30/528 477/18670 4.12 × 10−5 0.042 0.041
    BP GO:0031146 SCF-dependent proteasomal Ubiquitin-dependent protein catabolic process 11/528 95/18670 7.62 × 10−5 0.057 0.055
    CC GO:0005774 Vacuolar membrane 27/558 412/19717 5.09 × 10−5 0.021 0.019
    CC GO:0098852 Lytic vacuole membrane 24/558 355/19717 8.15 × 10−5 0.021 0.019
    CC GO:0098798 Mitochondrial protein complex 19/558 262/19717 1.81 × 10−4 0.021 0.019
    CC GO:0000152 Nuclear ubiquitin ligase complex 7/558 43/19717 1.86 × 10−4 0.021 0.019
    CC GO:0005765 Lysosomal membrane 23/558 354/19717 2.04 × 10−4 0.021 0.019
    MF GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor 10/530 60/17697 1.05 × 10−5 0.005 0.004
    MF GO:0016616 Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 14/530 119/17697 1.30 × 10−5 0.005 0.004
    MF GO:0004032 Alditol: NADP+ 1-oxidoreductase activity 5/530 13/17697 2.49 × 10−5 0.005 0.005
    MF GO:0016614 Oxidoreductase activity, acting on CH-OH group of donors 14/530 128/17697 3.00 × 10−5 0.005 0.005
    MF GO:0016627 Oxidoreductase activity, acting on the CH–CH group of donors 9/530 58/17697 5.22 × 10−5 0.007 0.007
    KEGG hsa05012 Parkinson disease 23/245 249/8076 1.72 × 10−6 4.73 × 10−4 4.35 × 10−4
    KEGG hsa05010 Alzheimer disease 28/245 369/8076 6.23 × 10−6 8.60 × 10−4 7.90 × 10−4
    KEGG hsa05020 Prion disease 21/245 273/8076 7.86 × 10−5 0.007 0.006
    KEGG hsa05022 Pathways of neurodegeneration—multiple diseases 30/245 475/8076 9.78 × 10−5 0.007 0.006
    KEGG hsa00190 Oxidative phosphorylation 13/245 133/8076 1.88 × 10−4 0.010 0.010
    • Abbreviations: BP, biological process; Bg, background; CC, cellular component; ES, enrichment score; FDR, false discovery rate; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function; NOM, nominal. Gene sets with NOM p-value < 0.05 and FDR q-value < 0.25 were considered as significantly enriched.
    TABLE 5. Gene sets enriched in the 38 genes at the intersection that were related to SYNGR2 and esophageal squamous cell carcinoma (ESCC) survival
    Ontology ID Description Gene ratio Bg ratio p-Value p-Adjust q-Value
    BP GO:0042670 Retinal cone cell differentiation 2/34 11/18670 1.75 × 10−4 0.061 0.050
    BP GO:0046549 Retinal cone cell development 2/34 11/18670 1.75 × 10−4 0.061 0.050
    BP GO:0000209 Protein polyubiquitination 5/34 310/18670 2.29 × 10−4 0.061 0.050
    BP GO:1902036 Regulation of hematopoietic stem cell differentiation 3/34 72/18670 3.02 × 10−4 0.061 0.050
    BP GO:0060218 Hematopoietic stem cell differentiation 3/34 83/18670 4.59 × 10−4 0.063 0.051
    MF GO:0015078 Proton transmembrane transporter activity 3/32 133/17697 0.002 0.093 0.066
    MF GO:0044769 ATPase activity, coupled to transmembrane movement of ions, rotational mechanism 2/32 36/17697 0.002 0.093 0.066
    MF GO:0019842 Vitamin binding 3/32 138/17697 0.002 0.093 0.066
    • Abbreviations: BP, biological process; CC, cellular component; ES, enrichment score. Gene sets with NOM p-value < 0.05 and FDR q value < 0.25 were considered as significantly enriched.

