1
|
Wang Z, Ma C, Teng Q, Man J, Zhang X, Liu X, Zhang T, Chong W, Chen H, Lu M. Identification of a ferroptosis-related gene signature predicting recurrence in stage II/III colorectal cancer based on machine learning algorithms. Front Pharmacol 2023; 14:1260697. [PMID: 37711170 PMCID: PMC10498388 DOI: 10.3389/fphar.2023.1260697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most prevalent cancer types globally. A survival paradox exists due to the inherent heterogeneity in stage II/III CRC tumor biology. Ferroptosis is closely related to the progression of tumors, and ferroptosis-related genes can be used as a novel biomarker in predicting cancer prognosis. Methods: Ferroptosis-related genes were retrieved from the FerrDb and KEGG databases. A total of 1,397 samples were enrolled in our study from nine independent datasets, four of which were integrated as the training dataset to train and construct the model, and validated in the remaining datasets. We developed a machine learning framework with 83 combinations of 10 algorithms based on 10-fold cross-validation (CV) or bootstrap resampling algorithm to identify the most robust and stable model. C-indice and ROC analysis were performed to gauge its predictive accuracy and discrimination capabilities. Survival analysis was conducted followed by univariate and multivariate Cox regression analyses to evaluate the performance of identified signature. Results: The ferroptosis-related gene (FRG) signature was identified by the combination of Lasso and plsRcox and composed of 23 genes. The FRG signature presented better performance than common clinicopathological features (e.g., age and stage), molecular characteristics (e.g., BRAF mutation and microsatellite instability) and several published signatures in predicting the prognosis of the CRC. The signature was further stratified into a high-risk group and low-risk subgroup, where a high FRG signature indicated poor prognosis among all collected datasets. Sensitivity analysis showed the FRG signature remained a significant prognostic factor. Finally, we have developed a nomogram and a decision tree to enhance prognosis evaluation. Conclusion: The FRG signature enabled the accurate selection of high-risk stage II/III CRC population and helped optimize precision treatment to improve their clinical outcomes.
Collapse
Affiliation(s)
- Ze Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Chenghao Ma
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Qiong Teng
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Jinyu Man
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xuening Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xinjie Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Tongchao Zhang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center of Shandong University, Jinan, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Hao Chen
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center of Shandong University, Jinan, China
| | - Ming Lu
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center of Shandong University, Jinan, China
| |
Collapse
|
2
|
Xin C, Lai Y, Ji L, Wang Y, Li S, Hao L, Zhang W, Meng R, Xu J, Hong Y, Lou Z. A novel 9-gene signature for the prediction of postoperative recurrence in stage II/III colorectal cancer. Front Genet 2023; 13:1097234. [PMID: 36704343 PMCID: PMC9871489 DOI: 10.3389/fgene.2022.1097234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Individualized recurrence risk prediction in patients with stage II/III colorectal cancer (CRC) is crucial for making postoperative treatment decisions. However, there is still a lack of effective approaches for identifying patients with stage II and III CRC at a high risk of recurrence. In this study, we aimed to establish a credible gene model for improving the risk assessment of patients with stage II/III CRC. Methods: Recurrence-free survival (RFS)-related genes were screened using Univariate Cox regression analysis in GSE17538, GSE39582, and GSE161158 cohorts. Common prognostic genes were identified by Venn diagram and subsequently subjected to least absolute shrinkage and selection operator (LASSO) regression analysis and multivariate Cox regression analysis for signature construction. Kaplan-Meier (K-M), calibration, and receiver operating characteristic (ROC) curves were used to assess the predictive accuracy and superiority of our risk model. Single-sample gene set enrichment analysis (ssGSEA) was employed to investigate the relationship between the infiltrative abundances of immune cells and risk scores. Genes significantly associated with the risk scores were identified to explore the biological implications of the 9-gene signature. Results: Survival analysis identified 347 RFS-related genes. Using these genes, a 9-gene signature was constructed, which was composed of MRPL41, FGD3, RBM38, SPINK1, DKK1, GAL3ST4, INHBB, CTB-113P19.1, and FAM214B. K-M curves verified the survival differences between the low- and high-risk groups classified by the 9-gene signature. The area under the curve (AUC) values of this signature were close to or no less than the previously reported prognostic signatures and clinical factors, suggesting that this model could provide improved RFS prediction. The ssGSEA algorithm estimated that eight immune cells, including regulatory T cells, were aberrantly infiltrated in the high-risk group. Furthermore, the signature was associated with multiple oncogenic pathways, including cell adhesion and angiogenesis. Conclusion: A novel RFS prediction model for patients with stage II/III CRC was constructed using multicohort validation. The proposed signature may help clinicians better manage patients with stage II/III CRC.
