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Wang Y, Cao Y, Wang Y, Sun J, Wang L, Song X, Zhao X. Construction and analysis of protein-protein interaction network for esophageal squamous cell carcinoma. Comput Biol Med 2024; 182:109156. [PMID: 39276610 DOI: 10.1016/j.compbiomed.2024.109156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 09/08/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a prevalent malignant tumor of the digestive tract. Clinical findings reveal that the five-year survival rate for mid-to late-stage ESCC patients is merely around 20 %, whereas those diagnosed at an early stage can achieve up to a 95 % survival rate. Consequently, early detection is paramount to improving ESCC patient survival. Protein markers are essential for diagnosing diseases, and the identification of new candidate proteins associated with ESCC through the protein-protein interaction (PPI) network is aimed for in this paper. The PPI network related to ESCC was constructed using protein data, comprising 2094 nodes and 19,660 edges. To assess the nodes' importance in the network, three metrics-degree centrality, betweenness centrality, and closeness centrality-were employed, leading to the identification of 81 key proteins. Subsequently, the biological significance of these proteins in the network was explored, combining biomedical knowledge from three perspectives: network, node, and cluster. The results demonstrated that 52 out of 81 key proteins were confirmed to be linked to ESCC. Among the remaining 29 unreported proteins, 18 displayed significant biological significance, indicating their potential as protein markers related to ESCC.
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Affiliation(s)
- Yanfeng Wang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Yuhan Cao
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Yingcong Wang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China.
| | - Junwei Sun
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Lidong Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Xueke Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
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Wei MX, Song X, Zhao XK, Han WL, Bao QD, Han XN, Xu RH, Li XM, Fan ZM, Wang R, Li XS, Hu JF, Li J, Li B, Tan HF, Gao SG, Zhou FY, Wang LD. Clinicopathological characteristics and postoperative prognosis of patients with nuclear pedigree of esophageal squamous cell carcinoma. Front Oncol 2023; 13:1190457. [PMID: 37538122 PMCID: PMC10396289 DOI: 10.3389/fonc.2023.1190457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/07/2023] [Indexed: 08/05/2023] Open
Abstract
The aim of this work is to analyze the clinicopathological characteristics and prognostic factors of patients with nuclear pedigree of esophageal cancer. The clinicopathological data and follow-up information of 3,260 patients from different nuclear pedigree of esophageal cancer who underwent radical resection of esophageal cancer were collected, and the clinicopathological characteristics and prognostic factors of the patients were analyzed. The male to female ratio of 3,260 patients with esophageal cancer was 1.7:1. The diagnosis age was ranged from 32 to 85 (60.2 ± 8.1) years old. About 53.8% of the patients were ≥ 60 years old; About 88.8% of the patients came from the high incidence area of esophageal cancer; About 82.5% of the tumors were located in the middle and lower segments of esophagus; Poor, moderate and well differentiation accounted for 26.6%, 61.9% and 11.5% respectively; The surgical margin accounted for 94.3%; 47.6% of the tumors were shorter than 4 cm in length; Clinicopathological TNM stage (0+I) accounted for 15.2%, and stage II, III and IV accounted for 54.5%, 29.9% and 0.4%, respectively. Cox analysis showed that male, diagnosed age ≥ 60 years, tumor located in neck and upper esophageal segments, poor differentiation, tumor length ≥ 4 cm, and advanced TNM were independent risk factors for the prognosis of patients in nuclear pedigree with esophageal cancer. Gender, diagnosis age, tumor location, degree of differentiation, tumor length and TNM stage are the influencing factors for the prognosis of patients with nuclear pedigree of esophageal cancer, which will provide important data for the future study of esophageal cancer family aggregation.
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Affiliation(s)
- Meng Xia Wei
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xue Ke Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Wen Li Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Qi De Bao
- Oncology Department, He’nan Puyang Municipal Any Ang Area Hospital, Anyang, China
| | - Xue Nan Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Rui Hua Xu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xin Min Li
- Department of Pathology, The Maternal and Child Health Care Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Zong Min Fan
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ran Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xing Song Li
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Jing Feng Hu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Jia Li
- Department of Language, Zhengzhou White Gown Translation Co., Ltd., Zhengzhou, China
| | - Bei Li
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Hui Fang Tan
- Department of Gastroenterology, People’s Hospital of Zhengzhou, Zhengzhou, China
| | - She Gan Gao
- Department of Oncology, the First Affiliated Hospital, Henan University of Science and Technology, Luoyang, China
| | - Fu You Zhou
- Oncology Prevention Office, Anyang Tumor Hospital, Anyang, China
| | - Li Dong Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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Zou B, Guo D, Kong P, Wang Y, Cheng X, Cui Y. Integrative Genomic Analyses of 1,145 Patient Samples Reveal New Biomarkers in Esophageal Squamous Cell Carcinoma. Front Mol Biosci 2022; 8:792779. [PMID: 35127817 PMCID: PMC8814608 DOI: 10.3389/fmolb.2021.792779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
Due to the lack of effective diagnostic markers and therapeutic targets, esophageal squamous cell carcinoma (ESCC) shows a poor 5 years survival rate of less than 30%. To explore the potential therapeutic targets of ESCC, we integrated and reanalyzed the mutation data of WGS (whole genome sequencing) or WES (whole exome sequencing) from a total of 1,145 samples in 7 large ESCC cohorts, including 270 ESCC gene expression data. Two new mutation signatures and 20 driver genes were identified in our study. Among them, AP3S1, MUC16, and RPS15 were reported for the first time. We also discovered that the KMT2D was associated with the multiple clinical characteristics of ESCC, and KMT2D knockdown cells showed enhanced cell migration and cell invasion. Furthermore, a few neoantigens were shared between ESCC patients. For ESCC, compared to TMB, neoantigen might be treated as a better immunotherapy biomarker. Our research expands the understanding of ESCC mutations and helps the identification of ESCC biomarkers, especially for immunotherapy biomarkers.