    3.7 Correlation of SYNGR2 expression with immune characteristics

    To explore the correlation between the expression level of SYNGR2 and the tumor immune response, we used the TIMER database to investigate immune infiltration in ESCC with different SYNGR2 expression levels. The expression of SYNGR2 was negatively correlated with T helper cells (Figure 7A). We further analyzed the correlation between the expression level of SYNGR2 and immune infiltration in ESCC, and the results showed that the expression level of SYNGR2 was negatively correlated with the infiltrating levels of T helper cells (r = −0.264, p = 0.017; Figure 7B). Therefore, we used TISIDB to analyze the correlation between the methylation level of SYNGR2 and immune cell chemokines and chemokine receptors in ESCC. The heatmap results showed that several chemokines and chemokine receptors were significantly correlated with the methylation level of SYNGR2 in ESCC (Figure 8A, B). These results demonstrate that SYNGR2 methylation may play an important role in tumor immunity. To further clarify the relationship between SYNGR2 methylation and immune cell migration, we comprehensively analyzed the correlation between SYNGR2 methylation and chemokine/chemokine receptors. The results showed that SYNGR2 methylation was positively correlated with CCL2 (r = 0.404, p < 1.6 × 10−8), CXCL12 (r = 0.393, p < 4.04 × 10−8), CCR1 (r = 0.321, p < 9.65 × 10−6) and CCR2 (r = 0.337, p < 3.21 × 10−14; Figure 8C–F). These data indicated that SYNGR2 methylation is positively correlated with the expression of chemokines/chemokine receptors in ESCC. Immune checkpoint inhibitors are a significantly novel strategy for tumor immunotherapy that has gradually improved the prognosis of patients with many types of cancers. Subsequently, we analyzed the correlation between SYNGR2 methylation and the expression of immunoinhibitors and immunostimulators in different types of human cancers using the TISIDB database (Figure 9A, B). Interestingly, SYNGR2 methylation was positively correlated with CCL12 (r = 0.393, p < 4.04 × 10−8), TNFRSF4 (r = 0.338, p < 3 × 10−6), CSF1R (r = 0.395, p < 3.5 × 10−8) and PDCD1LG2 (r = 0.348, p < 1.46 × 10−6) (Figures 9C–F). Therefore, these results suggest that SYNGR2 may play a role in regulating tumor immunity.

    Details are in the caption following the image
    The expression level of SYNGR2 was associated with immune infiltration in the tumor microenvironment. (A) Correlation between the relative abundances of 24 immune cells and SYNGR2 expression levels. The size of the dots shows the absolute value of the Spearman R. (B) Correlation diagrams showing the relationship between the T helper cell infiltration level and SYNGR2 expression.
    Details are in the caption following the image
    Correlation analysis between SYNGR2 methylation and chemokines and/or chemokine receptors. (A) Heatmap analysis of the correlation between SYNGR2 and chemokines in tumors. (B) Heatmap analysis of the correlation between SYNGR2 methylation and chemokine receptors in tumors. (C–F) SYNGR2 methylation in ESCC is positively correlated with CCL2, CXCL12, CCR1 and CCR2.
    Details are in the caption following the image
    Correlation analysis between SYNGR2 methylation and immunoinhibitors and immunostimulators. (A) Correlation between SYNGR2 and immunoinhibitors in tumors by heatmap analysis. (B) Correlation between SYNGR2 and immunostimulators in tumors by heatmap analysis. (C–F) SYNGR2 methylation in ESCC is positively correlated with CCL12, TNFRSF4, CSF1R and PDCD1LG2.

    4 DISCUSSION

    SYNGR2 plays an important role in biological processes such as cell exocytosis, the storage and transport of GLUT4 in the cytoplasmic membrane, and the formation and maturation of microvesicles in neuronal cells.16 A recent study indicated that SYNGR2 can be used as a promoter to enhance the infectivity of novel tick-borne bunyaviruses in humans.17 However, there are no reports of SYNGR2 in tumors. We integrated multiple bioinformatic analysis methods to determine the biological functions and potential regulatory pathways in ESCC. In this study, we first determined the expression and prognostic value of the SYNGR2 gene in cancer and found that the expression level of SYNGR2 was upregulated in ESCC. High SYNGR2 expression was associated with poorer OS in ESCC. Moreover, a high SYNGR2 expression level was associated with poorer T stage and poorer overall survival and disease-specific survival. In addition, we also found that SYNGR2 has an important reference value for the diagnosis of ESCC. These findings strongly suggest that SYNGR2 can be used as a biomarker for ESCC diagnosis and prognosis.

    To explain the underlying molecular mechanism by which SYNGR2 affects ESCC prognosis, we defined 38 genes in the SYNGR2 gene network as our hub genes, which included 913 genes closely associated with ESCC prognosis and 471 genes with the highest correlation with SYNGR2 intersection. Then, we further analyzed the biological processes and signaling pathways of the hub genes using GO functional enrichment and KEGG pathway analyses. The enrichment results suggested that most of the hub genes were related to biological processes such as protein polyubiquitination. Protein polyubiquitination is a common biological process in cells, and a large number of studies have suggested that it plays an important role in the progression of ESCC.30, 31 A study indicated that the protein FLOT1 in ESCC cells promotes the recruitment of tumor necrosis factor-alpha receptors to lipid rafts, promotes polyubiquitination of tumor necrosis factor receptor-associated factor 2 and receptor-interacting proteins, and persists in activating NF-κB.32 Zhao et al. pointed out that the protein FAM175B inhibits ATF4 ubiquitination and promotes ESCC cell apoptosis in a p53-independent manner.33 Therefore, SYNGR2 may be involved in regulating ESCC progression by regulating protein polyubiquitination.

