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Wang B, Zhou J, An N. Investigating molecular markers linked to acute myocardial infarction and cuproptosis: bioinformatics analysis and validation in the AMI mice model. PeerJ 2024; 12:e17280. [PMID: 38827298 PMCID: PMC11143973 DOI: 10.7717/peerj.17280] [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: 10/24/2023] [Accepted: 04/01/2024] [Indexed: 06/04/2024] Open
Abstract
Cuproptosis-related key genes play a significant role in the pathological processes of acute myocardial infarction (AMI). However, a complete understanding of the molecular mechanisms behind this participation remains elusive. This study was designed to identify genes and immune cells critical to AMI pathogenesis. Based on the GSE48060 dataset (31 AMI patients and 21 healthy persons, GPL570-55999), we identified genes associated with dysregulated cuproptosis and the activation of immune responses between normal subjects and patients with a first myocardial attack. Two molecular clusters associated with cuproptosis were defined in patients with AMI. Immune infiltration analysis showed that there was significant immunity heterogeneity among different clusters. Multiple immune responses were closely associated with Cluster2-specific differentially expressed genes (DEGs). The generalized linear model machine model presented the best discriminative performance with relatively lower residual and root mean square error, and a higher area under the curve (AUC = 0.870). A final two-gene-based generalized linear model was constructed, exhibiting satisfactory performance in two external validation datasets (AUC = 0.719, GSE66360 and AUC = 0.856, GSE123342). Column graph, calibration curve, and decision curve analyses also proved the accuracy of AMI prediction. We also constructed a mouse C57BL/6 model of AMI (3 h, 48 h, and 1 week) and used qRT-PCR and immunofluorescence to detect the expression changes of CBLB and ZNF302. In this study, we present a systematic analysis of the complex relationship between cuproptosis and a first AMI attack, and provide new insights into the diagnosis and treatment of AMI.
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Affiliation(s)
- Bingyu Wang
- Ningbo Medical Center Lihuili Hospital, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Jianqing Zhou
- Ningbo Medical Center Lihuili Hospital, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Ning An
- Ningbo Medical Center Lihuili Hospital, Medical School of Ningbo University, Ningbo, Zhejiang, China
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Wu YL, Liu W, Zhao T, Jin J. P4HA2 contributes to head and neck squamous cell carcinoma progression and EMT through PI3K/AKT signaling pathway. Med Oncol 2024; 41:163. [PMID: 38777998 PMCID: PMC11111551 DOI: 10.1007/s12032-024-02358-w] [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: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 05/25/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) can be defined as a deadly illness with a dismal prognosis in advanced stages. Therefore, we seek to examine P4HA2 expression and effect in HNSCC, along with the underlying mechanisms. This study utilized integrated bioinformatics analyses to evaluate the P4HA2 expression pattern, prognostic implication, and probable function in HNSCC. The study conducted various in vitro experiments, including colony formation, CCK-8, flow cytometry, wound healing, and transwell assays, on the human HNSCC cell line CAL-27 to examine the involvement of P4HA2 in HNSCC progression. Moreover, western blotting was used to investigate epithelial-mesenchymal transition (EMT) markers and PI3K/AKT pathway markers to elucidate the underlying mechanisms. P4HA2 expression was significantly enhanced in HNSCC, and its overexpression was correlated to tumor aggressiveness and a poor prognosis in patients. Based on in vitro experiments, the overexpressed P4HA2 enhanced cell proliferation, migration, invasion, as well as EMT while reducing apoptosis, whereas P4HA2 silencing exhibited the reverse effect. P4HA2 overexpression enhanced PI3K/AKT phosphorylation in HNSCC cells. Moreover, LY294002 was observed to counteract the effects of upregulated P4HA2 on proliferation, migration, invasion, and EMT in HNSCC. Collectively, we indicated that P4HA2 promoted HNSCC progression and EMT via PI3K/AKT signaling pathway.
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Affiliation(s)
- Yan-Ling Wu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, Guangdong, China
| | - Wan Liu
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, Guangdong, China
| | - Tingting Zhao
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, Guangdong, China
| | - Jing Jin
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, Guangdong, China.
