1
|
Wu N, Jing Z, Lv H, Liu Q, Gu M, Zhong Y, Xing P, Ma R, Jing Y. Expression characteristics of TBC1D4 activating protein molecule and identification of key module genes for preventing thyroid cancer progression. Int J Biol Macromol 2024; 278:134986. [PMID: 39181362 DOI: 10.1016/j.ijbiomac.2024.134986] [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: 06/27/2024] [Revised: 08/09/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Endocrine tumors like thyroid carcinoma are becoming more frequent. No clinically informative predictors were found. Thus, effective gene networks and representative biomarkers can illuminate thyroid cancer prevention molecular mechanisms. TBC1D4 is an activating protein molecule that plays an important role in regulating cell metabolism and signal transduction. The aim of this study was to investigate the expression characteristics of TBC1D4 activating protein molecules and identify key module genes that prevent thyroid cancer progression. GSE65144 data were downloaded from GEO. "limma" in R found DEGs with a false discovery rate < 0.05 and a log2 fold change <1. WGCNA builds gene co-expression networks, screens key modules, and filters hub genes. Overlapping genes become hub genes. Hub genes underwent GO and KEGG pathway enrichment analysis. We used Lasso to extract hub gene expression results' distinctive genes. Key genes. GEPIA database determined expression and survival impact. A total of 3220 DEGs. Thyroid cancer was mostly associated with darkred, darkturquoise, and green modules. Venn screened 639 hub genes. Cytokine-cytokine receptor interaction was the primary KEGG enrichment. Hub genes were 14. Finally, ARHGAP6, TBC1D4, and TC2N were important genes. Through gene screening and functional enrichment analysis, we identified a group of genes related to TBC1D4 activating protein and constructed the corresponding protein interaction network.
Collapse
Affiliation(s)
- Na Wu
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Zuoqian Jing
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Huina Lv
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Qun Liu
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Ming Gu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yifan Zhong
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Peng Xing
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Ruiyang Ma
- Department of Otorhinolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
| | - Yuchen Jing
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
| |
Collapse
|
2
|
Wang Z, Ren M, Liu W, Wu J, Tang P. Role of cell division cycle-associated proteins in regulating cell cycle and promoting tumor progression. Biochim Biophys Acta Rev Cancer 2024; 1879:189147. [PMID: 38955314 DOI: 10.1016/j.bbcan.2024.189147] [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: 12/19/2023] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
The cell division cycle-associated protein (CDCA) family is important in regulating cell division. High CDCA expression is significantly linked to tumor development. This review summarizes clinical and basic studies on CDCAs conducted in recent decades. Furthermore, it systematically introduces the molecular expression and function, key mechanisms, cell cycle regulation, and roles of CDCAs in tumor development, cell proliferation, drug resistance, invasion, and metastasis. Additionally, it presents the latest research on tumor diagnosis, prognosis, and treatment targeting CDCAs. These findings are pivotal for further in-depth studies on the role of CDCAs in promoting tumor development and provide theoretical support for their application as new anti-tumor targets.
Collapse
Affiliation(s)
- Zhaoyu Wang
- Department of Breast and Thyroid Surgery, Southwest Hospital, the First Affiliated Hospital of the Army Military Medical University, Chongqing 400038, China
| | - Minshijing Ren
- Department of Breast and Thyroid Surgery, Southwest Hospital, the First Affiliated Hospital of the Army Military Medical University, Chongqing 400038, China
| | - Wei Liu
- Department of Breast and Thyroid Surgery, Southwest Hospital, the First Affiliated Hospital of the Army Military Medical University, Chongqing 400038, China
| | - Jin Wu
- Department of Breast and Thyroid Surgery, Southwest Hospital, the First Affiliated Hospital of the Army Military Medical University, Chongqing 400038, China; Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
| | - Peng Tang
- Department of Breast and Thyroid Surgery, Southwest Hospital, the First Affiliated Hospital of the Army Military Medical University, Chongqing 400038, China.
| |
Collapse
|
3
|
Yu S, Jiang J. Immune infiltration-related genes regulate the progression of AML by invading the bone marrow microenvironment. Front Immunol 2024; 15:1409945. [PMID: 39072320 PMCID: PMC11272452 DOI: 10.3389/fimmu.2024.1409945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024] Open
Abstract
In this study, we try to find the pathogenic role of immune-related genes in the bone marrow microenvironment of AML. Through WGCNA, seven modules were obtained, among which the turquoise module containing 1793 genes was highly correlated with the immune infiltration score. By unsupervised clustering, the turquoise module was divided into two clusters: the intersection of clinically significant genes in the TCGA and DEGs to obtain 178 genes for mutation analysis, followed by obtaining 17 genes with high mutation frequency. Subsequently, these 17 genes were subjected to LASSO regression analysis to construct a riskscore model of 8 hub genes. The TIMER database, ImmuCellAI portal website, and ssGSEA elucidate that the hub genes and risk scores are closely related to immune cell infiltration into the bone marrow microenvironment. In addition, we also validated the relative expression levels of hub genes using the TCGA database and GSE114868, and additional expression levels of hub genes in AML cell lines in vitro. Therefore, we constructed an immune infiltration-related gene model that identify 8 hub genes with good risk stratification and predictive prognosis for AML.
Collapse
Affiliation(s)
- Shuangmei Yu
- Department of Radio-immunity, Heilongjiang Provincial Hospital, Harbin, China
| | - Jiquan Jiang
- Department of Laboratory Diagnosis, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
4
|
Huang B, Yu Z, Cui D, Du F. MAPKAP1 orchestrates macrophage polarization and lipid metabolism in fatty liver-enhanced colorectal cancer. Transl Oncol 2024; 45:101941. [PMID: 38692197 PMCID: PMC11070763 DOI: 10.1016/j.tranon.2024.101941] [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: 12/09/2023] [Revised: 03/02/2024] [Accepted: 03/16/2024] [Indexed: 05/03/2024] Open
Abstract
Various factors, including fatty liver and macrophage alterations, influence colorectal cancer (CRC). This study explores the mechanistic role of fatty liver in CRC progression, focusing on macrophage polarization and lipid metabolism. A murine fatty liver model was created with a high-fat diet (HFD), and CRC was induced using AOM and DSS. Single-cell transcriptome sequencing (scRNA-seq) identified MAPKAP1 as a critical gene promoting CRC via M2 macrophage polarization and lipid metabolism reprogramming. Prognosis analysis on the TCGA-CRC dataset confirmed MAPKAP1's significance. In vitro and in vivo experiments demonstrated that EVs from fatty liver cells enhanced MAPKAP1 expression, accelerating CRC development and metastasis. HFD exacerbated CRC, but fatty acid inhibitors delayed progression. Fatty liver upregulates MAPKAP1, driving M2 macrophage polarization and lipid metabolism changes, worsening CRC. These findings suggest potential therapeutic strategies for CRC, particularly targeting lipid metabolism and macrophage-mediated tumor promotion.
Collapse
Affiliation(s)
- Bo Huang
- Department of Hypertension, The Affiliated Hospital of Guizhou Medical University, No.28, Guimedical Street, Yunyan District, Guiyang City, Guizhou Province, PR China.
| | - Zhenqiu Yu
- Department of Hypertension, The Affiliated Hospital of Guizhou Medical University, No.28, Guimedical Street, Yunyan District, Guiyang City, Guizhou Province, PR China.
| | - Dejun Cui
- Department of Gastroenterology, Guizhou Provincial People's Hospital, PR China.
| | - Fawang Du
- Department of Hypertension, The Affiliated Hospital of Guizhou Medical University, No.28, Guimedical Street, Yunyan District, Guiyang City, Guizhou Province, PR China
| |
Collapse
|
5
|
Xia F, Zhang Q, Xia G, Ndhlovu E, Chen X, Huang Z, Zhang B, Zhu P. A pathologic scoring system for predicting postoperative prognosis in patients with ruptured hepatocellular carcinoma. Asian J Surg 2024; 47:3015-3025. [PMID: 38326117 DOI: 10.1016/j.asjsur.2024.01.139] [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: 10/30/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND The accuracy of pathological factors to predict the prognosis of patients with ruptured hepatocellular carcinoma (rHCC) is unclear. We aimed to develop and validate a novel scoring system based on pathological factors to predict the postoperative survival of patients with rHCC. METHOD Patients with rHCC who underwent hepatectomy were recruited from three hospitals and allocated to the training (n = 221) and validation (n = 194) cohorts. A new scoring system, namely the MSE (microvascular invasion-satellite foci-Edmondson Steiner) score, was established based on three pathological factors using univariate and multivariate Cox proportional hazards regression analyses, including microvascular invasion, satellite foci, and differentiation grade. Finally, patients were stratified into three groups based on their risk of prognosis (low, intermediate, or high) according to their MSE score. We also constructed MSE score-based nomograms. The performance of the nomograms was assessed by receiver operating characteristic and calibration curve analyses and validated using the validation cohort. RESULTS Three pathological factors were significantly correlated with overall survival (OS) and recurrence-free survival (RFS), three of which were included in the MSE score. The score can clearly stratify rHCC patients after hepatectomy (P < 0.05). And we established nomograms based on the MSE score (MSE score, Barcelona Clinic Liver Cancer stage, and alpha-fetoprotein concentration) to predict postoperative OS and RFS in patients with rHCC. The nomograms showed good discrimination, with C-indices over 0.760 for OS and RFS at 1, 3, and 5 years, respectively. The calibration curve showed excellent nomogram calibration, which was also verified in the validation cohort. CONCLUSION The clinical MSE score were accurate in predicting OS and RFS in patients with rHCC with resectable lesions after hepatectomy.
Collapse
Affiliation(s)
- Feng Xia
- Department of Hepatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongshan People's Hospital Affiliated to Guangdong Medical University, Guangdong, China
| | - Guobing Xia
- Department of Hepatobiliary and Pancreatic Surgery, Huangshi Central Hospital of Edong Healthcare Group, Hubei Polytechnic University.Huangshi, Hubei, China
| | - Elijah Ndhlovu
- Department of Hepatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Chen
- Department of Hepatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiyuan Huang
- Department of Hepatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Bixiang Zhang
- Department of Hepatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Peng Zhu
- Department of Hepatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| |
Collapse
|
6
|
Zhu N, Hou J, Si J, Yang N, Chen B, Wei X, Zhu L. SIRT1 and ZNF350 as novel biomarkers for osteoporosis: a bioinformatics analysis and experimental validation. Mol Biol Rep 2024; 51:530. [PMID: 38637425 DOI: 10.1007/s11033-024-09406-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/29/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Osteoporosis (OP) is characterized by bone mass decrease and bone tissue microarchitectural deterioration in bone tissue. This study identified potential biomarkers for early diagnosis of OP and elucidated the mechanism of OP. METHODS Gene expression profiles were downloaded from Gene Expression Omnibus (GEO) for the GSE56814 dataset. A gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA) to identify key modules associated with healthy and OP samples. Functional enrichment analysis was conducted using the R clusterProfiler package for modules to construct the transcriptional regulatory factor networks. We used the "ggpubr" package in R to screen for differentially expressed genes between the two samples. Gene set variation analysis (GSVA) was employed to further validate hub gene expression levels between normal and OP samples using RT-PCR and immunofluorescence to evaluate the potential biological changes in various samples. RESULTS There was a distinction between the normal and OP conditions based on the preserved significant module. A total of 100 genes with the highest MM scores were considered key genes. Functional enrichment analysis suggested that the top 10 biological processes, cellular component and molecular functions were enriched. The Toll-like receptor signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, osteoclast differentiation, JAK-STAT signaling pathway, and chemokine signaling pathway were identified by Kyoto Encyclopedia of Genes and Genomes pathway analysis. SIRT1 and ZNF350 were identified by Wilcoxon algorithm as hub differentially expressed transcriptional regulatory factors that promote OP progression by affecting oxidative phosphorylation, apoptosis, PI3K-Akt-mTOR signaling, and p53 pathway. According to RT-PCR and immunostaining results, SIRT1 and ZNF350 levels were significantly higher in OP samples than in normal samples. CONCLUSION SIRT1 and ZNF350 are important transcriptional regulatory factors for the pathogenesis of OP and may be novel biomarkers for OP treatment.
