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Chen H, Xu Y, Lin H, Wan S, Luo L. A prognostic framework for predicting lung signet ring cell carcinoma via a machine learning based cox proportional hazard model. J Cancer Res Clin Oncol 2024; 150:364. [PMID: 39052087 PMCID: PMC11272739 DOI: 10.1007/s00432-024-05886-0] [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: 08/05/2023] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
PURPOSE Signet ring cell carcinoma (SRCC) is a rare type of lung cancer. The conventional survival nomogram used to predict lung cancer performs poorly for SRCC. Therefore, a novel nomogram specifically for studying SRCC is highly required. METHODS Baseline characteristics of lung signet ring cell carcinoma were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Univariate and multivariate Cox regression and random forest analysis were performed on the training group data, respectively. Subsequently, we compared results from these two types of analyses. A nomogram model was developed to predict 1-year, 3-year, and 5-year overall survival (OS) for patients, and receiver operating characteristic (ROC) curves and calibration curves were used to assess the prediction accuracy. Decision curve analysis (DCA) was used to assess the clinical applicability of the proposed model. For treatment modalities, Kaplan-Meier curves were adopted to analyze condition-specific effects. RESULTS We obtained 731 patients diagnosed with lung signet ring cell carcinoma (LSRCC) in the SEER database and randomized the patients into a training group (551) and a validation group (220) with a ratio of 7:3. Eight factors including age, primary site, T, N, and M.Stage, surgery, chemotherapy, and radiation were included in the nomogram analysis. Results suggested that treatment methods (like surgery, chemotherapy, and radiation) and T-Stage factors had significant prognostic effects. The results of ROC curves, calibration curves, and DCA in the training and validation groups demonstrated that the nomogram we constructed could precisely predict survival and prognosis in LSRCC patients. Through deep verification, we found the constructed model had a high C-index, indicating that the model had a strong predictive power. Further, we found that all surgical interventions had good effects on OS and cancer-specific survival (CSS). The survival curves showed a relatively favorable prognosis for T0 patients overall, regardless of the treatment modality. CONCLUSIONS Our nomogram is demonstrated to be clinically beneficial for the prognosis of LSRCC patients. The surgical intervention was successful regardless of the tumor stage, and the Cox proportional hazard (CPH) model had better performance than the machine learning model in terms of effectiveness.
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Affiliation(s)
- Haixin Chen
- The First Clinical College, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Yanyan Xu
- The First Clinical College, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Haowen Lin
- The First Clinical College, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Lianxiang Luo
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
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Wei J, Wang M, Wu Y. A disulfidptosis-related lncRNAs cluster to forecast the prognosis and immune landscapes of ovarian cancer. Front Genet 2024; 15:1397011. [PMID: 39045330 PMCID: PMC11263023 DOI: 10.3389/fgene.2024.1397011] [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: 04/12/2024] [Accepted: 06/11/2024] [Indexed: 07/25/2024] Open
Abstract
Objective Disulfidptosis is a newly recognized form of regulated cell death that has been linked to cancer progression and prognosis. Despite this association, the prognostic significance, immunological characteristics and treatment response of disulfidptosis-related lncRNAs (DRLs) in ovarian cancer have not yet been elucidated. Methods The lncRNA data and clinical information for ovarian cancer and normal samples were obtained from the UCSC XENA. Differential expression analysis and Pearson analysis were utilized to identify core DRLs, followed by LASSO algorithm. Random Survival Forest was used to construct a prognostic model. The relationships between risk scores, RNA methylation, immune cell infiltration, mutation, responses to immunotherapy and drug sensitivity analysis were further examined. Additionally, qRT-PCR experiments were conducted to validate the expression of the core DRLs in human ovarian cancer cells and normal ovarian cells and the scRNA-seq data of the core DRLs were obtained from the GEO dataset, available in the TISCH database. Results A total of 8 core DRLs were obtained to construct a prognostic model for ovarian cancer, categorizing all patients into low-risk and high-risk groups using an optimal cutoff value. The AUC values for 1-year, 3-year and 5-year OS in the TCGA cohort were 0.785, 0.810 and 0.863 respectively, proving a strong predictive capability of the model. The model revealed the high-risk group patients exhibited lower overall survival rates, higher TIDE scores and lower TMB levels compared to the low-risk group. Variations in immune cell infiltration and responses to therapeutic drugs were observed between the high-risk and low-risk groups. Besides, our study verified the correlations between the DRLs and RNA methylation. Additionally, qRT-PCR experiments and single-cell RNA sequencing data analysis were conducted to confirm the significance of the core DRLs at both cellular and scRNA-seq levels. Conclusion We constructed a reliable and novel prognostic model with a DRLs cluster for ovarian cancer, providing a foundation for further researches in the management of this disease.