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Du Z, Zhang Q, Yang J. Prognostic related gene index for predicting survival and immunotherapeutic effect of hepatocellular carcinoma. Medicine (Baltimore) 2023; 102:e35820. [PMID: 37933057 PMCID: PMC10627638 DOI: 10.1097/md.0000000000035820] [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: 04/04/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common malignant liver tumor. It is an aggressive disease with high mortality rate. In this study, we investigated a new prognosis-related gene index (PRGI) that can predict the survival and efficacy of immunotherapy in patients with HCC. RNA-seq data and clinical data of HCC samples were obtained from the cancer genome atlas and ICGC databases. Prognosis-related genes were obtained using log-rank tests and univariate Cox proportional hazards regression. Univariate and multivariate analyses were performed on the overall survival rate of patients with prognosis-related genes and multiple clinicopathological factors, and a nomogram was constructed. A PRGI was then constructed based on least absolute shrinkage and selection operator or multivariate Cox Iterative Regression. The possible correlation between PRGI and immune cell infiltration or immunotherapy efficacy was discussed. Eight genes were identified to construct the PRGI. PRGI can predict the infiltration of immune cells into the tumor microenvironment of HCC and the response to immunotherapy. PRGI can accurately predict the survival rate of patients with HCC, reflect the immune microenvironment, and predict the efficacy of immunotherapy.
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Affiliation(s)
- Zhongxiang Du
- Clinical Laboratory, Danyang People’s Hospital of Jiangsu Province, Danyang Hospital Affiliated to Nantong University, Danyang, Jiangsu, China
| | - Qi Zhang
- Clinical Laboratory, Danyang People’s Hospital of Jiangsu Province, Danyang Hospital Affiliated to Nantong University, Danyang, Jiangsu, China
| | - Jie Yang
- Clinical Laboratory, Danyang People’s Hospital of Jiangsu Province, Danyang Hospital Affiliated to Nantong University, Danyang, Jiangsu, China
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Du R, Li J, Li F, Mi L, Dionigi G, Sun H, Liang N. Estimating disease-free survival of thyroid cancer based on novel cuprotosis-related gene model. Front Endocrinol (Lausanne) 2023; 14:1209172. [PMID: 37745716 PMCID: PMC10515282 DOI: 10.3389/fendo.2023.1209172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Background Cuprotosis is a newly discovered form of cell death that differs from other types of cell death. The aim of this study was to investigate the functional role and a possible prognostic model for thyroid cancer. Methods TCGA and GEO were used to investigate the differential expression of CRGs in THCA. KEGG and GO enrichment analyses were applied to investigate the possible molecular functions. The features of CRGs were selected by LASSO regression. 20 pairs of samples were randomly collected from the hospital to compare expression between tumor and normal. Results Among the 19 CRGs related to thyroid cancer recurrence, 16 genes were differentially expressed in thyroid cancer. KEGG analysis showed that the 19 CRGs were mainly enriched in cell death, cell cycle and ribosomal pathways. K-M survival analysis and subsequent multiple logistic regression revealed that the expression of BUB1 and GINS2 were potential risk factors for disease-free survival (DFS) of thyroid cancer. In addition, further LASSO-regression selected the following three DFS-related CRGs: FDX1, BUB1 and RPL3. A novel prognostic prediction model was constructed by nomogram, and the prediction probability for 1-, 3- and 5-year survival approached the actual time. As for the possible mechanisms, FDX1, BUB1 and RPL3 were associated with immune infiltration. The cell model experiment illustrated that the ATM signaling pathway might be involved in thyroid cancer cell death. Conclusion Three CRG models (FDX1, BUB1, RPL3) could better predict the prognosis of thyroid cancer. Immune cell infiltration and the ATM pathway were the possible mechanisms.
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Affiliation(s)
- Rui Du
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Jingting Li
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Fang Li
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Lusi Mi
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Gianlorenzo Dionigi
- Department of Pathophysiology and Transplantation, Division of Surgery, Istituto Auxologico Italiano IRCCS (Istituto di Ricovero e Cura a Carattere Scientifco), University of Milan, Milan, Italy
| | - Hui Sun
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Nan Liang
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
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Zheng Z, Li H, Yang R, Guo H. Role of the membrane-spanning 4A gene family in lung adenocarcinoma. Front Genet 2023; 14:1162787. [PMID: 37533433 PMCID: PMC10390740 DOI: 10.3389/fgene.2023.1162787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Lung adenocarcinoma, which is the second most prevalent cancer in the world, has a poor prognosis and a low 5-year survival rate. The MS4A protein family is crucial to disease development and progression, particularly for cancers, allergies, metabolic disorders, autoimmune diseases, infections, and neurodegenerative disorders. However, its involvement in lung adenocarcinoma remains unclear. In this study, we found that 11 MS4A family genes were upregulated or downregulated in lung adenocarcinoma. Furthermore, we described the genetic variation landscape of the MS4A family in lung adenocarcinoma. Notably, through functional enrichment analysis, we discovered that the MS4A family is involved in the immune response regulatory signaling pathway and the immune response regulatory cell surface receptor signaling pathway. According to the Kaplan-Meier curve, patients with lung adenocarcinoma having poor expression of MS4A2, MS4A7, MS4A14, and MS4A15 had a low overall survival rate. These four prognostic genes are substantially associated with immune-infiltrating cells, and a prognosis model incorporating them may more accurately predict the overall survival rate of patients with lung adenocarcinoma than current models. The findings of this study may offer creative suggestions and recommendations for the identification and management of lung adenocarcinoma.
