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Song XQ, Shao ZM. Identification of immune-related prognostic biomarkers in triple-negative breast cancer. Transl Cancer Res 2024; 13:1707-1720. [PMID: 38737702 PMCID: PMC11082668 DOI: 10.21037/tcr-23-1554] [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: 08/28/2023] [Accepted: 02/29/2024] [Indexed: 05/14/2024]
Abstract
Background Triple-negative breast cancer (TNBC), a type of breast cancer, lacks immune-related markers that can be used for prognosis or prediction. Therefore, we created a predictive framework for TNBC using a risk assessment. Methods Our previous study group consisted of 360 individuals who were diagnosed with TNBC through pathology using RNA sequencing and had clinical data from Fudan University Shanghai Cancer Center (FUSCC). A risk scoring model was constructed using the Cox regression method with the least absolute shrinkage and selection operator (LASSO). A multivariate Cox regression analysis was utilized to develop the prediction model, which was then assessed using the consistency index and calibration plots. The validation cohort of The Cancer Genome Atlas (TCGA) TNBC confirmed the strength of the signatures' predictive value. Results The prognostic risk score model included 12 genes: TDO2, CHIT1, CARML2, HLA-C, ADIRF, C19orf33, CA8, AHNAK2, RHOV, OPLAH, THEM6, and NEBL. The receiver operator characteristic (ROC) curves for survivability values at 1, 3, and 5 years in the FUSCC TNBC cohort demonstrated area under the curve (AUC) values of 0.78, 0.83, and 0.75, respectively. These results indicated a high level of accuracy in predicting outcomes, which was further confirmed through validation using TCGA database. The patients in the high-risk group showed worse prognoses and lower levels of immune cell infiltration, specifically CD8+ T cells, than those in the low-risk group. Furthermore, the low-risk group exhibited a significant upregulation of genes that encode immune checkpoints, including CD274 and CTLA4, suggesting that immunotherapy may yield enhanced efficacy within this particular group. Conclusions In conclusion, the prognostic signature consisting of 12 genes can assist in the choice of immunotherapy for TNBC.
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Affiliation(s)
- Xiao-Qing Song
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Li W, Wang X, Li C, Chen T, Zhou X, Li Z, Yang Q. Identification and validation of an m6A-related gene signature to predict prognosis and evaluate immune features of breast cancer. Hum Cell 2023; 36:393-408. [PMID: 36403174 DOI: 10.1007/s13577-022-00826-x] [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: 07/25/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022]
Abstract
Breast cancer is the most prevalent cancer, and it is accompanied by high heterogeneity. N6-methyladenosine (m6A) modification significantly contributes to breast cancer tumorigenesis and progression. However, how m6A-related genes affect the clinical outcomes and tumor immune microenvironment (TIME) of breast cancer is largely unknown. Our study developed an m6A-related gene signature on the basis of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The m6A-related gene signature was constructed using univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses. Breast cancer patients were classified into low- and high-risk groups depending on the median risk score. The reliability and efficiency of the signature were validated using Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, and principal component analysis (PCA). The risk score was validated as an independent indicator associated with overall survival, and a nomogram model was created to estimate the overall survival of patients with breast cancer. Functional annotation suggested that the risk score had a strong relationship with immune-related pathways. Different proportions of immune cell infiltration between the two groups were evaluated using various algorithms. The high-risk group had higher immune checkpoint expression levels. We discovered that one of the 6 prognostic genes, TMEM71, was downregulated in breast cancer tissues. In vitro experiments indicated that overexpression of TMEM71 suppressed breast cancer cell proliferation and migration. In conclusion, the m6A-related gene signature may be a sensitive biomarker for overall survival prediction and guide the individualized treatment for breast cancer patients.
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Affiliation(s)
- Wenhao Li
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China
| | - Chen Li
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China
| | - Tong Chen
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China
| | - Xianyong Zhou
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China
- Department of Breast Surgery, Binzhou People's Hospital, Binzhou, Shandong, China
| | - Zheng Li
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China.
- Department of Pathology Tissue Bank, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Wenhua Xi Road No. 107, Jinan, 250012, Shandong, China.
