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Lei Q, Wang Y, Li J, Wang S, Hu Y, Duan L, Huo Y, Wu Y, Liu H. Increased SEMA6B expression as a potential prognostic and immune cell infiltration biomarker in thyroid cancer patients. Aging (Albany NY) 2023; 15:3572-3585. [PMID: 37155149 PMCID: PMC10449300 DOI: 10.18632/aging.204691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Even today, thyroid cancer (THCA) remains an important threat to global health. For THCA patients, differentiated thyroid cancer is the most commonly identified pathological subtype, and those diagnosed with papillary thyroid cancer generally have good overall prognosis. For poorly differentiated subtype THCA, patients have aggressive disease course, higher risk of distant organ metastasis and inferior overall prognosis. METHODS RNA-seq data from TCGA and GTEx databases are collected and analyzed via R. The correlation between SEMA6B expression level and pathological as well as clinical parameters of THCA patients was respectively investigated. Gene expression profiling and subsequent functional clustering analysis was the performed utilizing GSEA. The receiver operating characteristic (ROC) curve was utilized to evaluate the diagnostic value of SEMA6B expression. RESULTS Increased SEMA6B expression was characteristic in THCA tumor samples and was associated with specific pathologic and clinical features for TCHA patients. Univariate and multivariate analysis indicated that SEMA6B was independent predictive marker for THCA patients' prognosis. Gene expression profiling and functional clustering analysis suggested that SEMA6B high-expression was related with increased expression of multiple signal pathways and signatures of multiple immune cell infiltration. CONCLUSIONS In this study, through bioinformatic analysis and clinical data investigation, we demonstrated the potential value of SEMA6B as diagnostic and prognostic marker in THCA patient treatment.
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Affiliation(s)
- Qinghua Lei
- Physical Examination Center, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Yunha Wang
- Department of Endocrinology, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing 100853, China
| | - Junhua Li
- Physical Examination Center, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Shanshan Wang
- Physical Examination Center, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Yanyan Hu
- Physical Examination Center, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Lihua Duan
- Department of Ultrasound Medicine, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Yanfei Huo
- Physical Examination Center, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Yiping Wu
- Department of Neurology, Handan Central Hospital, Congtai, Handan 056008, Hebei Province, China
| | - Hongzhou Liu
- Department of Endocrinology, First Hospital of Handan City, Congtai, Handan 056002, Hebei Province, China
- Department of Endocrinology, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing 100853, China
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Zhang W, Liu T, Li X, Li T, Ma X, Zhao D, Liu Y, Zheng X, Zhao X. Identification of novel immune-related molecular subtypes and a prognosis model to predict thyroid cancer prognosis and drug resistance. Front Pharmacol 2023; 14:1130399. [PMID: 37063290 PMCID: PMC10098004 DOI: 10.3389/fphar.2023.1130399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/06/2023] [Indexed: 04/01/2023] Open
Abstract
Background: Thyroid cancer is a common malignant tumor of the endocrine system that has shown increased incidence in recent decades. We explored the relationship between tumor-infiltrating immune cell classification and the prognosis of thyroid carcinoma.Methods: RNA-seq, SNV, copy number variance (CNV), and methylation data for thyroid cancer were downloaded from the TCGA dataset. ssGSEA was used to calculate pathway scores. Clustering was conducted using ConsensusClusterPlus. Immune infiltration was assessed using ESTIMATE and CIBERSORT. CNV and methylation were determined using GISTIC2 and the KNN algorithm. Immunotherapy was predicted based on TIDE analysis. Results: Three molecular subtypes (Immune-enrich(E), Stromal-enrich(E), and Immune-deprived(D)) were identified based on 15 pathways and the corresponding genes. Samples in Immune-E showed higher immune infiltration, while those in Immune-D showed increased tumor mutation burden (TMB) and mutations in tumor driver genes. Finally, Immune-E showed higher CDH1 methylation, higher progression-free survival (PFS), higher suitability for immunotherapy, and higher sensitivity to small-molecule chemotherapeutic drugs. Additionally, an immune score (IMScore) based on four genes was constructed, in which the low group showed better survival outcome, which was validated in 30 cancers. Compared to the TIDE score, the IMScore showed better predictive ability.Conclusion: This study constructed a prognostic evaluation model and molecular subtype system of immune-related genes to predict the thyroid cancer prognosis of patients. Moreover, the interaction network between immune genes may play a role by affecting the biological function of immune cells in the tumor microenvironment.