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Philip MM, Watts J, McKiddie F, Welch A, Nath M. Development and Validation of Prognostic Models Using Radiomic Features from Pre-Treatment Positron Emission Tomography (PET) Images in Head and Neck Squamous Cell Carcinoma (HNSCC) Patients. Cancers (Basel) 2024; 16:2195. [PMID: 38927901 PMCID: PMC11202084 DOI: 10.3390/cancers16122195] [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: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
High-dimensional radiomics features derived from pre-treatment positron emission tomography (PET) images offer prognostic insights for patients with head and neck squamous cell carcinoma (HNSCC). Using 124 PET radiomics features and clinical variables (age, sex, stage of cancer, site of cancer) from a cohort of 232 patients, we evaluated four survival models-penalized Cox model, random forest, gradient boosted model and support vector machine-to predict all-cause mortality (ACM), locoregional recurrence/residual disease (LR) and distant metastasis (DM) probability during 36, 24 and 24 months of follow-up, respectively. We developed models with five-fold cross-validation, selected the best-performing model for each outcome based on the concordance index (C-statistic) and the integrated Brier score (IBS) and validated them in an independent cohort of 102 patients. The penalized Cox model demonstrated better performance for ACM (C-statistic = 0.70, IBS = 0.12) and DM (C-statistic = 0.70, IBS = 0.08) while the random forest model displayed better performance for LR (C-statistic = 0.76, IBS = 0.07). We conclude that the ML-based prognostic model can aid clinicians in quantifying prognosis and determining effective treatment strategies, thereby improving favorable outcomes in HNSCC patients.
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Affiliation(s)
- Mahima Merin Philip
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Jessica Watts
- National Health Service Grampian, Aberdeen AB15 6RE, UK; (J.W.); (F.M.)
| | - Fergus McKiddie
- National Health Service Grampian, Aberdeen AB15 6RE, UK; (J.W.); (F.M.)
| | - Andy Welch
- Institute of Education in Healthcare and Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Mintu Nath
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
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Mohammadyari P, Vieceli Dalla Sega F, Fortini F, Minghini G, Rizzo P, Cimaglia P, Mikus E, Tremoli E, Campo G, Calore E, Schifano SF, Zambelli C. Deep-learning survival analysis for patients with calcific aortic valve disease undergoing valve replacement. Sci Rep 2024; 14:10902. [PMID: 38740898 DOI: 10.1038/s41598-024-61685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Calcification of the aortic valve (CAVDS) is a major cause of aortic stenosis (AS) leading to loss of valve function which requires the substitution by surgical aortic valve replacement (SAVR) or transcatheter aortic valve intervention (TAVI). These procedures are associated with high post-intervention mortality, then the corresponding risk assessment is relevant from a clinical standpoint. This study compares the traditional Cox Proportional Hazard (CPH) against Machine Learning (ML) based methods, such as Deep Learning Survival (DeepSurv) and Random Survival Forest (RSF), to identify variables able to estimate the risk of death one year after the intervention, in patients undergoing either to SAVR or TAVI. We found that with all three approaches the combination of six variables, named albumin, age, BMI, glucose, hypertension, and clonal hemopoiesis of indeterminate potential (CHIP), allows for predicting mortality with a c-index of approximately 80 % . Importantly, we found that the ML models have a better prediction capability, making them as effective for statistical analysis in medicine as most state-of-the-art approaches, with the additional advantage that they may expose non-linear relationships. This study aims to improve the early identification of patients at higher risk of death, who could then benefit from a more appropriate therapeutic intervention.
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Affiliation(s)
| | | | | | - Giada Minghini
- Department of Environmental and Prevention Sciences, Università di Ferrara, Ferrara, Italy
| | - Paola Rizzo
- Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy.
- Department of Translational Medicine, Università di Ferrara, Ferrara, Italy.
- Laboratory for Technologies of Advanced Therapies (LTTA), Ferrara, Italy.
| | - Paolo Cimaglia
- Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy
| | - Elisa Mikus
- Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy
| | - Elena Tremoli
- Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy
| | - Gianluca Campo
- Department of Translational Medicine, Università di Ferrara, Ferrara, Italy
- Azienda Ospedaliero-Universitaria di Ferrara, Ferrara, Italy
| | - Enrico Calore
- Istituto Nazionale di Fisica Nucleare (INFN), Ferrara, Italy
| | - Sebastiano Fabio Schifano
- Istituto Nazionale di Fisica Nucleare (INFN), Ferrara, Italy.
- Department of Environmental and Prevention Sciences, Università di Ferrara, Ferrara, Italy.