Collapse
Affiliation(s)
- Naiqiang Zhu
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Jingyi Hou
- Chengde Medical University, Chengde, 067000, China
| | - Jingyuan Si
- South Operation Department, The Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Ning Yang
- Central Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Bin Chen
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Xu Wei
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China.
| | - Liguo Zhu
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China.
| |
Collapse
|
7
|
Pan L, Zhang L, Fu J, Shen K, Zhang G. Integrated transcriptome sequencing and weighted gene co-expression network analysis reveals key genes of papillary thyroid carcinomas. Heliyon 2024; 10:e27928. [PMID: 38560266 PMCID: PMC10981042 DOI: 10.1016/j.heliyon.2024.e27928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Objective Papillary thyroid carcinoma (PTC) accounts for the majority of thyroid cancers and has a high recurrence rate. We aimed to screen key genes involved in PTC to provide novel insights into the mechanisms of PTC. Methods Seven microarray datasets of PTC were downloaded from gene expression omnibus database. Differentially expressed genes (DEGs) between PTC and normal samples were screened in the merged dataset. Then, protein-protein interaction (PPIs) functional modules analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify PTC-associated key genes. The identified key genes were then characterized from various aspects, including gene set enrichment analysis (GSEA) and the associations with immune infiltration, methylation levels and prognosis. Results A large numbers of DEGs were identified, and these DEGs are involved in several cancer pathways. Nine key genes (including down-regulated genes GNA14, AVPR1A, and WFS1, and up-regulated genes LAMB3, PLAU, MET, MFGE8, PRSS23, and SERPINA1) were identified. Patients in the AVPR1A and GNA14 high expression groups had better disease-free survival (DFS) than those in the low expression group. Key genes were mainly involved in P53 pathway, estrogen response, apoptosis, glycolysis, NOTCH signaling, epithelial mesenchymal transition, WNT_beta catenin signaling, and inflammatory response. The expression of key genes was associated with immune cell infiltration and corresponding methylation levels. The verification results of key gene proteins and mRNA expression levels using external validation datasets were consistent with our expectations, implying the involvements of key genes in PTC. Conclusion The key genes may serve as potential therapeutic targets for PTC. This study provides novel insights into the mechanisms underlying PTC development.
Collapse
Affiliation(s)
- Lingfeng Pan
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Lianbo Zhang
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Jingyao Fu
- Department of Thyroid Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Keyu Shen
- Department of Thyroid Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Guang Zhang
- Department of Thyroid Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| |
Collapse
|
8
|
Xu X, Lai C, Luo J, Shi J, Guo K, Hu J, Mulati Y, Xiao Y, Kong D, Liu C, Huang J, Xu K. The predictive significance of chromobox family members in prostate cancer in humans. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00929-7. [PMID: 38427207 DOI: 10.1007/s13402-024-00929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE The Chromobox (CBX) family proteins are crucial elements of the epigenetic regulatory machinery and play a significant role in the development and advancement of cancer. Nevertheless, there is limited understanding regarding the role of CBXs in development or progression of prostate cancer (PCa). Our objective is to develop a unique prognostic model associated with CBXs to improve the accuracy of predicting outcomes of patients with PCa. METHODS Data from TCGA and GEO databases were analyzed to assess differential expression, prognostic value, gene pathway enrichment, and immune cell infiltration. COX regression analysis was utilized to identify the independent prognostic factors that impact disease-free survival (DFS). The expression of CBX2 and FOXP3+ cells infiltration was verified by immunohistochemical staining of clinical tissue sections. In vitro proliferation, migration and invasion assay were conducted to examine the function of CBX2. RNA-seq was employed to examine the CBX2 related pathway enrichment. RESULTS CBX2, CBX3, CBX4, and CBX8 were upregulated, while CBX6 and CBX7 were downregulated in PCa tissues. CBXs expression varied by stage and grade. Elevated expression of CBX1, CBX2, CBX3, CBX4 and CBX8 is correlated with poor outcome. CBX2 expression, T stage, and Gleason score were independent prognostic factors. The expression level of CBX2 in PCa tissues was significantly higher than that in adjacent normal tissues. More Treg infiltration was observed in the group with high CBX2 expression. CBX2 expression affected PCa cell growth, migration, and invasion. CONCLUSIONS CBX2 is involved in the development and advancement of PCa, suggesting its potential as a reliable prognostic indicator for PCa patients.
Collapse
Affiliation(s)
- Xiaoting Xu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Urology, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Cong Lai
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiawen Luo
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Juanyi Shi
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaixuan Guo
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jintao Hu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yelisudan Mulati
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yunfei Xiao
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Degeng Kong
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng Liu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, China
| | - Jingang Huang
- Medical Research Center, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Kewei Xu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China.
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, China.
- Sun Yat-sen University School of Medicine, Sun Yat-sen University, Shenzhen, China.
| |
Collapse
|
9
|
Wang F, Kang X, Li Y, Lu J, Liu X, Yan H. Elucidating hepatocellular carcinoma progression: a novel prognostic miRNA-mRNA network and signature analysis. Sci Rep 2024; 14:5042. [PMID: 38424172 PMCID: PMC10904818 DOI: 10.1038/s41598-024-55806-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 02/28/2024] [Indexed: 03/02/2024] Open
Abstract
There is increasing evidence that miRNAs play an important role in the prognosis of HCC. There is currently a lack of acknowledged models that accurately predict patient prognosis. The aim of this study is to create a miRNA-based model to precisely forecast a patient's prognosis and a miRNA-mRNA network to investigate the function of a targeted mRNA. TCGA miRNA dataset and survival data of HCC patients were downloaded for differential analysis. The outcomes of variance analysis were subjected to univariate and multivariate Cox regression analyses and LASSO analysis. We constructed and visualized prognosis-related models and subsequently used violin plots to probe the function of miRNAs in tumor cells. We predicted the target mRNAs added those to the String database, built PPI protein interaction networks, and screened those mRNA using Cytoscape. The hub mRNA was subjected to GO and KEGG analysis to determine its biological role. Six of them were associated with prognosis: hsa-miR-139-3p, hsa-miR-139-5p, hsa-miR-101-3p, hsa-miR-30d-5p, hsa-miR-5003-3p, and hsa-miR-6844. The prognostic model was highly predictive and consistently performs, with the C index exceeding 0.7 after 1, 3, and 5 years. The model estimated significant differences in the Kaplan-Meier plotter and the model could predict patient prognosis independently of clinical indicators. A relatively stable miRNA prognostic model for HCC patients was constructed, and the model was highly accurate in predicting patients with good stability over 5 years. The miRNA-mRNA network was constructed to explore the function of mRNA.
Collapse
Affiliation(s)
- Fei Wang
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China
| | - Xichun Kang
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China
| | - Yaoqi Li
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China
| | - Jianhua Lu
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China
| | - Xiling Liu
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China
| | - Huimin Yan
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China.
| |
Collapse
|
10
|
Li MT, Zheng KF, Qiu YE. Identification of immune cell-related prognostic genes characterized by a distinct microenvironment in hepatocellular carcinoma. World J Clin Oncol 2024; 15:243-270. [PMID: 38455128 PMCID: PMC10915937 DOI: 10.5306/wjco.v15.i2.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND The development and progression of hepatocellular carcinoma (HCC) have been reported to be associated with immune-related genes and the tumor microenvironment. Nevertheless, there are not enough prognostic biomarkers and models available for clinical use. Based on seven prognostic genes, this study calculated overall survival in patients with HCC using a prognostic survival model and revealed the immune status of the tumor microenvironment (TME). AIM To develop a novel immune cell-related prognostic model of HCC and depict the basic profile of the immune response in HCC. METHODS We obtained clinical information and gene expression data of HCC from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. TCGA and ICGC datasets were used for screening prognostic genes along with developing and validating a seven-gene prognostic survival model by weighted gene coexpression network analysis and least absolute shrinkage and selection operator regression with Cox regression. The relative analysis of tumor mutation burden (TMB), TME cell infiltration, immune checkpoints, immune therapy, and functional pathways was also performed based on prognostic genes. RESULTS Seven prognostic genes were identified for signature construction. Survival receiver operating characteristic curve analysis showed the good performance of survival prediction. TMB could be regarded as an independent factor in HCC survival prediction. There was a significant difference in stromal score, immune score, and estimate score between the high-risk and low-risk groups stratified based on the risk score derived from the seven-gene prognostic model. Several immune checkpoints, including VTCN1 and TNFSF9, were found to be associated with the seven prognostic genes and risk score. Different combinations of checkpoint blockade targeting inhibitory CTLA4 and PD1 receptors and potential chemotherapy drugs hold great promise for specific HCC therapies. Potential pathways, such as cell cycle regulation and metabolism of some amino acids, were also identified and analyzed. CONCLUSION The novel seven-gene (CYTH3, ENG, HTRA3, PDZD4, SAMD14, PGF, and PLN) prognostic model showed high predictive efficiency. The TMB analysis based on the seven genes could depict the basic profile of the immune response in HCC, which might be worthy of clinical application.
Collapse
Affiliation(s)
- Meng-Ting Li
- Department of Gastroenterology, The Affiliated People's Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Kai-Feng Zheng
- Department of Gastroenterology, The Affiliated People's Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Yi-Er Qiu
- Department of Gastroenterology, The Affiliated People's Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| |
Collapse
|
11
|
Xu G, Jiang Y, Li Y, Ge J, Xu X, Chen D, Wu J. A novel immunogenic cell death-related genes signature for predicting prognosis, immune landscape and immunotherapy effect in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:16261-16277. [PMID: 37698679 DOI: 10.1007/s00432-023-05370-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
OBJECTIVE Immunogenic cell death (ICD) has emerged as a promising strategy to activate the adaptive immune response, modulate the tumor microenvironment (TME) and enhance the efficacy of immune therapy. However, the relationship between ICD and TME reprogramming in hepatocellular carcinoma (HCC) remains poorly understood. METHODS Transcriptional profiles and clinical spectrum of 486 HCC patients were obtained from TCGA and GEO databases. We utilized consensus clustering analysis to construct two distinct molecular subtypes and established an ICD-based scoring system (named ICD score) via WGCNA and LASSO Cox regression to predict the prognosis of the HCC cohort. Then we employed CIBERSORT and ESTIMATE methods to analyze the immune landscape of ICD score in HCC. Subsequently, the immunophenoscore (IPS) and tumor immune dysfunction and rejection (TIDE) analyses were performed to determine whether the ICD score could influence the immune therapeutic effect. Based on the ICD scoring system, a novel nomogram was generated to provide a numerical probability of HCC patients' overall survival (OS). RESULTS We identified two independent ICD clusters (cluster A/B), and cluster B possessed a worse prognosis and higher immune cell infiltration. Using ICD scoring system, the HCC patients were divided into high- and low-ICD-score groups. Through integrative analyses, the high-ICD cohort owned advanced TNM stage, high pathologic grade and increased suppressive immune cell enrichment. We developed a nomogram containing the ICD score, demonstrating a high predictive accuracy with a C-index of 0.703. We further discovered that PSMD2 and PSMD14 could serve as ICD-associated prognostic biomarkers and therapeutic targets in HCC. CONCLUSION The ICD score exhibits a high degree of reliability for predicting prognosis and may provide valuable guidance for the selection of immunotherapy for HCC patients. This novel scoring system enables the estimation of clinical immunotherapy response for HCC patients, offering new opportunities for personalized immunotherapy.
Collapse
Affiliation(s)
- Guangming Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China
| | - Yifan Jiang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China
| | - Yu Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China
| | - Jiangzhen Ge
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China
| | - Xiaofeng Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China
| | - Diyu Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China.
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province, Hangzhou, 310003, China.
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, 310003, China.
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China.
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Zhejiang Province, Hangzhou, 310003, China.
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province, Hangzhou, 310003, China.
| |
Collapse
|
12
|
Wang D, Ding D, Ying J, Qin Y. Bioinformatics identification of a T-cell-related signature for predicting prognosis and drug sensitivity in hepatocellular carcinoma. IET Syst Biol 2023; 17:366-377. [PMID: 37935646 PMCID: PMC10725711 DOI: 10.1049/syb2.12082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a fatal disease with poor clinical outcomes. T cells play a vital role in the crosstalk between the tumour microenvironment and HCC. Single-cell RNA sequencing data were downloaded from the GSE149614 dataset. The T-cell-related prognostic signature (TRPS) was developed with the integrative procedure including 10 machine learning algorithms. The TRPS was established using 7 T-cell-related markers in the Cancer Genome Atlas cohort with 1-, 2- and 3-year area under curve values of 0.820, 0.725 and 0.678, respectively. TRPS acted as an independent risk factor for HCC patients. HCC patients with a high TRPS-based risk score had a higher Tumour Immune Dysfunction and Exclusion score, lower PD1 and CTLA4 immunophenoscore and lower level of immunoactivated cells, including CD8+ T cells and NK cells. The response rate was significantly higher in patients with low-risk scores in immunotherapy cohorts, including IMigor210 and GSE91061. The TRPS-based nomogram had a relatively good predictive value in evaluating the mortality risk at 1, 3 and 5 years in HCC. Overall, this study develops a TRPS by integrated bioinformatics analysis. This TRPS acted as an independent risk factor for the OS rate of HCC patients. It can screen for HCC patients who might benefit from immunotherapy, chemotherapy and targeted therapy.