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Peng Q, Jiang X, Tan S, Xu X, Xia L, Wu N, Lin J, Oyang L, Tang Y, Peng M, Su M, Luo X, Han Y, Liao Q, Zhou Y. Clinical significance and integrative analysis of the cuproptosis-associated genes in head and neck squamous cell carcinoma. Aging (Albany NY) 2023; 15:1964-1976. [PMID: 36947706 PMCID: PMC10085596 DOI: 10.18632/aging.204579] [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: 11/16/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023]
Abstract
Head and neck squamous cell carcinoma (HNSC) is a kind of malignant tumor originating from the oropharynx, larynx, nasopharynx and oral cavity. The incidence of HNSC is increasing and it is the sixth malignant tumor in the world at present. "Cuprotosis" is a novel cuper-dependent cell death mode that is closely related to mitochondrial respiration. Tumorigenesis is closely related to the dysregulation of cell death. However, the relationship between cuprotosis and HNSC remains unclear. Here, we investigated the association between 10 cuprotosis-associated genes (CAGs) and HNSC using multi-omics public data. We found that CAGs had abnormal expression and significant genetic changes in HNSC, especially CDKN2A with 54% mutation rate. Expression of CAGs significantly correlates with the prognosis of HNSC patients. Moreover, the CAGs expression is correlated with the immune checkpoints expression and immune cells infiltration. These CAGs expression was associated with multiple drugs sensitivity of cancer cells, such as cisplatin and docetaxel. These findings indicate that CAGs are likely to serve an essential role in the diagnosis, prognosis, immunotherapy and drug therapy prediction of HNSC.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xuemeng Xu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Mingjing Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha 410013, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha 410013, Hunan, China
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Screening of the Key Genes for the Progression of Liver Cirrhosis to Hepatocellular Carcinoma Based on Bioinformatics. JOURNAL OF ONCOLOGY 2022; 2022:2515513. [PMID: 36199789 PMCID: PMC9529408 DOI: 10.1155/2022/2515513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC), which is among the most globally prevalent cancers, is strongly associated with liver cirrhosis. Using a bioinformatics approach, we have identified and investigated the hub genes responsible for the progression of cirrhosis into HCC. We analyzed the Gene Expression Omnibus (GEO) microarray datasets, GSE25097 and GSE17549, to identify differentially expressed genes (DEGs) in these two conditions and also performed protein-protein interaction (PPI) network analysis. STRING database and Cytoscape software were used to analyze the modules and locate hub genes following which the connections between hub genes and the transition from cirrhosis to HCC, progression of HCC, and prognosis of HCC were investigated. We used the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to detect the molecular mechanisms underlying the action of the primary hub genes. In all, 239 DEGs were obtained, with 94 of them showing evidence of upregulation and 145 showing evidence of downregulation in HCC tissues as compared to cirrhotic liver tissues. We identified six hub genes, namely, BUB1B, NUSAP1, TTK, HMMR, CCNA2, and KIF2C, which were upregulated and had a high diagnostic value for HCC. Besides, these six hub genes were positively related to immune cell infiltration. Since these genes may play a direct role in the progression of cirrhosis to HCC, they can be considered as potential novel molecular indicators for the onset and development of HCC.