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Affiliation(s)
- Binbin Zou
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Dinghe Guo
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Yanqiang Wang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
- *Correspondence: Xiaolong Cheng, ; Yongping Cui,
| | - Yongping Cui
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
- Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Xiaolong Cheng, ; Yongping Cui,
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Yu J, Liang LL, Liu J, Liu TT, Li J, Xiu L, Zeng J, Wang TT, Wang D, Liang LJ, Xie DW, Chen DX, An JS, Wu LY. Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer. Front Genet 2021; 12:733715. [PMID: 34630524 PMCID: PMC8493221 DOI: 10.3389/fgene.2021.733715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background: 5-Methylcytidine (m5C) is the most common RNA modification and plays an important role in multiple tumors including cervical cancer (CC). We aimed to develop a novel gene signature by identifying m5C modification subtypes of CC to better predict the prognosis of patients. Methods: We obtained the expression of 13 m5C regulatory factors from The Cancer Genome Atlas (TCGA all set, 257 patients) to determine m5C modification subtypes by the "nonnegative matrix factorization" (NMF). Then the "limma" package was used to identify differentially expressed genes (DEGs) between different subtypes. According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients). We also verified the risk prediction effect of gene signature in TCGA test set (129 patients), TCGA all set (257 patients) and GSE44001 (300 patients). Furthermore, a nomogram including this gene signature and clinicopathological parameters was established to predict the individual survival rate. Finally, the expression and function of these signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, colony formation, migration and invasion assays. Results: Based on consistent clustering of 13 m5C-modified genes, CC was divided into two subtypes (C1 and C2) and the C1 subtype had a worse prognosis. The 4-gene signature comprising FNDC3A, VEGFA, OPN3 and CPE was constructed. In TCGA training set and three validation sets, we found the prognosis of patients in the low-risk group was much better than that in the high-risk group. A nomogram incorporating the gene signature and T stage was constructed, and the calibration plot suggested that it could accurately predict the survival rate. The expression levels of FNDC3A, VEGFA, OPN3 and CPE were all high in cervical cancer tissues. Downregulation of FNDC3A, VEGFA or CPE expression suppressed the proliferation, migration and invasion of SiHa cells. Conclusions: Two m5C modification subtypes of CC were identified and then a 4-gene signature was established, which provide new feasible methods for clinical risk assessment and targeted therapies for CC.
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Affiliation(s)
- Jing Yu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei-Lei Liang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Liu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting-Ting Liu
- Department of Blood Grouping, Beijing Red Cross Blood Center, Beijing, China
| | - Jian Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Xiu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia Zeng
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tian-Tian Wang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Di Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Jun Liang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Da-Wei Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ding-Xiong Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ju-Sheng An
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ling-Ying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Wang W, Li D, Zheng L, Zhan H. Oesophageal squamous cell carcinoma mimicking submucosal tumour. BMC Gastroenterol 2021; 21:150. [PMID: 33794790 PMCID: PMC8017772 DOI: 10.1186/s12876-021-01731-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/22/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Oesophageal submucosal tumours are usually benign. We report a rare case of esophageal squamous cell carcinoma presenting as a submucosal tumour. CASE PRESENTATION A 58-year-old man undergoing screening oesophago-gastroduodenoscopy was found to have a smooth-surfaced 0.6-cm sized submucosal tumour in the oesophagus 30 cm from the incisor. Endoscopic ultrasonography showed the tumour to be located in the muscularis mucosa; the lesion was heterogeneously hypoechoic and had a clear boundary. With a provisional diagnosis of leiomyoma, the tumour was removed by endoscopic submucosal dissection. Pathological examination showed it to be a moderately differentiated infiltrating squamous cell carcinoma, with normal overlying squamous epithelium. Immunohistochemistry indicated that it was caused by malignant transformation in mucosal glandular duct epithelium. Positron emission tomography-computer tomography showed no tumour spread to any other site. The patient was treated by oesophageal resection. CONCLUSION The clinician should be aware that oesophageal submucosal tumours with smooth overlying mucosa may not always be benign; malignancy must be ruled out.
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Affiliation(s)
- Wen Wang
- Fuzhou General Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Gastroenterology, 900Th Hospital of People's Liberation Army, 156 North Road, West second Ring Road, Gulou District, Fuzhou, 350025, China
- Oriental Hospital Affiliated To Xiamen University, Fuzhou, 350025, China
| | - Dazhou Li
- Fuzhou General Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Gastroenterology, 900Th Hospital of People's Liberation Army, 156 North Road, West second Ring Road, Gulou District, Fuzhou, 350025, China
- Oriental Hospital Affiliated To Xiamen University, Fuzhou, 350025, China
| | - Linfu Zheng
- Fuzhou General Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China.
- Department of Gastroenterology, 900Th Hospital of People's Liberation Army, 156 North Road, West second Ring Road, Gulou District, Fuzhou, 350025, China.
- Oriental Hospital Affiliated To Xiamen University, Fuzhou, 350025, China.
| | - Hongli Zhan
- Department of Gastroenterology, 900Th Hospital of People's Liberation Army, 156 North Road, West second Ring Road, Gulou District, Fuzhou, 350025, China
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