Collapse
Affiliation(s)
- Dianqian Wang
- Health Science CenterNingbo UniversityNingboZhejiangChina
| | - Dongxiao Ding
- Department of Thoracic SurgeryThe People's Hospital of Beilun DistrictNingboZhejiangChina
| | - Junjie Ying
- Department of Thoracic SurgeryThe People's Hospital of Beilun DistrictNingboZhejiangChina
| | - Yunsheng Qin
- Department of Hepatobiliary and Pancreatic SurgeryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Department of Hepatobiliary SurgeryThe People's Hospital of Beilun DistrictNingboZhejiangChina
| |
Collapse
|
13
|
Kuang T, Ma W, Zhang J, Yu J, Deng W, Dong K, Wang W. Construction of a Nomogram to Predict Overall Survival in Patients with Early-Onset Hepatocellular Carcinoma: A Retrospective Cohort Study. Cancers (Basel) 2023; 15:5310. [PMID: 38001570 PMCID: PMC10670167 DOI: 10.3390/cancers15225310] [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: 10/18/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a widespread and impactful cancer which has pertinent implications worldwide. Although most cases of HCC are typically diagnosed in individuals aged ≥60 years, there has been a notable rise in the occurrence of HCC among younger patients. However, there is a scarcity of precise prognostic models available for predicting outcomes in these younger patients. A retrospective analysis was conducted to investigate early-onset hepatocellular carcinoma (EO-LIHC) using data from the Surveillance, Epidemiology, and End Results (SEER) database from 2004 to 2018. The analysis included 1392 patients from the SEER database and our hospital. Among them, 1287 patients from the SEER database were assigned to the training cohort (n = 899) and validation cohort 1 (n = 388), while 105 patients from our hospital were assigned to validation cohort 2. A Cox regression analysis showed that age, sex, AFP, grade, stage, tumor size, surgery, and chemotherapy were independent risk factors. The nomogram developed in this study demonstrated its discriminatory ability to predict the 1-, 3-, and 5-year overall survival (OS) rates in EO-LIHC patients based on individual characteristics. Additionally, a web-based OS prediction model specifically tailored for EO-LIHC patients was created and validated. Overall, these advancements contribute to improved decision-making and personalized care for individuals with EO-LIHC.
Collapse
Affiliation(s)
- Tianrui Kuang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Wangbin Ma
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jiacheng Zhang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jia Yu
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Wenhong Deng
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Keshuai Dong
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Weixing Wang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| |
Collapse
|
14
|
Jiang L, Wang C, Tong Y, Jiang J, Zhao D. Web-based nomogram and risk stratification system constructed for predicting the overall survival of older adults with primary kidney cancer after surgical resection. J Cancer Res Clin Oncol 2023; 149:11873-11889. [PMID: 37410141 DOI: 10.1007/s00432-023-05072-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Kidney cancer (KC) is one of the most common malignant tumors in adults which particularly affects the survival of elderly patients. We aimed to construct a nomogram to predict overall survival (OS) in elderly KC patients after surgery. METHODS Information on all primary KC patients aged more than 65 years and treated with surgery between 2010 and 2015 was downloaded from the Surveillance, Epidemiology, and End Results (SEER) database. Univariate and multivariate Cox regression analysis was used to identify the independent prognostic factors. Consistency index (C-index), receiver operating characteristic curve (ROC), the area under curve (AUC), and calibration curve were used to assess the accuracy and validity of the nomogram. Comparison of the clinical benefits of nomogram and the TNM staging system is done by decision curve analysis (DCA) and time-dependent ROC. RESULTS A total of 15,989 elderly KC patients undergoing surgery were included. All patients were randomly divided into training set (N = 11,193, 70%) and validation set (N = 4796, 30%). The nomogram produced C-indexes of 0.771 (95% CI 0.751-0.791) and 0.792 (95% CI 0.763-0.821) in the training and validation sets, respectively, indicating that the nomogram has excellent predictive accuracy. The ROC, AUC, and calibration curves also showed the same excellent results. In addition, DCA and time-dependent ROC showed that the nomogram outperformed the TNM staging system with better net clinical benefits and predictive efficacy. CONCLUSIONS Independent influencing factors for postoperative OS in elderly KC patients were sex, age, histological type, tumor size, grade, surgery, marriage, radiotherapy, and T-, N-, and M-stage. The web-based nomogram and risk stratification system could assist surgeons and patients in clinical decision-making.
Collapse
Affiliation(s)
- Liming Jiang
- Department of Orthopedics, The China-Japan Union Hospital of Jilin University, Changchun, 130000, China
| | - Chengcheng Wang
- Department of Oncology, The First People's Hospital of Liangshan Yi Autonomous Prefecture, Xichang, 615099, China
| | - Yuexin Tong
- Department of Orthopedics, The China-Japan Union Hospital of Jilin University, Changchun, 130000, China
| | - Jiajia Jiang
- Department of Orthopedics, The China-Japan Union Hospital of Jilin University, Changchun, 130000, China
| | - Dongxu Zhao
- Department of Orthopedics, The China-Japan Union Hospital of Jilin University, Changchun, 130000, China.
| |
Collapse
|
15
|
Hu Y, Zhang X, Li Q, Zhou Q, Fang D, Lu Y. An immune and epigenetics-related scoring model and drug candidate prediction for hepatic carcinogenesis via dynamic network biomarker analysis and connectivity mapping. Comput Struct Biotechnol J 2023; 21:4619-4633. [PMID: 37817777 PMCID: PMC10561057 DOI: 10.1016/j.csbj.2023.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/12/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high mortality. This study aimed to build a prognostic signature for HCC patients based on immune-related genes (IRGs) and epigenetics-related genes (EPGs). RNA-seq data from Gene Expression Omnibus were used for dynamic network biomarker (DNB) analysis to identify 56 candidate IRG-EPG-DNBs and their first-neighbor genes. These genes were screened using LASSO-Cox regression analysis to finally obtain five candidate genes-RNF2, YBX1, EZH2, CAD, and PSMD1-which constituted the prognostic signature panel. According to this panel, patients in The Cancer Genome Atlas and International Cancer Genome Consortium were divided into high- and low-risk groups. The prognosis, clinicopathological features, and immune cell infiltration significantly differed between the two risk groups. The prognostic ability of the signature panel and expression profiling were further validated using online databases. We used an independent cohort of patients to validate the expression profiles of the five genes using reverse transcription-PCR. CMap and CellMiner predicted four small molecule drug-protein pairs based on the five prognostic genes. Of them, two market drugs approved by the Food and Drug Administration (AT-13387 and KU-55933) have emerged as candidates for HCC study. This new signature panel may serve as a potential prognostic marker, engendering the possibility of novel personalized therapy with classification of HCC patients.
Collapse
Affiliation(s)
- Yuting Hu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xingli Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qingya Li
- Henan University of Chinese Medicine, Henan 450046, China
| | - Qianmei Zhou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dongdong Fang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yiyu Lu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| |
Collapse
|
16
|
Yao Y, Lv J, Wang G, Hong X. Multi-omics analysis and validation of the tumor microenvironment of hepatocellular carcinoma under RNA modification patterns. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:18318-18344. [PMID: 38052560 DOI: 10.3934/mbe.2023814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
BACKGROUND Multiple types of RNA modifications are associated with the prognosis of hepatocellular carcinoma (HCC) patients. However, the overall mediating effect of RNA modifications on the tumor microenvironment (TME) and the prognosis of patients with HCC is unclear. METHODS Thoroughly analyze the TME, biological processes, immune infiltration and patient prognosis based on RNA modification patterns and gene patterns. Construct a prognostic model (RNA modification score, RNAM-S) to predict the overall survival (OS) in HCC patients. Analyze the immune status, cancer stem cell (CSC), mutations and drug sensitivity of HCC patients in both the high and low RNAM-S groups. Verify the expression levels of the four characteristic genes of the prognostic RNAM-S using in vitro cell experiments. RESULTS Two modification patterns and two gene patterns were identified in this study. Both the high-expression modification pattern and the gene pattern exhibited worse OS. A prognostic RNAM-S model was constructed based on four featured genes (KIF20A, NR1I2, NR2F1 and PLOD2). Cellular experiments suggested significant dysregulation of the expression levels of these four genes. In addition, validation of the RNAM-S model using each data set showed good predictive performance of the model. The two groups of HCC patients (high and low RNAM-S groups) exhibited significant differences in immune status, CSC, mutation and drug sensitivity. CONCLUSION The findings of the study demonstrate the clinical value of RNA modifications, which provide new insights into the individualized treatment for patients with HCC.
Collapse
Affiliation(s)
- Yuanqian Yao
- Guangxi University of Chinese medicine, NanNing 530000, China
| | - Jianlin Lv
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530000, China
| | - Guangyao Wang
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530000, China
| | - Xiaohua Hong
- Guangxi University of Chinese medicine, NanNing 530000, China
| |
Collapse
|
17
|
Feng Q, Huang Z, Song L, Wang L, Lu H, Wu L. Combining bulk and single-cell RNA-sequencing data to develop an NK cell-related prognostic signature for hepatocellular carcinoma based on an integrated machine learning framework. Eur J Med Res 2023; 28:306. [PMID: 37649103 PMCID: PMC10466881 DOI: 10.1186/s40001-023-01300-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND The application of molecular targeting therapy and immunotherapy has notably prolonged the survival of patients with hepatocellular carcinoma (HCC). However, multidrug resistance and high molecular heterogeneity of HCC still prevent the further improvement of clinical benefits. Dysfunction of tumor-infiltrating natural killer (NK) cells was strongly related to HCC progression and survival benefits of HCC patients. Hence, an NK cell-related prognostic signature was built up to predict HCC patients' prognosis and immunotherapeutic response. METHODS NK cell markers were selected from scRNA-Seq data obtained from GSE162616 data set. A consensus machine learning framework including a total of 77 algorithms was developed to establish the gene signature in TCGA-LIHC data set, GSE14520 data set, GSE76427 data set and ICGC-LIRI-JP data set. Moreover, the predictive efficacy on ICI response was externally validated by GSE91061 data set and PRJEB23709 data set. RESULTS With the highest C-index among 77 algorithms, a 11-gene signature was established by the combination of LASSO and CoxBoost algorithm, which classified patients into high- and low-risk group. The prognostic signature displayed a good predictive performance for overall survival rate, moderate to high predictive accuracy and was an independent risk factor for HCC patients' prognosis in TCGA, GEO and ICGC cohorts. Compared with high-risk group, low-risk patients showed higher IPS-PD1 blocker, IPS-CTLA4 blocker, common immune checkpoints expression but lower TIDE score, which indicated low-risk patients might be prone to benefiting from ICI treatment. Moreover, a real-world cohort, PRJEB23709, also revealed better immunotherapeutic response in low-risk group. CONCLUSIONS Overall, the present study developed a gene signature based on NK cell-related genes, which offered a novel platform for prognosis and immunotherapeutic response evaluation of HCC patients.
Collapse
Affiliation(s)
- Qian Feng
- Department of Emergency, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Zhihao Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1st min de Road, Nanchang, 330000, China
| | - Lei Song
- Department of General Practice, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Le Wang
- Department of Blood Transfusion, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Hongcheng Lu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1st min de Road, Nanchang, 330000, China.
| | - Linquan Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1st min de Road, Nanchang, 330000, China.
| |
Collapse
|
18
|
Jiang W, Wang L, Zhang Y, Li H. Identification and verification of novel immune-related ferroptosis signature with excellent prognostic predictive and clinical guidance value in hepatocellular carcinoma. Front Genet 2023; 14:1112744. [PMID: 37671041 PMCID: PMC10475594 DOI: 10.3389/fgene.2023.1112744] [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: 11/30/2022] [Accepted: 05/25/2023] [Indexed: 09/07/2023] Open
Abstract
Background: Immunity and ferroptosis often play a synergistic role in the progression and treatment of hepatocellular carcinoma (HCC). However, few studies have focused on identifying immune-related ferroptosis gene biomarkers. Methods: We performed weighted gene co-expression network analysis (WGCNA) and random forest to identify prognostic differentially expressed immune-related genes (PR-DE-IRGs) highly related to HCC and characteristic prognostic differentially expressed ferroptosis-related genes (PR-DE-FRGs) respectively to run co-expression analysis for prognostic differentially expressed immune-related ferroptosis characteristic genes (PR-DE-IRFeCGs). Lasso regression finally identified 3 PR-DE-IRFeCGs for us to construct a prognostic predictive model. Differential expression and prognostic analysis based on shared data from multiple sources and experimental means were performed to further verify the 3 modeled genes' biological value in HCC. We ran various performance testing methods to test the model's performance and compare it with other similar signatures. Finally, we integrated composite factors to construct a comprehensive quantitative nomogram for accurate prognostic prediction and evaluated its performance. Results: 17 PR-DE-IRFeCGs were identified based on co-expression analysis between the screened 17 PR-DE-FRGs and 34 PR-DE-IRGs. Multi-source sequencing data, QRT-PCR, immunohistochemical staining and testing methods fully confirmed the upregulation and significant prognostic influence of the three PR-DE-IRFeCGs in HCC. The model performed well in the performance tests of multiple methods based on the 5 cohorts. Furthermore, our model outperformed other related models in various performance tests. The immunotherapy and chemotherapy guiding value of our signature and the comprehensive nomogram's excellent performance have also stood the test. Conclusion: We identified a novel PR-DE-IRFeCGs signature with excellent prognostic prediction and clinical guidance value in HCC.