    Numerous studies have pointed out that the development of cancer is closely related to the tumor microenvironment.34 The tumor microenvironment is composed of immune cells, extracellular matrix and inflammatory mediators, which interact with each other to promote the growth, survival and metastasis of tumor cells.35, 36 Although an effective immune response can produce antitumor effects, cancer cells can evade attack by immune cells through antigen presentation dysfunction and the recruitment of immunosuppressive cells.37, 38 Previous studies have reported that the degree of immune cell infiltration in tumors can affect the prognosis of patients, and the grade of tumor-infiltrating lymphocytes is an independent predictor of the prognosis of tumor patients.39, 40 This study explored the correlation between SYNGR2 expression and the level of immune infiltration in ESCC. Our results showed that the expression of SYNGR2 was negatively correlated with the infiltration level of T helper cells. Studies have shown that the frequency of Th cells in ESCC patients is significantly reduced, and the average expression of IFN-γ in Th cells is also greatly reduced, indicating that the dysregulation of Th-cell subsets contributes to the occurrence and development of ESCC.14, 41, 42 These findings suggest that SYNGR2 may play an important regulatory role in the tumor immune microenvironment and ESCC development.

    Chemokines and their receptors play an important role in the directed migration of immune cells. In this study, the TISIDB database was used to analyze the correlation between the methylation level of SYNGR2 and the expression of immune cell chemokines and chemokine receptors in ESCC. The results showed that the methylation level of SYNGR2 was positively correlated with the expression of CCL2, CXCL12, CCR1 and CCR2, suggesting that the methylation of SYNGR2 may inhibit the migration of immune cells to the tumor microenvironment. The CCL2–CCR2 axis, one of the major chemokine signaling pathways, increases tumor cell proliferation and invasiveness during tumor progression and creates the tumor microenvironment by increasing angiogenesis and recruitment of immunosuppressive cells.43-45 The interaction of CXCL12 and its receptor CXCR4 stimulates downstream signaling pathways, which affect tumor angiogenesis, tumor cell proliferation and chemotherapy resistance.46-48 In addition, studies have pointed out that CCL3/CCR1 can promote the chemotaxis of monocytes in tumors and affect tumor angiogenesis and cell proliferation.49, 50 This may explain the mechanism by which SYNGR2 regulates immune infiltration in ESCC.

    In conclusion, our study found that the expression of SYNGR2 was significantly upregulated and closely related to the poor prognosis of ESCC patients. SYNGR2 has a certain reference value for the diagnosis and prognosis of ESCC. SYNGR2 may affect ESCC progression through immune infiltration and it could serve as a novel premarker for ESCC patients.

    However, even though we systematically analyzed SYNGR2 and performed cross-validation using different databases, this study has limitations. First, the role of SYNGR2 in ESCC may vary in the reproducibility of microarray data generated by different laboratories. Second, we need in vivo and in vitro experiments to demonstrate the effect of SYNGR2 on ESCC to increase the reliability of our results. Third, our results show that the AUC area of SYNGR2 is 0.881, indicating that SYNGR2 has a good diagnostic effect on esophageal cancer. At present, the relevant experiments for detecting SYNGR2 in peripheral blood and liver tissues are in progress, and the relevant research results will be published in the follow-up research reports. Finally, although we concluded that SYNGR2 is closely associated with immune infiltration and prognosis in ESCC, we lack direct evidence that SYNGR2 affects prognosis through its involvement in immune infiltration. We will further explore these questions in future experiments.

    ACKNOWLEDGEMENTS

    This study was supported by Science and Technology Key Research and Development Program of Gansu Province (no. 20YF3FA032) and Key Talent Project of Gansu Province (no. Gan Zu Tong Zi (2021) 17 Hao).

      CONFLICT OF INTEREST

      The authors declare that they have no competing interests.

      AUTHOR CONTRIBUTIONS

      B.L., MY.R., YZ.C. and YQ.M. wrote the main manuscript text and prepared Figures 1-9, B.L., TN.S., ZP.S. and B.Y. prepared Tables 1–5. All authors reviewed the manuscript.

      DATA AVAILABILITY STATEMENT

      All datasets used and/or analyzed during the current study are available from the public database.

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