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Li M, Mao S, Li L, Wei M. Hypoxia-related LncRNAs signature predicts prognosis and is associated with immune infiltration and progress of head and neck squamous cell carcinoma. Biochem Biophys Rep 2022; 31:101304. [PMID: 35818500 PMCID: PMC9270212 DOI: 10.1016/j.bbrep.2022.101304] [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: 05/11/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 12/21/2022] Open
Abstract
Background Disclosing prognostic information is necessary to enable good treatment selection and improve patient outcomes. Previous studies suggest that hypoxia is associated with an adverse prognosis in patients with HNSCC and that long non-coding RNAs (lncRNAs) show functions in hypoxia-associated cancer biology. Nevertheless, the understanding of lncRNAs in hypoxia related HNSCC progression remains confusing. Methods Data were downloaded from TCGA and GEO database. Bioinformatic tools including R packages GEOquery, limma, pheatmap, ggplot2, clusterProfiler, survivalROC and survcomp and LASSO cox analysis were utilized. Si-RNA transfection, CCK8 and real-time quantified PCR were used in functional study. Results GEO data (GSE182734) revealed that lncRNA regulation may be important in hypoxia related response of HNSCC cell lines. Further analysis in TCGA data identified 314 HRLs via coexpression analysis between differentially expressed lncRNAs and hypoxia-related mRNAs. 23 HRLs were selected to build the prognosis predicting model using lasso Cox regression analyses. Our model showed excellent performance in predicting survival outcomes among patients with HNSCC in both the training and validation sets. We also found that the risk scores were related to tumor stage and to tumor immune infiltration. Moreover, LINC01116 were selected as a functional study target. The knockdown of LINC01116 significantly inhibited the proliferation of HNSCC cells and effected the hypoxia induced immune and the NF-κB/AKT signaling. Conclusions Data analysis of large cohorts and functional experimental validation in our study suggest that hypoxia related lncRNAs play an important role in the progression of HNSCC, and its expression model can be used for prognostic prediction. NcRNAs regulations showed significance in hypoxia related response in HNSCC. 314 lncRNAs coexpressed with hypoxia marker genes were identified as HRLs. An effective HRLs prognosis prediction model had been constructed and validated. Immune cells and pathways paly roles in hypoxia related progress of HNSCC. LINC01116 regulates HNSCC through hypoxia related immune and NF-κB/AKT signaling.
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Affiliation(s)
- Minhan Li
- School of Stomatology, Shandong University, Jinan, Shandong, China
| | - Shaowei Mao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
| | - Lixing Li
- Department of General Surgery, Shanghai Xuhui District Central Hospital, Shanghai, China
| | - Muyun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
- Corresponding author. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
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Yang L, Xu P, Li M, Wang M, Peng M, Zhang Y, Wu T, Chu W, Wang K, Meng H, Zhang L. PET/CT Radiomic Features: A Potential Biomarker for EGFR Mutation Status and Survival Outcome Prediction in NSCLC Patients Treated With TKIs. Front Oncol 2022; 12:894323. [PMID: 35800046 PMCID: PMC9253544 DOI: 10.3389/fonc.2022.894323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Backgrounds Epidermal growth factor receptor (EGFR) mutation profiles play a vital role in treatment strategy decisions for non–small cell lung cancer (NSCLC). The purpose of this study was to evaluate the predictive efficacy of baseline 18F-FDG PET/CT-based radiomics analysis for EGFR mutation status, mutation site, and the survival benefit of targeted therapy. Methods A sum of 313 NSCLC patients with pre-treatment 18F-FDG PET/CT scans and genetic mutations detection were retrospectively studied. Clinical and PET metabolic parameters were incorporated into independent predictors of determining mutation status and mutation site. The dataset was randomly allocated into the training and the validation sets in a 7:3 ratio. Three-dimensional (3D) radiomics features were extracted from each PET- and CT-volume of interests (VOI) singularly, and then a radiomics signature (RS) associated with EGFR mutation profiles is built by feature selection. Three different prediction models based on support vector machine (SVM), decision tree (DT), and random forest (RF) classifiers were established. Furthermore, nomograms for estimation of overall survival (OS) and progression-free survival (PFS) were established by integrating PET/CT radiomics score (Rad-score), metabolic parameters, and clinical factors. Predictive performance was assessed by the receiver operating characteristic (ROC) analysis and the calibration curve analysis. The decision curve analysis (DCA) was applied to estimate and compare the clinical usefulness of nomograms. Results Three hundred thirteen NSCLC patients were classified into a training set (n=218) and a validation set (n=95). Multivariate analysis demonstrated that SUVmax and sex were independent indicators of EGFR mutation status and mutation site. Eight CT-derived RS, six PET-derived RS, and two clinical factors were retained to develop integrated models, which exhibited excellent ability to distinguish between EGFR wild type (EGFR-WT), EGFR 19 mutation type (EGFR-19-MT), and EGFR 21 mutation type (EGFR-21-MT). The SVM model outperformed the RF model and the DT model, yielding training area under the curves (AUC) of EGFR-WT, EGFR-19-WT, and EGFR-21-WT, with 0.881, 0.851, and 0.849, respectively, and validation AUCs of 0.926, 0.805 and 0.859, respectively. For prediction of OS, the integrated nomogram is superior to the clinical nomogram and the radiomics nomogram, with C-indexes of 0.80 in the training set and 0.83 in the validation set, respectively. Conclusions The PET/CT-based radiomics analysis might provide a novel approach to predict EGFR mutation status and mutation site in NSCLC patients and could serve as useful predictors for the patients’ survival outcome of targeted therapy in clinical practice.