Collapse
Affiliation(s)
- Wenxiu Jiang
- Department of Infectious Diseases, The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, China
| | - Lili Wang
- Department of Clinical Research, The Second Hospital of Nanjing, Nanjing Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Yajuan Zhang
- General Medicine, Pingjiang Xincheng Community Health Service Center, Suzhou, China
| | - Hongliang Li
- Department of Infectious Diseases, The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, China
| |
Collapse
|
19
|
Meiser P, Knolle MA, Hirschberger A, de Almeida GP, Bayerl F, Lacher S, Pedde AM, Flommersfeld S, Hönninger J, Stark L, Stögbauer F, Anton M, Wirth M, Wohlleber D, Steiger K, Buchholz VR, Wollenberg B, Zielinski CE, Braren R, Rueckert D, Knolle PA, Kaissis G, Böttcher JP. A distinct stimulatory cDC1 subpopulation amplifies CD8 + T cell responses in tumors for protective anti-cancer immunity. Cancer Cell 2023; 41:1498-1515.e10. [PMID: 37451271 DOI: 10.1016/j.ccell.2023.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Type 1 conventional dendritic cells (cDC1) can support T cell responses within tumors but whether this determines protective versus ineffective anti-cancer immunity is poorly understood. Here, we use imaging-based deep learning to identify intratumoral cDC1-CD8+ T cell clustering as a unique feature of protective anti-cancer immunity. These clusters form selectively in stromal tumor regions and constitute niches in which cDC1 activate TCF1+ stem-like CD8+ T cells. We identify a distinct population of immunostimulatory CCR7neg cDC1 that produce CXCL9 to promote cluster formation and cross-present tumor antigens within these niches, which is required for intratumoral CD8+ T cell differentiation and expansion and promotes cancer immune control. Similarly, in human cancers, CCR7neg cDC1 interact with CD8+ T cells in clusters and are associated with patient survival. Our findings reveal an intratumoral phase of the anti-cancer T cell response orchestrated by tumor-residing cDC1 that determines protective versus ineffective immunity and could be exploited for cancer therapy.
Collapse
Affiliation(s)
- Philippa Meiser
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Moritz A Knolle
- Institute for Artificial Intelligence in Medicine & Healthcare, School of Medicine, TUM, Munich, Germany; Institute for Diagnostic and Interventional Radiology, School of Medicine, TUM, Munich, Germany; Department of Computing, Imperial College London, London, UK
| | - Anna Hirschberger
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Gustavo P de Almeida
- Institute of Animal Physiology and Immunology, School of Life Science, TUM, Freising, Germany; Institute of Virology, School of Medicine, TUM, Munich, Germany
| | - Felix Bayerl
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sebastian Lacher
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Anna-Marie Pedde
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sophie Flommersfeld
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, TUM, Munich, Germany
| | - Julian Hönninger
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany; Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, TUM, Munich, Germany
| | - Leonhard Stark
- Department of Otolaryngology Head and Neck Surgery, School of Medicine, TUM, Munich, Germany
| | - Fabian Stögbauer
- Institute of Pathology, School of Medicine, TUM, Munich, Germany
| | - Martina Anton
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Markus Wirth
- Department of Otolaryngology Head and Neck Surgery, School of Medicine, TUM, Munich, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine, TUM, Munich, Germany; Comparative Experimental Pathology, School of Medicine, TUM, Munich, Germany; German Cancer Consortium, partner site Munich, Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, TUM, Munich, Germany
| | - Barbara Wollenberg
- Department of Otolaryngology Head and Neck Surgery, School of Medicine, TUM, Munich, Germany
| | - Christina E Zielinski
- Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Rickmer Braren
- Institute for Diagnostic and Interventional Radiology, School of Medicine, TUM, Munich, Germany
| | - Daniel Rueckert
- Institute for Artificial Intelligence in Medicine & Healthcare, School of Medicine, TUM, Munich, Germany; Department of Computing, Imperial College London, London, UK; Chair for Artificial Intelligence in Medicine and Healthcare, School of Medicine and School of Computation, Information and Technology, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany; Institute of Molecular Immunology, School of Life Science, TUM, Freising, Germany; German Center for Infection Research, Munich site, Munich, Germany
| | - Georgios Kaissis
- Institute for Artificial Intelligence in Medicine & Healthcare, School of Medicine, TUM, Munich, Germany; Institute for Diagnostic and Interventional Radiology, School of Medicine, TUM, Munich, Germany; Department of Computing, Imperial College London, London, UK
| | - Jan P Böttcher
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich (TUM), Munich, Germany.
| |
Collapse
|
20
|
Wang MD, Xiang H, Hong TY, Mierxiati A, Yan FH, Zhang L, Wang C. Integrated analysis of intratumoral biomarker and tumor-associated macrophage to improve the prognosis prediction in cancer patients. BMC Cancer 2023; 23:593. [PMID: 37370037 DOI: 10.1186/s12885-023-11027-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The lack of effective and accurate predictive indicators remains a major bottleneck for the improvement of the prognosis of patients with hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Hepatitis B virus X (HBx) has been widely suggested as a critical pathogenic protein for HBV-driven liver carcinogenesis, while tumor-associated macrophage (TAM) infiltration is also closely related to the tumorigenesis and progression of HCC. However, few studies have determined whether combining HBx expression with TAM populations could increase the accuracy of prognostic prediction for HBV-related HCC. METHODS The study cohort enrolling 251 patients with HBV-related HCC was randomly split into a training and a validation group (ratio 1:1). The expression levels of HBx and TAM marker CD68 in HCC samples were detected by immunohistochemistry. Kaplan-Meier curves, Cox regression and Harrell's concordance index (C-index) analysis were conducted to evaluate the prognostic significance of these indicators alone or in combination. RESULTS The expression level of HBx was strongly correlated with CD68+ TAM infiltration in HCC tissues. Elevated HBx or CD68 expression indicated poorer overall survival (OS) and progression-free survival (PFS) after hepatectomy, and both of them were independent risk factors for postoperative survival. Meanwhile, patients with both high HBx and CD68 levels had worst clinical outcomes. Moreover, integrating HBx and CD68 expression with clinical indicators (tumor size and micro-vascular invasion) showed the best prognostic potential with highest C-index value for survival predictivity, and this proposed model also performed better than several conventional classifications of HCC. CONCLUSION Combining the expression of intratumoral HBx, CD68+ TAM population and clinical variables could enable better prognostication for HBV-related HCC after hepatectomy, thus providing novel insights into developing more effective clinical prediction model based on both molecular phenotypes and tumor-immune microenvironment.
Collapse
Affiliation(s)
- Ming-Da Wang
- Shanghai Health Commission Key Lab of Artificial Intelligence-Based Management of Inflammation and Chronic Diseases, Gongli Hospital, Navy Medical University, 219 Miaopu Road, Shanghai, 200135, China
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, 200433, China
| | - Hao Xiang
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Guizhou, 563000, China
| | - Tian-Yu Hong
- Shanghai Health Commission Key Lab of Artificial Intelligence-Based Management of Inflammation and Chronic Diseases, Gongli Hospital, Navy Medical University, 219 Miaopu Road, Shanghai, 200135, China
| | - Abudurexiti Mierxiati
- Shanghai Health Commission Key Lab of Artificial Intelligence-Based Management of Inflammation and Chronic Diseases, Gongli Hospital, Navy Medical University, 219 Miaopu Road, Shanghai, 200135, China
| | - Fei-Hu Yan
- Department of Colorectal Surgery, Shanghai Changhai Hospital, Navy Medical University, Shanghai, 200433, China.
| | - Ling Zhang
- Department of Obstetrics and Gynecology, School of Medicine, Chengdu Women's and Children's Central Hospital, University of Electronic Science and Technology of China, Sichuan, 610000, China.
| | - Chao Wang
- Shanghai Health Commission Key Lab of Artificial Intelligence-Based Management of Inflammation and Chronic Diseases, Gongli Hospital, Navy Medical University, 219 Miaopu Road, Shanghai, 200135, China.
- Department of Urinary Surgery, Gongli Hospital, Navy Medical University, Shanghai, 200135, China.
| |
Collapse
|
21
|
Chen X, Peng C, Chen Y, Ding B, Liu S, Song Y, Li Y, Sun B, Yang R. A T-cell-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma based on transcriptomics and single-cell sequencing. BMC Bioinformatics 2023; 24:216. [PMID: 37231356 DOI: 10.1186/s12859-023-05344-7] [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: 03/09/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed malignancy and the third leading cause of cancer death globally. T cells are significantly correlated with the progression, therapy and prognosis of cancer. Limited systematic studies regarding the role of T-cell-related markers in HCC have been performed. METHODS T-cell markers were identified with single-cell RNA sequencing (scRNA-seq) data from the GEO database. A prognostic signature was developed with the LASSO algorithm in the TCGA cohort and verified in the GSE14520 cohort. Another three eligible immunotherapy datasets, GSE91061, PRJEB25780 and IMigor210, were used to verify the role of the risk score in the immunotherapy response. RESULTS With 181 T-cell markers identified by scRNA-seq analysis, a 13 T-cell-related gene-based prognostic signature (TRPS) was developed for prognostic prediction, which divided HCC patients into high-risk and low-risk groups according to overall survival, with AUCs of 1 year, 3 years, and 5 years of 0.807, 0.752, and 0.708, respectively. TRPS had the highest C-index compared with the other 10 established prognostic signatures, suggesting a better performance of TRPS in predicting the prognosis of HCC. More importantly, the TRPS risk score was closely correlated with the TIDE score and immunophenoscore. The high-risk score patients had a higher percentage of SD/PD, and CR/PR occurred more frequently in patients with low TRPS-related risk scores in the IMigor210, PRJEB25780 and GSE91061 cohorts. We also constructed a nomogram based on the TRPS, which had high potential for clinical application. CONCLUSION Our study proposed a novel TRPS for HCC patients, and the TRPS could effectively indicate the prognosis of HCC. It also served as a predictor for immunotherapy.
Collapse
Affiliation(s)
- Xu Chen
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Chuang Peng
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Yu Chen
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Bai Ding
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Sulai Liu
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Yinghui Song
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Yuhang Li
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Bo Sun
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China.
| | - Ranzhiqiang Yang
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China.
| |
Collapse
|
22
|
Liu J, Chen L, Zheng X, Guo C. Identification of immune-related genes in acute myocardial infarction based on integrated bioinformatical methods and experimental verification. PeerJ 2023; 11:e15058. [PMID: 37214088 PMCID: PMC10198157 DOI: 10.7717/peerj.15058] [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: 08/23/2022] [Accepted: 02/22/2023] [Indexed: 05/24/2023] Open
Abstract
Background Acute myocardial infarction (AMI) is one of the leading causes of death worldwide. The etiology of AMI is complex and has not been fully defined. In recent years, the role of immune response in the development, progression and prognosis of AMI has received increasing attention. The aim of this study was to identify key genes associated with the immune response in AMI and to analyze their immune infiltration. Methods The study included a total of two GEO databases, containing 83 patients with AMI and 54 healthy individuals. We used the linear model of microarray data (limma) package to find the differentially expressed genes associated with AMI, performing weighted gene co-expression analysis (WGCNA) to further identify the genes associated with inflammatory response to AMI. We found the final hub genes through the protein-protein interaction (PPI) network and least absolute shrinkage and selection operator (LASSO) regression model. To verify the above conclusions, we constructed mice AMI model, extracting myocardial tissue to perform qRT-PCR. Furthermore, the CIBERSORT tool for immune cells infiltration analysis was also carried out. Results A total of 5,425 significant up-regulated and 2,126 down-regulated genes were found in GSE66360 and GSE24519. A total of 116 immune-related genes in close association with AMI were screened by WGCNA analysis. These genes were mostly clustered in the immune response on the basis of GO and KEGG enrichment. With construction of PPI network and LASSO regression analysis, this research found three hub genes (SOCS2, FFAR2, MYO10) among these differentially expressed genes. The immune cell infiltration results revealed that significant differences could be found on T cells CD4 memory activated, Tregs (regulatory T cells), macrophages M2, neutrophils, T cells CD8, T cells CD4 naive, eosinophils between controls and AMI patients.