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Affiliation(s)
- Wei Zhang
- Department of Endocrinology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ting Liu
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinyi Li
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tianshu Li
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiangchi Ma
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dongxu Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yueyang Liu
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xueke Zheng
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xudong Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Xudong Zhao,
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Li M, Zhang J, Zhang Z, Qian Y, Qu W, Jiang Z, Zhao B. Identification of Transcriptional Pattern Related to Immune Cell Infiltration With Gene Co-Expression Network in Papillary Thyroid Cancer. Front Endocrinol (Lausanne) 2022; 13:721569. [PMID: 35185791 PMCID: PMC8854657 DOI: 10.3389/fendo.2022.721569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/06/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A growing body of evidence suggests that immune cell infiltration in cancer is closely related to clinical outcomes. However, there is still a lack of research on papillary thyroid cancer (PTC). METHODS Based on single-sample gene set enrichment analysis (SSGSEA) algorithm and weighted gene co-expression network analysis (WGCNA) tool, the infiltration level of immune cell and key modules and genes associated with the level of immune cell infiltration were identified using PTC gene expression data from The Cancer Genome Atlas (TCGA) database. In addition, the co-expression network and protein-protein interactions network analysis were used to identify the hub genes. Moreover, the immunological and clinical characteristics of these hub genes were verified in TCGA and GSE35570 datasets and quantitative real-time polymerase chain reaction (PCR). Finally, receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value of hub genes. RESULTS Activated B cell, activated dendritic cell, CD56bright natural killer cell, CD56dim natural killer cell, Eosinophil, Gamma delta T cell, Immature dendritic cell, Macrophage, Mast cell, Monocyte, Natural killer cell, Neutrophil and Type 17 T helper cell were significantly changed between PTC and adjacent normal groups. WGCNA results showed that the black model had the highest correlation with the infiltration level of activated dendritic cells. We found 14 hub genes whose expression correlated to the infiltration level of activated dendritic cells in both TCGA and GSE35570 datasets. After validation in the TCGA dataset, the expression level of only 5 genes (C1QA, HCK, HLA-DRA, ITGB2 and TYROBP) in 14 hub genes were differentially expressed between PTC and adjacent normal groups. Meanwhile, the expression levels of these 5 hub genes were successfully validated in GSE35570 dataset. Quantitative real-time PCR results showed the expression of these 4 hub genes (except C1QA) was consistent with the results in TCGA and GSE35570 dataset. Finally, these 4 hub genes had diagnostic value to distinguish PTC and adjacent normal controls. CONCLUSIONS HCK, HLA-DRA, ITGB2 and TYROBP may be key diagnostic biomarkers and immunotherapy targets in PTC.
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Affiliation(s)
- Meiye Li
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Jimei Zhang
- School of Pharmacy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Zongjing Zhang
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Ying Qian
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Wei Qu
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Zhaoshun Jiang
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
- *Correspondence: Baochang Zhao, ; Zhaoshun Jiang,
| | - Baochang Zhao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
- *Correspondence: Baochang Zhao, ; Zhaoshun Jiang,
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Huang Y, Yi T, Liu Y, Yan M, Peng X, Lv Y. The landscape of tumors-infiltrate immune cells in papillary thyroid carcinoma and its prognostic value. PeerJ 2021; 9:e11494. [PMID: 34055497 PMCID: PMC8142931 DOI: 10.7717/peerj.11494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Introduction Thyroid cancer is a very common malignant tumor in the endocrine system, while the incidence of papillary thyroid carcinoma (PTC) throughout the world also shows a trend of increase year by year. In this study, we constructed two models: ICIscore and Riskscore. Combined with these two models, we can make more accurate and reasonable inferences about the prognosis of PTC patients. Methods We selected 481 PTC samples from TCGA and 147 PTC samples from GEO (49 samples in GSE33630, 65 samples in GSE35570 and 33 samples in GSE60542). We performed consistent clustering for them and divided them into three subgroups and screened differentially expressed genes from these three subgroups. Then we divided the differential genes into three subtypes. We also distinguished the up-regulated and down-regulated genes and calculated ICIscore for each PTC sample. ICIscore consists of two parts: (1) the PCAu was calculated from up-regulated genes. (2) the PCAd was calculated from down-regulated genes. The PCAu and PCAd of each sample were the first principal component of the relevant gene. What’s more, we divided the patients into two groups and constructed mRNA prognostic signatures. Additionally we also verified the independent prognostic value of the signature. Results Though ICIscore, we were able to observe the relationship between immune infiltration and prognosis. The result suggests that the activation of the immune system may have both positive and negative consequences. Though Riskscore, we could make more accurate predictions about the prognosis of patients with PTC. Meanwhile, we also generated and validated the ICIscore group and Riskscore group respectively. Conclusion All the research results show that by combining the two models constructed, ICIscore and Riskscore, we can make a more accurate and reasonable inference about the prognosis of patients with clinical PTC patients. This suggests that we can provide more effective and reasonable treatment plan for clinical PTC patients.
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Affiliation(s)
- Yanyi Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Nanchang University, The Second Clinical Medicine College, Nanchang, Jiangxi, China
| | - Tao Yi
- Department of Otolaryngology, People's Hospital of Yichun, Yichun, Jiangxi, China
| | - Yushu Liu
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Nanchang University, The Second Clinical Medicine College, Nanchang, Jiangxi, China
| | - Mengyun Yan
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Nanchang University, The First Clinical Medicine College, Nanchang, Jiangxi, China
| | - Xinli Peng
- Department of Otolaryngology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yunxia Lv
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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