- Research Institute of Breast Cancer, Shandong University, Wenhua Xi Road No. 107, JinanShandong, 250012, China.
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Huang W, Kong F, Li R, Chen X, Wang K. Emerging Roles of m 6A RNA Methylation Regulators in Gynecological Cancer. Front Oncol 2022; 12:827956. [PMID: 35155260 PMCID: PMC8831694 DOI: 10.3389/fonc.2022.827956] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
Gynecological cancers seriously affect the reproductive system of females; diseases include ovarian tumors, uterine tumors, endometrial cancers, cervical cancers, and vulva and vaginal tumors. At present, the diagnosis methods of gynecological cancer are insufficiently sensitive and specific, leading to failure of early disease detection. N6-methyladenosine (m6A) plays various biological functions in RNA modification and is currently studied extensively. m6A modification controls the fate of transcripts and regulates RNA metabolism and biological processes through the interaction of m6A methyltransferase (“writer”) and demethylase (“erasers”) and the binding protein decoding m6A methylation (“readers”). In the field of epigenetics, m6A modification is a dynamic process of reversible regulation of target RNA through its regulatory factors. It plays an important role in many diseases, especially cancer. However, its role in gynecologic cancers has not been fully investigated. Thus, we review the regulatory mechanism, biological functions, and therapeutic prospects of m6A RNA methylation regulators in gynecological cancers.
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Affiliation(s)
- Wanjun Huang
- Department of Obstetrics and Gynecology, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Fanhua Kong
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, China
| | - Ruolan Li
- Department of Obstetrics and Gynecology, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Xiang Chen
- Department of Anesthesiology, Xiangya Hospital of Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Kunpeng Wang
- Department of General Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
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Zhang Y, He R, Lei X, Mao L, Jiang P, Ni C, Yin Z, Zhong X, Chen C, Zheng Q, Li D. A Novel Pyroptosis-Related Signature for Predicting Prognosis and Indicating Immune Microenvironment Features in Osteosarcoma. Front Genet 2021; 12:780780. [PMID: 34899864 PMCID: PMC8662937 DOI: 10.3389/fgene.2021.780780] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is a common malignant bone tumor with a propensity for drug resistance, recurrence, and metastasis. A growing number of studies have elucidated the dual role of pyroptosis in the development of cancer, which is a gasdermin-regulated novel inflammatory programmed cell death. However, the interaction between pyroptosis and the overall survival (OS) of osteosarcoma patients is poorly understood. This study aimed to construct a prognostic model based on pyroptosis-related genes to provide new insights into the prognosis of osteosarcoma patients. We identified 46 differentially expressed pyroptosis-associated genes between osteosarcoma tissues and normal control tissues. A total of six risk genes affecting the prognosis of osteosarcoma patients were screened to form a pyroptosis-related signature by univariate and LASSO regression analysis and verified using GSE21257 as a validation cohort. Combined with other clinical characteristics, including age, gender, and metastatic status, we found that the pyroptosis-related signature score, which we named “PRS-score,” was an independent prognostic factor for patients with osteosarcoma and that a low PRS-score indicated better OS and a lower risk of metastasis. The result of ssGSEA and ESTIMATE algorithms showed that a lower PRS-score indicated higher immune scores, higher levels of tumor infiltration by immune cells, more active immune function, and lower tumor purity. In summary, we developed and validated a pyroptosis-related signature for predicting the prognosis of osteosarcoma, which may contribute to early diagnosis and immunotherapy of osteosarcoma.
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Affiliation(s)
- Yiming Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Rong He
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Xuan Lei
- Department of Burn and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lianghao Mao
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Pan Jiang
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China.,Guizhou Orthopedics Hospital, Guiyang, China
| | - Chenlie Ni
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Zhengyu Yin
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xinyu Zhong
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Chen Chen
- Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University Zhenjiang, Guiyang, China
| | - Qiping Zheng
- Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University Zhenjiang, Guiyang, China.,Shenzhen Academy of Peptide Targeting Technology at Pingshan, and Shenzhen Tyercan Bio-Pharm Co., Ltd., Shenzhen, China
| | - Dapeng Li
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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