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Affiliation(s)
- Liping Yang
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Panpan Xu
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mengyue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Menglu Wang
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mengye Peng
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ying Zhang
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tingting Wu
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wenjie Chu
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kezheng Wang
- Positron Emission Tomography/Computed Tomography (PET-CT)/MR Department, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Lingbo Zhang, ; Kezheng Wang, ; Hongxue Meng,
| | - Hongxue Meng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Lingbo Zhang, ; Kezheng Wang, ; Hongxue Meng,
| | - Lingbo Zhang
- Oral Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Lingbo Zhang, ; Kezheng Wang, ; Hongxue Meng,
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Yao Q, Zhang X, Chen D. Emerging Roles and Mechanisms of lncRNA FOXD3-AS1 in Human Diseases. Front Oncol 2022; 12:848296. [PMID: 35280790 PMCID: PMC8914342 DOI: 10.3389/fonc.2022.848296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 01/02/2023] Open
Abstract
Numerous long noncoding RNAs (lncRNAs) have been identified as powerful regulators of human diseases. The lncRNA FOXD3-AS1 is a novel lncRNA that was recently shown to exert imperative roles in the initialization and progression of several diseases. Emerging studies have shown aberrant expression of FOXD3-AS1 and close correlation with pathophysiological traits of numerous diseases, particularly cancers. More importantly, FOXD3-AS1 was also found to ubiquitously impact a range of biological functions. This study aims to summarize the expression, associated clinicopathological features, major functions and molecular mechanisms of FOXD3-AS1 in human diseases and to explore its possible clinical applications.
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Affiliation(s)
- Qinfan Yao
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Xiuyuan Zhang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Dajin Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
- *Correspondence: Dajin Chen,
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Chen Y, Zhao Y, Lu R, Zhao H, Guo Y. Identification and Validation of a Novel Genomic Instability-Associated Long Non-Coding RNA Prognostic Signature in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2022; 9:787766. [PMID: 35127708 PMCID: PMC8812830 DOI: 10.3389/fcell.2021.787766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most aggressive malignant cancers worldwide, and accurate prognostic models are urgently needed. Emerging evidence revealed that long non-coding RNAs (lncRNAs) are related to genomic instability. We sought to identify and validate a genomic instability-associated lncRNA prognostic signature to assess HNSCC patient survival outcomes. Methods: RNA-sequencing data, somatic mutation files, and patient clinical data were downloaded from The Cancer Genome Atlas database. A total of 491 patients with completely clinical files were randomly divided into training and testing sets. In the training set, genomic instability-associated lncRNAs were screened through univariate Cox regression analyses and least absolute shrinkage and selection operator regression analyses to build a genomic instability-associated lncRNA signature (GILncSig). In addition, time-dependent receiver operating characteristic (ROC) curve, Kaplan-Meier survival curve, and clinical stratification analyses were used to evaluate the signature’s reliability. Finally, in situ hybridization experiments were performed to validate GILncSig expression levels between adjacent non-tumor tissues and tumor tissues from HNSCC patients. Results: Four genomic instability-associated lncRNAs (AC023310.4, AC091729.1, LINC01564, and MIR3142HG) were selected for the prognostic signature. The model was successfully validated using the testing cohort. ROC analysis demonstrated its strong predictive ability for HNSCC prognosis. Univariate and multivariate Cox analyses revealed that the GILncSig was an independent predictor of prognosis. HNSCC patients with a low-risk score showed a substantially better prognosis than the high-risk groups. The in situ hybridization experiments using human HNSCC tissue revealed high GILncSig expression in HNSCC tissues compared with adjacent non-tumor tissues. Conclusion: We developed a novel GILncSig for prognosis prediction in HNSCC patients, and the components of that signature might be therapeutic targets for HNSCC.
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Affiliation(s)
- Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ruohuang Lu
- Department of Stomatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose and Throat Hospital of Fudan University, Shanghai, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- *Correspondence: Han Zhao, ; Yue Guo,
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Han Zhao, ; Yue Guo,
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