Collapse
Affiliation(s)
- Jian Liu
- Cardiovascular Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lu Chen
- Cardiovascular Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiang Zheng
- Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Caixia Guo
- Cardiovascular Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
23
|
Li X, Kang J, Yue J, Xu D, Liao C, Zhang H, Zhao J, Liu Q, Jiao J, Wang L, Li G. Identification and validation of immunogenic cell death-related score in uveal melanoma to improve prediction of prognosis and response to immunotherapy. Aging (Albany NY) 2023; 15:3442-3464. [PMID: 37142279 PMCID: PMC10449274 DOI: 10.18632/aging.204680] [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: 02/13/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Immunogenic cell death (ICD) could activate innate and adaptive immune response. In this work, we aimed to develop an ICD-related signature in uveal melanoma (UVM) patients and facilitate assessment of their prognosis and immunotherapy. METHODS A set of machine learning methods, including non-negative matrix factorization (NMF) method and least absolute shrinkage and selection operator (LASSO) logistic regression model, and bioinformatics analytic tools were integrated to construct an ICD-related risk score (ICDscore). CIBERSORT and ESTIMATE algorithms were used to evaluate the infiltration of immune cells. The Genomics of Drug Sensitivity in Cancer (GDSC), cellMiner and tumor immune dysfunction and exclusion (TIDE) databases were used for therapy sensitivity analyses. The predictive performance between ICDscore with other mRNA signatures was also compared. RESULTS The ICDscore could predict the prognosis of UVM patients in both the training and four validating cohorts. The ICDscore outperformed 19 previously published signatures. Patients with high ICDscore exhibited a substantial increase in immune cell infiltration and expression of immune checkpoint inhibitor-related genes, leading to a higher response rate to immunotherapy. Furthermore, the downregulation of poly (ADP-ribose) polymerase family member 8 (PARP8), a critical gene involved in the development of the ICDscore, resulted in decreased cell proliferation and slower migration of UVM cells. CONCLUSION In conclusion, we developed a robust and powerful ICD-related signature for evaluating the prognosis and benefits of immunotherapy that could serve as a promising tool to guide decision-making and surveillance for UVM patients.
Collapse
Affiliation(s)
- Xiaoyan Li
- Department of Central Laboratory, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, China
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, China
| | - Jing Kang
- Department of Clinical Laboratory, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jing Yue
- Department of Clinical Laboratory, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Dawei Xu
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, China
| | - Chunhua Liao
- Department of Physiotherapy and Rehabilitation, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Huina Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jin Zhao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qiongwen Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinke Jiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Lin Wang
- Department of Geriatrics, Xijing Hospital, The Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Shaanxi Normal University, Xi’an, Shaanxi, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
24
|
Lei L, Du LX, He YL, Yuan JP, Wang P, Ye BL, Wang C, Hou Z. Dictionary learning LASSO for feature selection with application to hepatocellular carcinoma grading using contrast enhanced magnetic resonance imaging. Front Oncol 2023; 13:1123493. [PMID: 37091168 PMCID: PMC10118007 DOI: 10.3389/fonc.2023.1123493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/17/2023] [Indexed: 04/09/2023] Open
Abstract
IntroductionThe successful use of machine learning (ML) for medical diagnostic purposes has prompted myriad applications in cancer image analysis. Particularly for hepatocellular carcinoma (HCC) grading, there has been a surge of interest in ML-based selection of the discriminative features from high-dimensional magnetic resonance imaging (MRI) radiomics data. As one of the most commonly used ML-based selection methods, the least absolute shrinkage and selection operator (LASSO) has high discriminative power of the essential feature based on linear representation between input features and output labels. However, most LASSO methods directly explore the original training data rather than effectively exploiting the most informative features of radiomics data for HCC grading. To overcome this limitation, this study marks the first attempt to propose a feature selection method based on LASSO with dictionary learning, where a dictionary is learned from the training features, using the Fisher ratio to maximize the discriminative information in the feature.MethodsThis study proposes a LASSO method with dictionary learning to ensure the accuracy and discrimination of feature selection. Specifically, based on the Fisher ratio score, each radiomic feature is classified into two groups: the high-information and the low-information group. Then, a dictionary is learned through an optimal mapping matrix to enhance the high-information part and suppress the low discriminative information for the task of HCC grading. Finally, we select the most discrimination features according to the LASSO coefficients based on the learned dictionary.Results and discussionThe experimental results based on two classifiers (KNN and SVM) showed that the proposed method yielded accuracy gains, compared favorably with another 5 state-of-the-practice feature selection methods.
Collapse
Affiliation(s)
- Lei Lei
- College of Information Science and Engineering, Jiaxing University, Jiaxing, China
- *Correspondence: Lei Lei, ; Ying-Long He,
| | - Li-Xin Du
- Medical Imaging Department, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Ying-Long He
- School of Mechanical Engineering Sciences, University of Surrey, Guildford, United Kingdom
- *Correspondence: Lei Lei, ; Ying-Long He,
| | - Jian-Peng Yuan
- Department of Radiology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Pan Wang
- Medical Imaging Department, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Bao-Lin Ye
- College of Information Science and Engineering, Jiaxing University, Jiaxing, China
| | - Cong Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - ZuJun Hou
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| |
Collapse
|
25
|
Wei D, Chen X, Xu J, He W. Identification of molecular subtypes of ischaemic stroke based on immune-related genes and weighted co-expression network analysis. IET Syst Biol 2023; 17:58-69. [PMID: 36802116 PMCID: PMC10116020 DOI: 10.1049/syb2.12059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/20/2023] Open
Abstract
Immune system has been reported to play a key role in the development of ischaemic stroke (IS). Nevertheless, its exact immune-related mechanism has not yet been fully revealed. Gene expression data of IS and healthy control samples was downloaded from Gene Expression Omnibus database and differentially expressed genes (DEGs) was obtained. Immune-related genes (IRGs) data was downloaded from the ImmPort database. The molecular subtypes of IS were identified based on IRGs and weighted co-expression network analysis (WGCNA). 827 DEGs and 1142 IRGs were obtained in IS. Based on 1142 IRGs, 128 IS samples were clustered into two molecular subtypes: clusterA and clusterB. Based on the WGCNA, the authors found that the blue module had the highest correlation with IS. In the blue module, 90 genes were screened as candidate genes. The top 55 genes were selected as the central nodes according to gene degree in protein-protein interactions network of all genes in blue module. Through taking overlap, nine real hub genes were obtained that might distinguish between clusterA subtype and clusterB subtype of IS. The real hub genes (IL7R, ITK, SOD1, CD3D, LEF1, FBL, MAF, DNMT1, and SLAMF1) may be associated with molecular subtypes and immune regulation of IS.
Collapse
Affiliation(s)
- Duncan Wei
- Department of PharmacyFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Xiaopu Chen
- Department of NeurologyFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Jing Xu
- Department of PharmacyFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Wenzhen He
- Department of NeurologyFirst Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| |
Collapse
|
26
|
Chen R, Wei JM. Integrated analysis identifies oxidative stress-related lncRNAs associated with progression and prognosis in colorectal cancer. BMC Bioinformatics 2023; 24:76. [PMID: 36869292 PMCID: PMC9985255 DOI: 10.1186/s12859-023-05203-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers in the world. Oxidative stress reactions have been reportedly associated with oncogenesis and tumor progression. By analyzing mRNA expression data and clinical information from The Cancer Genome Atlas (TCGA), we aimed to construct an oxidative stress-related long noncoding RNA (lncRNA) risk model and identify oxidative stress-related biomarkers to improve the prognosis and treatment of CRC. RESULTS Differentially expressed oxidative stress-related genes (DEOSGs) and oxidative stress-related lncRNAs were identified by using bioinformatics tools. An oxidative stress-related lncRNA risk model was constructed based on 9 lncRNAs (AC034213.1, AC008124.1, LINC01836, USP30-AS1, AP003555.1, AC083906.3, AC008494.3, AC009549.1, and AP006621.3) by least absolute shrinkage and selection operator (LASSO) analysis. The patients were then divided into high- and low-risk groups based on the median risk score. The high-risk group had a significantly worse overall survival (OS) (p < 0.001). Receiver operating characteristic (ROC) and calibration curves displayed the favorable predictive performance of the risk model. The nomogram successfully quantified the contribution of each metric to survival, and the concordance index and calibration plots demonstrated its excellent predictive capacity. Notably, different risk subgroups showed significant differences in terms of their metabolic activity, mutation landscape, immune microenvironment and drug sensitivity. Specifically, differences in the immune microenvironment implied that CRC patients in certain subgroups might be more responsive to immune checkpoint inhibitors. CONCLUSIONS Oxidative stress-related lncRNAs can predict the prognosis of CRC patients, which provides new insight for future immunotherapies based on potential oxidative stress targets.
Collapse
Affiliation(s)
- Rui Chen
- Department of Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jun-Min Wei
- Department of Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
| |
Collapse
|
27
|
Xu X, Wang J. Prognostic prediction and multidimensional dissections of a macrophages M0-related gene signature in liver cancer. Front Endocrinol (Lausanne) 2023; 14:1153562. [PMID: 37033261 PMCID: PMC10080084 DOI: 10.3389/fendo.2023.1153562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Liver hepatocellular carcinoma (LIHC) is the seventh most commonly diagnosed malignancy and the third leading cause of all cancer death worldwide. The undifferentiated macrophages M0 can be induced into polarized M1 and M2 to exert opposite effects in tumor microenvironment. However, the prognostic value of macrophages M0 phenotype remains obscure in LIHC. METHODS The transcriptome data of LIHC was obtained from TCGA database and ICGC database. 365 LIHC samples from TCGA database and 231 LIHC samples from ICGC database were finally included. Macrophages M0-related genes (MRGs) were screened by Pearson correlation analysis and univariate Cox regression analysis based on the infiltration level of Macrophages M0. LASSO regression analysis was employed to construct a prognostic signature based on MRGs, and risk scores were accordingly calculated. Then we investigated the MRGs-based prognostic signature with respects to prognostic value, clinical significance, strengthened pathways, immune infiltration, gene mutation and drug sensitivity. Furthermore, the expression pattern of MRGs in the tumor microenvironment were also detected in LIHC. RESULTS A ten-MRG signature was developed and clarified as independent prognostic predictors in LIHC. The risk score-based nomogram showed favorable capability in survival prediction. Several substance metabolism activities like fatty acid/amino acid metabolism were strengthened in low-risk group. Low risk group was deciphered to harbor TTN mutation-driven tumorigenesis, while TP53 mutation was dominant in high-risk group. We also ascertained that the infiltration levels of immune cells and expressions of immune checkpoints are significantly influenced by the risk score. Besides, we implied that patients in low-risk group may be more sensitive to several anti-cancer drugs. What's more important, single-cell analysis verified the expression of MRGs in the tumor microenvironment of LIHC. CONCLUSION Multidimensional evaluations verified the clinical utility of the macrophages M0-related gene signature to predict prognosis, assist risk decision and guide treatment strategy for patients with LIHC.
Collapse
Affiliation(s)
- Xiaoming Xu
- Department of Gastroenterology, Jining First People’s Hospital, Jining, China
| | - Jingzhi Wang
- Department of Radiotherapy Oncology, The Affiliated Yancheng First Hospital of Nanjing University Medical School, The First People’s Hospital of Yancheng, Yancheng, China
- *Correspondence: Jingzhi Wang,
| |
Collapse
|
28
|
Tang L, Yu S, Zhang Q, Cai Y, Li W, Yao S, Cheng H. Identification of hub genes related to CD4 + memory T cell infiltration with gene co-expression network predicts prognosis and immunotherapy effect in colon adenocarcinoma. Front Genet 2022; 13:915282. [PMID: 36105107 PMCID: PMC9465611 DOI: 10.3389/fgene.2022.915282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Background: CD4+ memory T cells (CD4+ MTCs), as an important part of the microenvironment affecting tumorigenesis and progression, have rarely been systematically analyzed. Our purpose was to comprehensively analyze the effect of CD4+ MTC infiltration on the prognosis of colon adenocarcinoma (COAD). Methods: Based on RNA-Seq data, weighted gene co-expression network analysis (WGCNA) was used to screen the CD4+ MTC infiltration genes most associated with colon cancer and then identify hub genes and construct a prognostic model using the least absolute shrinkage and selection operator algorithm (LASSO). Finally, survival analysis, immune efficacy analysis, and drug sensitivity analysis were performed to evaluate the role of the prognostic model in COAD. Results: We identified 929 differentially expressed genes (DEGs) associated with CD4+ MTCs and constructed a prognosis model based on five hub genes (F2RL2, TGFB2, DTNA, S1PR5, and MPP2) to predict overall survival (OS) in COAD. Kaplan-Meier analysis showed poor prognosis in the high-risk group, and the analysis of the hub gene showed that overexpression of TGFB2, DTNA, S1PR5, or MPP2 was associated with poor prognosis. Clinical prediction nomograms combining CD4+ MTC-related DEGs and clinical features were constructed to accurately predict OS and had high clinical application value. Immune efficacy and drug sensitivity analysis provide new insights for individualized treatment. Conclusion: We constructed a prognostic risk model to predict OS in COAD and analyzed the effects of risk score on immunotherapy efficacy or drug sensitivity. These studies have important clinical significance for individualized targeted therapy and prognosis.