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Li J, Ye Y, Cai Y, Ji H, Qin W, Luo Y, Zhou X, Zhang Z, Xiao X, Zhang B. Triglyceride-inflammation score established on account of random survival forest for predicting survival in patients with nasopharyngeal carcinoma: a retrospective study. Front Immunol 2024; 15:1375931. [PMID: 38736892 PMCID: PMC11082337 DOI: 10.3389/fimmu.2024.1375931] [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] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024] Open
Abstract
Objective This study aimed to establish an effective prognostic model based on triglyceride and inflammatory markers, including neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), and platelet-to-lymphocyte ratio (PLR), to predict overall survival (OS) in patients with nasopharyngeal carcinoma (NPC). Additionally, we aimed to explore the interaction and mediation between these biomarkers in their association with OS. Methods A retrospective review was conducted on 259 NPC patients who had blood lipid markers, including triglyceride and total cholesterol, as well as parameters of peripheral blood cells measured before treatment. These patients were followed up for over 5 years, and randomly divided into a training set (n=155) and a validation set (n=104). The triglyceride-inflammation (TI) score was developed using the random survival forest (RSF) algorithm. Subsequently, a nomogram was created. The performance of the prognostic model was measured by the concordance index (C-index), time-dependent receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). The interaction and mediation between the biomarkers were further analyzed. Bioinformatics analysis based on the GEO dataset was used to investigate the association between triglyceride metabolism and immune cell infiltration. Results The C-index of the TI score was 0.806 in the training set, 0.759 in the validation set, and 0.808 in the entire set. The area under the curve of time-dependent ROC of TI score in predicting survival at 1, 3, and 5 years were 0.741, 0.847, and 0.871 respectively in the training set, and 0.811, 0.837, and 0.758 in the validation set, then 0.771, 0.848, and 0.862 in the entire set, suggesting that TI score had excellent performance in predicting OS in NPC patients. Patients with stage T1-T2 or M0 had significantly lower TI scores, NLR, and PLR, and higher LMR compared to those with stage T3-T3 or M1, respectively. The nomogram, which integrated age, sex, clinical stage, and TI score, demonstrated good clinical usefulness and predictive ability, as evaluated by the DCA. Significant interactions were found between triglyceride and NLR and platelet, but triglyceride did not exhibit any medicating effects in the inflammatory markers. Additionally, NPC tissues with active triglyceride synthesis exhibited high immune cell infiltration. Conclusion The TI score based on RSF represents a potential prognostic factor for NPC patients, offering convenience and economic advantages. The interaction between triglyceride and NLR may be attributed to the effect of triglyceride metabolism on immune response.
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Affiliation(s)
- Jun Li
- Department of Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Yinxin Ye
- Department of Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Yonglin Cai
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Huojin Ji
- Department of Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Weiling Qin
- Department of Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Yonglin Luo
- Department of Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Xiaoying Zhou
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
| | - Zhe Zhang
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xue Xiao
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Bin Zhang
- Department of Radiation Oncology, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
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Gu Y, Wang M, Gong Y, Li X, Wang Z, Wang Y, Jiang S, Zhang D, Li C. Unveiling breast cancer risk profiles: a survival clustering analysis empowered by an online web application. Future Oncol 2023; 19:2651-2667. [PMID: 38095059 DOI: 10.2217/fon-2023-0736] [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] [Indexed: 12/23/2023] Open
Abstract
Aim: To develop a shiny app for doctors to investigate breast cancer treatments through a new approach by incorporating unsupervised clustering and survival information. Materials & methods: Analysis is based on the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset, which contains 1726 subjects and 22 variables. Cox regression was used to identify survival risk factors for K-means clustering. Logrank tests and C-statistics were compared across different cluster numbers and Kaplan-Meier plots were presented. Results & conclusion: Our study fills an existing void by introducing a unique combination of unsupervised learning techniques and survival information on the clinician side, demonstrating the potential of survival clustering as a valuable tool in uncovering hidden structures based on distinct risk profiles.
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Affiliation(s)
- Yuan Gu
- Department of Statistics, The George Washington University, Washington, DC 20052, USA
| | - Mingyue Wang
- Department of Mathematics, Syracuse University, Syracuse, NY 13244, USA
| | - Yishu Gong
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, NY 02115, USA
| | - Xin Li
- Department of Statistics, The George Washington University, Washington, DC 20052, USA
| | - Ziyang Wang
- Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Yuli Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Song Jiang
- Department of Biochemistry, Huzhou Institute of Biological Products Co., Ltd., 313017, China
| | - Dan Zhang
- Department of Information Science and Engineering, Shandong University, Shan Dong, China
| | - Chen Li
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, 14195, Germany
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