Collapse
Affiliation(s)
- Cheng Xin
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Yi Lai
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | | | - Ye Wang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Shihao Li
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Liqiang Hao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Ronggui Meng
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Jun Xu
- Department of Gastrointestinal Surgery, Changhai Hospital, Shanghai, China,*Correspondence: Jun Xu, ; Yonggang Hong, ; Zheng Lou,
| | - Yonggang Hong
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China,*Correspondence: Jun Xu, ; Yonggang Hong, ; Zheng Lou,
| | - Zheng Lou
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China,*Correspondence: Jun Xu, ; Yonggang Hong, ; Zheng Lou,
| |
Collapse
|
3
|
Liu Z, Lu T, Li J, Wang L, Xu K, Dang Q, Liu L, Guo C, Jiao D, Sun Z, Han X. Clinical Significance and Inflammatory Landscape of aNovel Recurrence-Associated Immune Signature in Stage II/III Colorectal Cancer. Front Immunol 2021; 12:702594. [PMID: 34394098 PMCID: PMC8358813 DOI: 10.3389/fimmu.2021.702594] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/19/2021] [Indexed: 01/31/2023] Open
Abstract
Background A considerable number of patients with stage II/III colorectal cancer (CRC) will relapse within 5 years after surgery, which is a leading cause of death in early-stage CRC. The current TNM stage system is limited due to the heterogeneous clinical outcomes displayed in patients of same stage. Therefore, searching for a novel tool to identify patients at high recurrence-risk for improving post-operative individual management is an urgent need. Methods Using four independent public cohorts and qRT-PCR data from 66 tissues, we developed and validated a recurrence-associated immune signature (RAIS) based on global immune genes. The clinical and molecular features, tumor immune microenvironment landscape, and immune checkpoints profiles of RAIS were also investigated. Results In five independent cohorts, this novel scoring system was proven to be an independent recurrent factor and displayed excellent discrimination and calibration in predicting the recurrence-risk at 1~5 years. Further analysis revealed that the high-risk group displayed high mutation rate of TP53, while the low-risk group had more abundance of activated CD4+/CD8+ T cells and high expression of PD-1/PD-L1. Conclusions The RAIS model is highly predictive of recurrence in patients with stage II/III CRC, which might serve as a powerful tool to further optimize decision-making in adjuvant chemotherapy and immunotherapy, as well as tailor surveillance protocol for individual patients.
Collapse
Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Taoyuan Lu
- Department of Cerebrovascular Disease, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Jing Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kaihao Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dechao Jiao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| |
Collapse
|
4
|
Nishiuchi A, Hisamori S, Sakaguchi M, Fukuyama K, Hoshino N, Itatani Y, Honma S, Maekawa H, Nishigori T, Tsunoda S, Obama K, Miyoshi H, Shimono Y, Taketo MM, Sakai Y. MicroRNA-9-5p-CDX2 Axis: A Useful Prognostic Biomarker for Patients with Stage II/III Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11121891. [PMID: 31783700 PMCID: PMC6966658 DOI: 10.3390/cancers11121891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 01/15/2023] Open
Abstract
A lack of caudal-type homeobox transcription factor 2 (CDX2) protein expression has been proposed as a prognostic biomarker for colorectal cancer (CRC). However, the relationship between CDX2 levels and the survival of patients with stage II/III CRC along with the relationship between microRNAs (miRs) and CDX2 expression are unclear. Tissue samples were collected from patients with stage II/III CRC surgically treated at Kyoto University Hospital. CDX2 expression was semi-quantitatively evaluated by immunohistochemistry (IHC). The prognostic impacts of CDX2 expression on overall survival (OS) and relapse-free survival (RFS) were evaluated by multivariable statistical analysis. The expression of miRs regulating CDX2 expression and their prognostic impacts were analyzed using The Cancer Genome Atlas Program for CRC (TCGA-CRC). Eleven of 174 CRC tissues lacked CDX2 expression. The five-year OS and RFS rates of patients with CDX2-negative CRC were significantly lower than those of CDX2-positive patients. Multivariate analysis of clinicopathological features revealed that CDX2-negative status is an independent marker of poor prognosis in stage II/III CRC. miR-9-5p was shown to regulate CDX2 expression. TCGA-CRC analysis showed that high miR-9-5p expression was significantly associated with poor patient prognosis in stage II/III CRC. In conclusion, CDX2, the post-transcriptional target of microRNA-9-5p, is a useful prognostic biomarker in patients with stage II/III CRC.
Collapse
Affiliation(s)
- Aya Nishiuchi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Shigeo Hisamori
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
- Correspondence: ; Tel.: +81-075-751-3445
| | - Masazumi Sakaguchi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
- Department of Gastroenterological Surgery, Osaka Red Cross Hospital, Osaka 543-8555, Japan
| | - Keita Fukuyama
- Department of Clinical Oncology, Kyoto University Hospital, Kyoto 606-8507, Japan;
| | - Nobuaki Hoshino
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Yoshiro Itatani
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Shusaku Honma
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Hisatsugu Maekawa
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Tatsuto Nishigori
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Shigeru Tsunoda
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| | - Hiroyuki Miyoshi
- Division of Experimental Therapeutics, Department of Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan;
| | - Yohei Shimono
- Department of Biochemistry, School of Medicine, Fujita Health University, Aichi 470-1192, Japan;
| | - M. Mark Taketo
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan;
| | - Yoshiharu Sakai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (A.N.); (M.S.); (N.H.); (Y.I.); (S.H.); (H.M.); (T.N.); (S.T.); (K.O.); (Y.S.)
| |
Collapse
|