Collapse
Affiliation(s)
- Lingxue Tang
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| | - Sheng Yu
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| | - Qianqian Zhang
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| | - Yinlian Cai
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| | - Wen Li
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| | - Senbang Yao
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| | - Huaidong Cheng
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Anhui Medical University, Hefei, China
| |
Collapse
|
29
|
ASPN Is a Potential Biomarker and Associated with Immune Infiltration in Endometriosis. Genes (Basel) 2022; 13:genes13081352. [PMID: 36011263 PMCID: PMC9407481 DOI: 10.3390/genes13081352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: Endometriosis is a benign gynecological disease characterized by distant metastasis. Previous studies have discovered abnormal numbers and function of immune cells in endometriotic lesions. We aimed to find potential biomarkers of endometriosis and to explore the relationship between ASPN and the immune microenvironment of endometriosis. Methods: We obtained the GSE141549 and GSE7305 datasets containing endometriosis and normal endometrial samples from the Gene Expression Omnibus database (GEO). In the GSE141549 dataset, differentially expressed genes (DEGs) were found. The Least Absolute Shrinkage and Selection Operator (Lasso) regression and generalized linear models (GLMs) were used to screen new biomarkers. The expression levels and diagnostic utility of biomarkers were assessed in GSE7305, and biomarker expression levels were further validated using qRT-PCR and western blot. We identified DEGs between high and low expression groups of key biomarkers. Enrichment analysis was carried out to discover the target gene’s biological function. We analyzed the relationship between key biomarker expression and patient clinical features. Finally, the immune cells that infiltrate endometriosis were assessed using the Microenvironment Cell Population-Counter (MCP-counter), and the correlation of biomarker expression with immune cell infiltration and immune checkpoints genes was studied. Results: There were a total of 38 DEGs discovered. Two machine learning techniques were used to identify 10 genes. Six biomarkers (SCG2, ASPN, SLIT2, GEM, EGR1, and FOS) had good diagnostic efficiency (AUC > 0.7) by internal and external validation. We excluded previously reported related genes (SLIT2, EGR1, and FOS). ASPN was the most significantly differentially expressed biomarker between normal and ectopic endometrial tissues, as verified by qPCR. The western blot assay revealed a significant upregulation of ASPN expression in endometriotic tissues. The investigation for DEGs in the ASPN high- and low-expression groups revealed that the DEGs were particularly enriched in extracellular matrix tissue, vascular smooth muscle contraction, cytokine interactions, the calcium signaling pathway, and the chemokine signaling pathway. High ASPN expression was related to r-AFS stage (p = 0.006), age (p = 0.03), and lesion location (p < 0.001). Univariate and multivariate logistic regression analysis showed that ASPN expression was an independent influencing factor in patients with endometriosis. Immune cell infiltration analysis revealed a significant increase in T-cell, B-cell, and fibroblast infiltration in endometriosis lesions; cytotoxic lymphocyte, NK-cell, and endothelial cell infiltration were reduced. Additionally, the percentage of T cells, B cells, fibroblasts, and endothelial cells was favorably connected with ASPN expression, while the percentage of cytotoxic lymphocytes and NK cells was negatively correlated. Immune checkpoint gene (CTLA4, LAG3, CD27, CD40, and ICOS) expression and ASPN expression were positively associated. Conclusions: Increased expression of ASPN is associated with immune infiltration in endometriosis, and ASPN can be used as a diagnostic biomarker as well as a potential immunotherapeutic target in endometriosis.
Collapse
|
30
|
Construction of a Novel Clinical Stage-Related Gene Signature for Predicting Outcome and Immune Response in Hepatocellular Carcinoma. J Immunol Res 2022; 2022:6535009. [PMID: 35865652 PMCID: PMC9296277 DOI: 10.1155/2022/6535009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors. However, there were no studies to create a clinical stage-related gene signature for HCC patients. Differentially expressed genes (DEGs) associated with clinical stage of HCC were analyzed based on TCGA datasets. Functional enrichment analysis was carried out by the use of stage-related DEGs. Then, the least absolute shrinkage and selection operator (LASSO) regression and univariate Cox regression were performed to reduce the overfit and the number of genes for further analysis. Next, survival and ROC assays were carried out to demonstrate the model using TCGA. Functional analysis and immune microenvironment analysis related to stage-related DEGs were performed. Reverse transcriptase polymerase chain reaction (RT-PCR) and Cell Counting Kit-8 (CCK-8) assays were applied to examine the expression and function of PNCK in HCC. In this research, there were 21 DEGs between HCC specimens with stage (I-II) and HCC specimens with stage (III-IV), including 20 increased genes and 1 decreased genes. A novel seven-gene signature (including PITX2, PNCK, GLIS1, SCNN1G, MMP1, ZNF488, and SHISA9) was created for the prediction of outcomes of HCC patients. The ROC curves confirmed the prognostic value of the new model. Cox assays demonstrated that the seven-gene signature can independently forecast overall survival. The immune analysis revealed that patients with low risk score exhibited more immune activities. Moreover, we confirmed that PNCK expressions were distinctly increased in HCC, and its silence suppressed the proliferation of HCC cells. Overall, our research offered a robust and reliable gene signature which displayed an important value in the prediction of overall survival of HCC patients and might deliver more effective personalized therapies.
Collapse
|
31
|
Abstract
The tumor microenvironment (TME) is a well-recognized system that plays an essential role in tumor initiation, development, and progression. Intense intercellular communication between tumor cells and other cells (especially macrophages) occurs in the TME and is mediated by cell-to-cell contact and/or soluble messengers. Emerging evidence indicates that noncoding RNAs (ncRNAs) are critical regulators of the relationship between cells within the TME. In this review, we provide an update on the regulation of ncRNAs (primarily micro RNAs [miRNAs], long ncRNAs [lncRNAs], and circular RNAs [circRNAs]) in the crosstalk between macrophages and tumor cells in hepatocellular carcinoma (HCC). These ncRNAs are derived from macrophages or tumor cells and act as oncogenes or tumor suppressors, contributing to tumor progression not only by regulating the physiological and pathological processes of tumor cells but also by controlling macrophage infiltration, activation, polarization, and function. Herein, we also explore the options available for clinical therapeutic strategies targeting crosstalk-related ncRNAs to treat HCC. A better understanding of the relationship between macrophages and tumor cells mediated by ncRNAs will uncover new diagnostic biomarkers and pharmacological targets in cancer.
Collapse
|
32
|
Wang T, Dai L, Shen S, Yang Y, Yang M, Yang X, Qiu Y, Wang W. Comprehensive Molecular Analyses of a Macrophage-Related Gene Signature With Regard to Prognosis, Immune Features, and Biomarkers for Immunotherapy in Hepatocellular Carcinoma Based on WGCNA and the LASSO Algorithm. Front Immunol 2022; 13:843408. [PMID: 35693827 PMCID: PMC9186446 DOI: 10.3389/fimmu.2022.843408] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
Macrophages have been reported to exert a crucial role in hepatocellular carcinoma (HCC). This study aimed to explore the macrophage-related genes and establish a macrophage-related signature (MRS) model to predict the overall survival (OS) of patients with HCC based on these genes’ expression. We screened the macrophage-related gene module by weighted gene coexpression network analysis (WGCNA), the least absolute shrinkage and selection operator (LASSO) Cox regression analysis was utilized for further selection, and the selected genes were entered into stepwise regression to develop the MRS model, which was further validated in the Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC) datasets. We analyzed the biological phenotypes associated with macrophages in terms of functional enrichment, tumor immune signature, and tumor mutational signature. The patient’s response to immunotherapy was inferred by the tumor immune dysfunction and exclusion (TIDE) score, the immunophenotype score (IPS), and the IMvigor210 dataset. A novel MRS model was established based on the LASSO regression coefficients of the genes PON1, IL15RA, NEIL3, HILPDA, PFN2, HAVCR1, ANXA10, CDCA8, EPO, S100A9, TTK, KLRB1, SPP1, STC2, CYP26B1, GPC1, G6PD, and CBX2. In either dataset, MRS was identified as an independent risk factor for OS in HCC patients. Additionally, our research indicated that a high-risk score in the MRS model was significantly correlated with tumor staging, pathological grade, tumor–node–metastasis (TNM) stage, and survival. Several genes of the human leukocyte antigen (HLA) family and immune checkpoints were highly expressed in the high-risk group. In addition, the frequency of tumor mutations was also higher in the high-risk group. According to our analyses, a higher risk score in the MRS model may predict a better response to immunotherapy.
Collapse
Affiliation(s)
- Tao Wang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liqun Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shu Shen
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Yang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Ming Yang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Xianwei Yang
- Department of Thyroid Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiwen Qiu
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Wentao Wang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Wentao Wang,
| |
Collapse
|
33
|
He K, Liu X, Hoffman RD, Shi RZ, Lv GY, Gao JL. G-CSF/GM-CSF-induced hematopoietic dysregulation in the progression of solid tumors. FEBS Open Bio 2022; 12:1268-1285. [PMID: 35612789 PMCID: PMC9249339 DOI: 10.1002/2211-5463.13445] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 11/06/2022] Open
Abstract
There are two types of abnormal hematopoiesis in solid tumor occurrence and treatment: pathological hematopoiesis, and myelosuppression induced by radiotherapy and chemotherapy. In this review, we primarily focus on the abnormal pathological hematopoietic differentiation in cancer induced by tumor-released granulocyte colony stimulating factor (G-CSF) and granulocyte-macrophage colony stimulating factor (GM-CSF). As key factors in hematopoietic development, G-CSF/GM-CSF are well-known facilitators of myelopoiesis and mobilization of hematopoietic stem cells (HSCs). In addition, these two cytokines can also promote or inhibit tumors, dependent on tumor type. In multiple cancer types, hematopoiesis is greatly enhanced and abnormal lineage differentiation is induced by these two cytokines. Here, dysregulated hematopoiesis induced by G-CSF/GM-CSF in solid tumors and its mechanism are summarized, and the prognostic value of G-CSF/GM-CSF-associated dysregulated hematopoiesis for tumor metastasis is also briefly highlighted.
Collapse
Affiliation(s)
- Kai He
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Xi Liu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Robert D Hoffman
- Yo San University of Traditional Chinese Medicine, Los Angeles, CA, 90066, USA
| | - Rong-Zhen Shi
- Tangqi Branch of Traditional Chinese Medicine Hospital of Yuhang District, Hangzhou, Zhejiang, 311106, China
| | - Gui-Yuan Lv
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University Hangzhou, Zhejiang, 310053, China
| | - Jian-Li Gao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University Hangzhou, Zhejiang, 310053, China
| |
Collapse
|
34
|
Fu Y, Wei XD, Guo L, Wu K, Le J, Ma Y, Kong X, Tong Y, Wu H. The Metabolic and Non-Metabolic Roles of UCK2 in Tumor Progression. Front Oncol 2022; 12:904887. [PMID: 35669416 PMCID: PMC9163393 DOI: 10.3389/fonc.2022.904887] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
Enhanced nucleoside metabolism is one of the hallmarks of cancer. Uridine-cytidine kinase 2 (UCK2) is a rate-limiting enzyme of the pyrimidine salvage synthesis pathway to phosphorylate uridine and cytidine to uridine monophosphate (UMP) and cytidine monophosphate (CMP), respectively. Recent studies have shown that UCK2 is overexpressed in many types of solid and hematopoietic cancers, closely associates with poor prognosis, and promotes cell proliferation and migration in lung cancer and HCCs. Although UCK2 is thought to catalyze sufficient nucleotide building blocks to support the rapid proliferation of tumor cells, we and other groups have recently demonstrated that UCK2 may play a tumor-promoting role in a catalytic independent manner by activating oncogenic signaling pathways, such as STAT3 and EGFR-AKT. By harnessing the catalytic activity of UCK2, several cytotoxic ribonucleoside analogs, such as TAS-106 and RX-3117, have been developed for UCK2-mediated cancer chemotherapy. Moreover, we have demonstrated that the concurrent targeting of the catalytic dependent and independent features of UCK2 could synergistically inhibit tumor growth. These findings suggest that UCK2 may serve as a potential therapeutic target for cancer treatment. In this mini-review, we introduced the genomic localization and protein structure of UCK2, described the role of UCK2 in tumor development, discussed the application of UCK2 in anti-tumor treatment, and proposed concurrent targeting of the catalytic and non-catalytic roles of UCK2 as a potential therapeutic strategy for cancer treatment.
Collapse
Affiliation(s)
- Yi Fu
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Xin-dong Wei
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Central Laboratory, Department of Liver Diseases, Institute of Clinical Immunology, ShuGuang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Luoting Guo
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Kai Wu
- School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Jiamei Le
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Yujie Ma
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Xiaoni Kong
- Central Laboratory, Department of Liver Diseases, Institute of Clinical Immunology, ShuGuang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Tong
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- *Correspondence: Hailong Wu, ; Ying Tong,
| | - Hailong Wu
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, China
- *Correspondence: Hailong Wu, ; Ying Tong,
| |
Collapse
|
35
|
Yang Y, Gao L, Chen J, Xiao W, Liu R, Kan H. Lamin B1 is a potential therapeutic target and prognostic biomarker for hepatocellular carcinoma. Bioengineered 2022; 13:9211-9231. [PMID: 35436411 PMCID: PMC9161935 DOI: 10.1080/21655979.2022.2057896] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive malignancy. Previous studies have found that lamin B1 (LMNB1) contributes to the development of human cancers. However, the biological functions and prognostic values of LMNB1 in HCC have not been adequately elucidated. In our present research, the expression pattern of LMNB1 was analyzed. The prognostic values of LMNB1 were evaluated by Kaplan-Meier survival analysis and Cox proportional hazards regression analysis. The effects of LMNB1 on HCC progression were assessed by Cell Counting Kit-8 (CCK-8), colony formation, wound healing, Transwell and in vivo xenograft assays. The mechanisms of LMNB1 in HCC progression were elucidated by gene set enrichment analysis (GSEA) and loss-of-function assays. Besides, a nomogram for predicting overall survival (OS) was constructed. The results demonstrated that LMNB1 was overexpressed in HCC and that increased LMNB1 expression predicted a dismal prognosis. Further experiments showed that LMNB1 facilitated cell proliferation and metastasis in HCC. Functional enrichment analysis revealed that LMNB1 modulated metastasis-associated biological functions such as focal adhesion, extracellular matrix, cell junctions and cell adhesion. Mechanistically, we revealed that LMNB1 promoted HCC progression by regulating the phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) pathways. Moreover, incorporating LMNB1, Ki67 and Barcelona Clinic Liver Cancer (BCLC) stage into a nomogram showed better predictive accuracy than the Tumor-Node-Metastasis (TNM) stage and BCLC stage. In conclusion, LMNB1 may serve as an effective therapeutic target as well as a reliable prognostic biomarker for HCC.
Collapse
Affiliation(s)
- Yongyu Yang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Gao
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junzhang Chen
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wang Xiao
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ruoqi Liu
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Heping Kan
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
36
|
Cai D, Zhao Z, Hu J, Dai X, Zhong G, Gong J, Qi F. Identification of the Tumor Immune Microenvironment and Therapeutic Biomarkers by a Novel Molecular Subtype Based on Aging-Related Genes in Hepatocellular Carcinoma. Front Surg 2022; 9:836080. [PMID: 35392063 PMCID: PMC8980463 DOI: 10.3389/fsurg.2022.836080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
BackgroundHepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors with poor prognosis. Increasing evidence has revealed that immune cells and checkpoints in the tumor microenvironment (TME) and aging are associated with the prognosis of HCC. However, the association between aging and the tumor immune microenvironment (TIME) in HCC is still unclear.MethodsRNA expression profiles and clinical data concerning HCC were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Based on differentially expressed aging-related genes (DEAGs), unsupervised clustering was used to identify a novel molecular subtype in HCC. The features of immune cell infiltration and checkpoints were further explored through CIBERSORTx. Enrichment analysis and both univariate and multivariate Cox analyses were conducted to construct a 3-gene model for predicting prognosis and chemosensitivity. Finally, the mRNA and protein expression levels of the 3 genes were verified in HCC and other cancers through database searches and experiments.ResultsEleven differentially expressed AGs (GHR, APOC3, FOXM1, PON1, TOP2A, FEN1, HELLS, BUB1B, PPARGC1A, PRKDC, and H2AFX) correlated with the prognosis of HCC were used to divide HCC into two subtypes in which the prognosis was different. In cluster 2, which had a poorer prognosis, the infiltration of naive B cells and monocytes was lower in the TCGA and GEO cohorts, while the infiltration of M0 macrophages was higher. In addition, the TCGA cohort indicated that the microenvironment of cluster 2 had more immunosuppression through immune checkpoints. Enrichment analysis suggested that the MYC and E2F targets were positively associated with cluster 2 in the TCGA and GEO cohorts. Additionally, 3 genes (HMGCS2, SLC22A1, and G6PD) were screened to construct the prognostic model through univariate/multivariate Cox analysis. Then, the model was validated through the TCGA validation set and GEO dataset (GSE54236). Cox analysis indicated that the risk score was an independent prognostic factor and that patients in the high-risk group were sensitive to multiple targeted drugs (sorafenib, gemcitabine, rapamycin, etc.). Finally, significantly differential expression of the 3 genes was detected across cancers.ConclusionWe systematically described the immune differences in the TME between the molecular subtypes based on AGs and constructed a novel three-gene signature to predict prognosis and chemosensitivity in patients with HCC.
Collapse
|
37
|
You JA, Gong Y, Wu Y, Jin L, Chi Q, Sun D. WGCNA, LASSO and SVM Algorithm Revealed RAC1 Correlated M0 Macrophage and the Risk Score to Predict the Survival of Hepatocellular Carcinoma Patients. Front Genet 2022; 12:730920. [PMID: 35493265 PMCID: PMC9044718 DOI: 10.3389/fgene.2021.730920] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
Background: RAC1 is involved in the progression of HCC as a regulator, but its prognostic performance and the imbalance of immune cell infiltration mediated by it are still unclear. We aim to explore the prognostic and immune properties of RAC1 in HCC. Methods: We separately downloaded the data related to HCC from the Cancer Genome Atlas (TCGA) and GEO database. CIBERSORT deconvolution algorithm, weighted gene co-expression network analysis (WGCNA) and LASSO algorithm participate in identifying IRGs and the construction of prognostic signatures. Results: The study discovered that RAC1 expression was linked to the severity of HCC lesions, and that its high expression was linked to a poor prognosis. Cox analysis confirmed that RAC1 is a clinically independent prognostic marker. M0, M1 and M2 macrophages’ abundance are significantly different in HCC. We found 828 IRGs related to macrophage infiltration, and established a novel 11-gene signature with excellent prognostic performance. RAC1-based risk score and M0 macrophage has a good ability to predict overall survival. Conclusion: The immune state of irregular macrophage infiltration may be one of the precursors to carcinogenesis. The RAC1 correlated with M0 macrophage and the risk score to show a good performance to predict the survival of HCC patients.
Collapse
Affiliation(s)
- Ji-An You
- College of Technology, Hubei Engineering University, Xiaogan, China
| | - Yuhan Gong
- Department of Geotechnical Engineering, Wuhan University of Technology, Wuhan, China
| | - Yongzhe Wu
- Department of Mechanics and Engineering Structure, Wuhan University of Technology, Wuhan, China
| | - Libo Jin
- Institute of Life Sciences and Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, China
| | - Qingjia Chi
- Department of Mechanics and Engineering Structure, Wuhan University of Technology, Wuhan, China
- *Correspondence: Qingjia Chi, ; Da Sun,
| | - Da Sun
- Institute of Life Sciences and Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, China
- *Correspondence: Qingjia Chi, ; Da Sun,
| |
Collapse
|
38
|
Qiu ZQ, Wang X, Ji XW, Jiang FJ, Han XY, Zhang WL, An YH. The clinical relevance of epithelial-mesenchymal transition and its correlations with tumorigenic immune infiltrates in hepatocellular carcinoma. Immunology 2022; 166:185-196. [PMID: 35274290 DOI: 10.1111/imm.13465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a cancer with extremely high mortality. Epithelial-mesenchymal transition (EMT) may play an important role in the occurrence, invasion, and prognosis of HCC; however, its relationship with immunity in HCC has not yet been studied. Therefore, we investigated the diagnostic and prognostic values of EMT and explored its potential connections with tumorigenic immune infiltrates in HCC. We first proposed a quantitative metric of EMT activity, the EMT score. After applying this metric to 20 datasets from the Integrative Molecular Database of Hepatocellular Carcinoma, The Cancer Genome Atlas, and the Gene Expression Omnibus, we explored the ability of the EMT score to stratify across sample types. We then applied the EMT score for survival analysis and to differentiate patients with/without vascular invasion to test its prognostic value. We also collected and calculated data on the abundance of immune cells and immune cell markers in HCC and investigated their correlations with EMT scores. Finally, we synthesized and analyzed 20 datasets and constructed an EMT-gene-immune linkage network. The results showed higher EMT scores in HCC samples than in cirrhotic and normal livers. The cases with higher EMT scores also showed poorer performance in terms of prognostic factors such as vascular invasion and overall survival time. Our research demonstrated a broad correlation between EMT and the tumor immune microenvironment, and we uncovered multiple potential linkers associated with both EMT and immunity. Studying EMT has clinical relevance and high diagnostic and prognostic value for HCC.
Collapse
Affiliation(s)
- Zhi-Qiang Qiu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Xiang-Wen Ji
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
| | - Fen-Jun Jiang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China.,Department of Research and Development, Beijing Yihua Biological Technology Co., Ltd, Beijing, 100041, China
| | - Xin-Ye Han
- Department of Research and Development, Beijing Yihua Biological Technology Co., Ltd, Beijing, 100041, China
| | - Wei-Li Zhang
- Department of Inpatient Administration and Medical Record Management, Third Medical Center, General Hospital of Chinese PLA, Beijing, 100039, China
| | - Yi-Hua An
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| |
Collapse
|
39
|
Identification of Biomarkers Associated with Cancerous Change in Oral Leukoplakia Based on Integrated Transcriptome Analysis. JOURNAL OF ONCOLOGY 2022; 2022:4599305. [PMID: 35096060 PMCID: PMC8791753 DOI: 10.1155/2022/4599305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/04/2022] [Indexed: 12/21/2022]
Abstract
Objective Oral leukoplakia (OLK) is the most common precancerous lesion in the oral cavity. This study aimed to explore key biomarkers for monitoring OLK for early diagnosis of oral squamous cell carcinoma (OSCC) and screen small-molecule drugs for the prevention of OSCC. Method The Gene Expression Omnibus (GEO) database was explored to extract two microarray datasets, namely, GSE85195 and GSE25099. The data of the normal group, OLK group, and OSCC group were analyzed by weighted gene coexpression network analysis (WGCNA) to identify the most significant gene module and differentially expressed genes (DEGs). The intersection genes were extracted as the key genes of OLK carcinogenesis. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed in the module. Connectivity Map and molecular docking were used to screen small-molecule drugs. The diagnostic values of four key genes were identified and verified in the GSE26549 dataset. Results WGCNA obtained the red module (r = −0.91, p < 0.05) with the strongest correlation with cancerous phenotype. GO enrichment analysis showed 60 pathways, including 28 biological processes, 11 cell components, and 21 molecular functions, and KEGG enrichment analysis showed 4 pathways (p < 0.05). In the differential expression analysis, there was no intersection between the upregulated genes and the red module genes. However, the intersection of the downregulated genes and the red module genes yielded 4 key genes: dopachrome tautomerase (DCT), keratin 3 (KRT3), keratin 76 (KRT76), and FAM3 metabolic regulation signal molecule B (FAM3B). The area under the curve of the diagnostic model constructed by these four genes was 0.963 (CI = 0.913–1.000). The sensitivity was 0.933, and the specificity was 0.923. The diagnostic model was successfully verified in GSE26549 (AUC = 0.745, CI = 0.638–0.851). Compared with the diagnostic models of the previous studies, the diagnostic efficiency of this model was the highest. The small-molecule drugs, selumetinib and benidipine, were selected according to the gene expression profile and showed binding activity when docking with the above molecules. Conclusions This study provides new targets and drugs for OLK. These targets could be used as the key diagnostic molecules for long-term follow-up of OLK. The small-molecule drugs selumetinib and benidipine could be used for the prevention and treatment of OSCC.
Collapse
|
40
|
Zhang D, Yin H, Bauer TL, Rogers MP, Velotta JB, Morgan CT, Du W, Xu P, Qian X. Development of a novel miR-3648-related gene signature as a prognostic biomarker in esophageal adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2022; 9:1702. [PMID: 34988211 PMCID: PMC8667142 DOI: 10.21037/atm-21-6237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/06/2022]
Abstract
Background Esophageal adenocarcinoma (EA) is a typical immunogenic malignant tumor with a dismal 5-year survival rate lower than 20%. Although miRNA-3648 (miR-3648) is expressed abnormally in EA, its impact on the tumor immune microenvironment remains unknown. In this study, we sought to identify immune-related genes (IRGs) that are targeted by miR-3648 and develop an EA multigene signature. Methods The gene expression data of 87 EA tumor samples and 67 normal tissue samples from The Cancer Genome Atlas (TCGA) database and the Genotype-Tissue Expression (GTEx) database were downloaded, respectively. Weighted gene co-expression network analysis (WGCNA), the CIBERSORT algorithm, and Cox regression analysis were applied to identify IRGs and to construct a prognostic signature and nomogram. Results MiR-3648 was expectedly highly expressed in EA tumor tissues (P=2.6e-8), and related to the infiltration of activated natural killer cells (NK cells) and activated CD4 T lymphocytes (CD4 cells). A total of 70 miR-3648-targeted genes related to immune cell infiltration were identified. Among them, 4 genes (C10orf55, DLL4, PANX2, and NKAIN1) were closely related to overall survival (OS), and were thus selected to construct a 4-gene risk score (RS). The RS had a superior capability to predict OS [area under the curve (AUC) =0.740 for 1 year; AUC =0.717 for 3 years; AUC =0.622 for 5 years]. A higher score was indicative of a poorer prognosis than a lower score [hazard ratio (HR) =2.71; 95% confidence interval (CI): 1.45-5.09; P=0.002]. Furthermore, the nomogram formed by combining the RS and the TNM classification of malignant tumors (TNM stage) improved the accuracy of survival prediction [Harrell's concordance index (C-index) =0.698]. Conclusions MiR-3648 may play a critical role in EA pathogenesis. The novel 4-gene signature may serve as a prognostic tool to manage patients with EA.
Collapse
Affiliation(s)
- Donglei Zhang
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hang Yin
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Thomas L Bauer
- Department of General Surgery, Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Michael P Rogers
- Department of Surgery, University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Jeffrey B Velotta
- Department of Thoracic Surgery, Oakland Medical Center, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Clinton T Morgan
- Division of Cardiothoracic Surgery, Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Weijia Du
- Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ping Xu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiaozhe Qian
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
41
|
Hu H, Zhang F, Li L, Liu J, Ao Q, Li P, Zeng J, Li L. Identification and Validation of ATF3 Serving as a Potential Biomarker and Correlating With Pharmacotherapy Response and Immune Infiltration Characteristics in Rheumatoid Arthritis. Front Mol Biosci 2021; 8:761841. [PMID: 34966780 PMCID: PMC8710747 DOI: 10.3389/fmolb.2021.761841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Although disease-modifying antirheumatic drugs (DMARDs) have significantly improved the prognosis of patients with rheumatoid arthritis (RA), approximately 40% of RA patients have limited response. Therefore, it was essential to explore new biomarkers to improve the therapeutic effects on RA. This study aimed to develop a new biomarker and validate it by an in vitro study. Methods: The RNA-seq and the clinicopathologic data of RA patients were downloaded from Gene Expression Omnibus (GEO) databases. Differentially expressed genes were screened in the GPL96 and GPL570 databases. Then, weighted gene co-expression network analysis (WGCNA) was used to explore the most correlated gene modules to normal and RA synovium in the GPL96 and GPL570 databases. After that, the differentially expressed genes were intersected with the correlated gene modules to find the potential biomarkers. The CIBERSORT tool was applied to investigate the relationship between activated transcription factor 3 (ATF3) expression and the immune cell infiltration, and Gene Set Enrichment Analysis (GSEA) was used to investigate the related signaling pathways of differentially expressed genes in the high and low ATF3 groups. Furthermore, the relationships between ATF3 expression and clinical parameters were also explored in the GEO database. Finally, the role of ATF3 was verified by in vitro cell experiments. Results: We intersected the differentially expressed genes and the most correlated gene modules in the GPL570 and GPL96 databases and identified that ATF3 is a significant potential biomarker and correlates with some clinical–pharmacological variables. Immune infiltration analysis showed that activated mast cells had a significant infiltration in the high ATF3 group in the two databases. GSEA showed that metabolism-associated pathways belonged to the high ATF3 groups and that inflammation and immunoregulation pathways were enriched in the low ATF3 group. Finally, we validated that ATF3 could promote the proliferation, migration, and invasion of RA fibroblast-like synoviocyte (FLS) and MH7A. Flow cytometry showed that ATF3 expression could decrease the proportion of apoptotic cells and increase the proportion of S and G2/M phase cells. Conclusion: We successfully identified and validated that ATF3 could serve as a novel biomarker in RA, which correlated with pharmacotherapy response and immune cell infiltration.
Collapse
Affiliation(s)
- Huan Hu
- Department of Rheumatology and Immunology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Facai Zhang
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Li Li
- Medical Intensive Care Unit, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jun Liu
- Department of Rheumatology and Immunology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qin Ao
- Department of Rheumatology and Immunology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Ping Li
- Department of Cardiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jiashun Zeng
- Department of Rheumatology and Immunology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Long Li
- Department of Rheumatology and Immunology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| |
Collapse
|
42
|
Huang C, Zhang C, Sheng J, Wang D, Zhao Y, Qian L, Xie L, Meng Z. Identification and Validation of a Tumor Microenvironment-Related Gene Signature in Hepatocellular Carcinoma Prognosis. Front Genet 2021; 12:717319. [PMID: 34899826 PMCID: PMC8662347 DOI: 10.3389/fgene.2021.717319] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/25/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a typical inflammatory-related malignant tumor with complex immune tolerance microenvironment and poor prognosis. In this study, we aimed to construct a novel immune-related gene signature for the prognosis of HCC patients, exploring tumor microenvironment (TME) cell infiltration characterization and potential mechanisms. Methods: A total of 364 HCC samples with follow-up information in the TCGA-LIHC dataset were analyzed for the training of the prognostic signature. The Least Absolute Shrinkage and Selector Operation (LASSO) regression based on the IRGs was conducted to identify the prognostic genes and establish an immune risk signature. The immune cell infiltration in TME was estimated via the CIBERSORT method. Gene Set Variation Analysis (GSVA) was conducted to compare the biological pathways involved in the low-risk and high-risk groups. Furthermore, paraffin sections of HCC tissue microarrays containing 77 patients from Fudan University Shanghai Cancer Center were used for IHC staining. The clinical characteristics of the 77 HCC patients were collected and summarized for survival analysis validation via the Kaplan-Meier (KM) method. Results: Three-gene signature with close immune correlation (Risk score = EPO * 0.02838 + BIRC5 * 0.02477 + SPP1 * 0.0002044) was constructed eventually and proven to be an effective prognostic factor for HCC patients. The patients were divided into a high-risk and a low-risk group according to the optimal cutoff, and the survival analysis revealed that HCC samples with high-risk immuno-score had significantly poorer outcomes than the low-risk group (p < 0.0001). The results of CIBERSORT suggested that the immune cell activation was relatively higher in the low-risk group with better prognosis. Besides, GSVA analysis showed multiple signaling differences between the high- and low-risk group, indicating that the three-gene prognostic model can affect the prognosis of patients by affecting immune-related mechanisms. Tissue microarray (TMA) results further confirmed that the expression of three genes in HCC tissues was closely related to the prognosis of patients, respectively. Conclusion: In this study, we constructed and validated a robust three-gene signature with close immune correlation in HCC, which presented a reliable performance in the prediction of HCC patients' survival.
Collapse
Affiliation(s)
- Changjing Huang
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenyue Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jie Sheng
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dan Wang
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yingke Zhao
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ling Qian
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lin Xie
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
43
|
Gao L, Xue J, Liu X, Cao L, Wang R, Lei L. A risk model based on autophagy-related lncRNAs for predicting prognosis and efficacy of immunotherapy and chemotherapy in gastric cancer patients. Aging (Albany NY) 2021; 13:25453-25465. [PMID: 34897033 PMCID: PMC8714132 DOI: 10.18632/aging.203765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/29/2021] [Indexed: 12/29/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNAs essential to the occurrence and development of gastric cancer (GC). We aimed to identify critical lncRNA pairs to construct a prognostic model and assess its performances in prognosis and efficacy prediction in GC patients receiving immunotherapy and chemotherapy. We searched transcriptome and clinical data of GC patients from The Cancer Genome Atlas (TCGA) database. Autophagy-related lncRNAs were identified using co-expression network analysis, and lncRNA pairs with prognostic value were selected using pairwise transcriptome analysis. The gene pairs were subjected to LASSO algorithm for identification of optimal gene pairs for risk model construction. Patients were classified into the low-risk and high-risk groups with the RiskScore as a cutoff. Finally, 9 optimal gene pairs were identified in the LASSO algorithm model for construction of a lncRNA prognostic risk model. For predictive performances, it successfully predicted a shorter survival of high-risk patients than that obtained in low-risk individuals (P < 0.001). It showed moderate AUC (area under the curve) values for 1-, 2-, and 3-year overall survival prediction of 0.713 and could serve as an independent predictor for GC prognosis. Compared to the low-risk group, high-risk patients had higher expressions of marker genes for immune checkpoint inhibitors (ICIs) and showed higher sensitivity to the chemotherapy agents, rapamycin, bexarotene, and bicalutamide. Our findings demonstrate a robust prognostic model based on nine autophagy-related lncRNA pairs for GC. It acts as an independent predictor for survival and efficacy prediction of immunotherapy and chemotherapy in GC patients.
Collapse
Affiliation(s)
- Lei Gao
- Department of Gastroenterology, The First Affiliated Hospital, And College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Juan Xue
- Department of Clinical Laboratory, The First Affiliated Hospital, And College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Xiaomin Liu
- Department of Gastroenterology, The First Affiliated Hospital, And College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Lei Cao
- Department of Gastroenterology, The First Affiliated Hospital, And College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Ruifang Wang
- Department of Gastroenterology, The First Affiliated Hospital, And College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Liangliang Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, And College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
44
|
Identification of Biomarkers Related to Immune Cell Infiltration with Gene Coexpression Network in Myocardial Infarction. DISEASE MARKERS 2021; 2021:2227067. [PMID: 34777632 PMCID: PMC8589498 DOI: 10.1155/2021/2227067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
Background There is evidence that the immune system plays a key critical role in the pathogenesis of myocardial infarction (MI). However, the exact mechanisms associated with immunity have not been systematically uncovered. Methods This study used the weighted gene coexpression network analysis (WGCNA) and the CIBERSORT algorithm to analyze the MI expression data from the Gene Expression Omnibus database and then identify the module associated with immune cell infiltration. In addition, we built the coexpression network and protein-protein interactions network analysis to identify the hub genes. Furthermore, the relationship between hub genes and NK cell resting was validated by using another dataset GSE123342. Finally, receiver operating characteristic (ROC) curve analyses were used to assess the diagnostic value of verified hub genes. Results Monocytes and neutrophils were markedly increased, and T cell CD8, T cell CD4 naive, T cell CD4 memory resting, and NK cell resting were significantly decreased in MI groups compared with stable coronary artery disease (CAD) groups. The WGCNA results showed that the pink model had the highest correlation with the NK cell resting infiltration level. We identified 11 hub genes whose expression correlated to the NK cell resting infiltration level, among which, 7 hub genes (NKG7, TBX21, PRF1, CD247, KLRD1, FASLG, and EOMES) were successfully validated in GSE123342. And these 7 genes had diagnostic value to distinguish MI and stable CAD. Conclusions NKG7, TBX21, PRF1, CD247, KLRD1, FASLG, and EOMES may be a diagnostic biomarker and therapeutic target associated with NK cell resting infiltration in MI.
Collapse
|
45
|
Zhang T, Nie Y, Gu J, Cai K, Chen X, Li H, Wang J. Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular Carcinoma. Front Oncol 2021; 11:587479. [PMID: 33868990 PMCID: PMC8047479 DOI: 10.3389/fonc.2021.587479] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of tumor-associated deaths worldwide. Despite great progress in early diagnosis and multidisciplinary tumor management, the long-term prognosis of HCC remains poor. Currently, metabolic reprogramming during tumor development is widely observed to support rapid growth and proliferation of cancer cells, and several metabolic targets that could be used as cancer biomarkers have been identified. The liver and mitochondria are the two centers of human metabolism at the whole organism and cellular levels, respectively. Thus, identification of prognostic biomarkers based on mitochondrial-related genes (Mito-RGs)—the coding-genes of proteins located in the mitochondria—that reflect metabolic changes associated with HCC could lead to better interventions for HCC patients. In the present study, we used HCC data from The Cancer Genome Atlas (TCGA) database to construct a classifier containing 10 Mito-RGs (ACOT7, ADPRHL2, ATAD3A, BSG, FAM72A, PDK3, PDSS1, RAD51C, TOMM34, and TRMU) for predicting the prognosis of HCC by using 10-fold Least Absolute Shrinkage and Selection Operation (LASSO) cross-validation Cox regression. Based on the risk score calculated by the classifier, the samples were divided into high- and low-risk groups. Gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), t-distributed stochastic neighbor embedding (t-SNE), and consensus clusterPlus algorithms were used to identify metabolic pathways that were significantly different between the high- and low-risk groups. We further investigated the relationship between metabolic status and infiltration of immune cells into HCC tumor samples by using the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm combined with the Tumor Immune Estimation Resource (TIMER) database. Our results showed that the classifier based on Mito-RGs could act as an independent biomarker for predicting survival of HCC patients. Repression of primary bile acid biosynthesis plays a vital role in the development and poor prognosis of HCC, which provides a potential approach to treatment. Our study revealed cross-talk between bile acid and infiltration of tumors by immune cells, which may provide novel insight into immunotherapy of HCC. Furthermore, our research may provide a novel method for HCC metabolic therapy based on modulation of mitochondrial function.
Collapse
Affiliation(s)
- Tao Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingli Nie
- Department of Dermatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian Gu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kailin Cai
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huili Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiliang Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|