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Gul S, Pang J, Yuan H, Chen Y, Yu Q, Wang H, Tang W. Stemness signature and targeted therapeutic drugs identification for Triple Negative Breast Cancer. Sci Data 2023; 10:815. [PMID: 37985782 PMCID: PMC10662149 DOI: 10.1038/s41597-023-02709-8] [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: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and carries the worst prognosis, characterized by the lack of progesterone, estrogen, and HER2 gene expression. This study aimed to analyze cancer stemness-related gene signature to determine patients' risk stratification and prognosis feature with TNBC. Here one-class logistic regression (OCLR) algorithm was applied to compute the stemness index of TNBC patients. Cox and LASSO regression analysis was performed on stemness-index related genes to establish 16 genes-based prognostic signature, and their predictive performance was verified in TCGA and METABERIC merged data cohort. We diagnosed the expression level of prognostic genes signature in the tumor immune microenvironment, analyzed the TNBC scRNA-seq GSE176078 dataset, and further validated the expression level of prognostic genes using the HPA database. Finally, the small molecular compounds targeted at the anti-tumor effect of predictive genes were screened by molecular docking; this novel stemness-based prognostic genes signature study could facilitate the prognosis of patients with TNBC and thus provide a feasible therapeutic target for TNBC.
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Affiliation(s)
- Samina Gul
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Jianyu Pang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Hongjun Yuan
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Yongzhi Chen
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Qian Yu
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Hui Wang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Wenru Tang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China.
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Mo C, Wu Y, Ma J, Xie L, Huang Y, Xu Y, Peng H, Chen Z, Zeng M, Mao R. Clinicopathological value of the upregulation of cyclin-dependent kinases regulatory subunit 2 in osteosarcoma. BMC Med Genomics 2022; 15:81. [PMID: 35410253 PMCID: PMC9004629 DOI: 10.1186/s12920-022-01234-8] [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: 11/08/2021] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background Cyclin-dependent kinase subunit 2 (CKS2) is a member of cyclin dependent kinase subfamily and the relationship between CKS2 and osteosarcoma (OS) remains to be further analyzed. Methods 80 OS and 41 non-tumor tissue samples were arranged to perform immunohistochemistry (IHC) to evaluate CKS2 expression between OS and non-tumor samples. The standard mean deviation (SMD) was calculated based on in-house IHC and tissue microarrays, and exterior high-throughput datasets for further verification of CKS2 expression trend in OS. The effect of CKS2 expression on clinicopathological parameters of OS patients, and single-cell in OS tissues was analyzed through public high-throughput datasets and functional enrichment analysis was conducted for co-expression genes of CKS2 in accordance with weighted correlation network analysis. Results A total of 217 OS samples and 87 non-tumor samples (including tissue and cell line) were obtained from in-house IHC, microarrays and exterior high-throughput datasets. The analysis of integrated expression status demonstrated up-regulation of CKS2 in OS (SMD = 1.57, 95%CI [0.27–2.86]) and the significant power of CKS2 expression in distinguishing OS samples from non-tumor samples (AUC = 0.97 95%CI [0.95–0.98]). Clinicopathological analysis of GSE21257 indicated that OS patients with higher CKS2 expression was more likely to suffer OS metastasis. Although Kaplan–Meier curves showed no remarkable difference of overall survival rate between OS patients with high and low-CKS2, CKS2 was found up-regulated in proliferating osteosarcoma cells. Co-expression genes of CKS2 were mainly assembled in function and pathways such as cell cycle, cell adhesion, and intercellular material transport. Conclusions In summary, up-regulation of CKS2 expression in OS tissue was found through multiple technical approaches. In addition, scRNA-seq and co-expression analysis showed that CKS2 may have an impact on important biological process linked with cell cycle, cell adhesion, and intercellular material transport. Present study on CKS2 in OS indicated a promising prospect for CKS2 as a biomarker for OS. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01234-8.
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Affiliation(s)
- Chaohua Mo
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Yanxing Wu
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Le Xie
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Yingxin Huang
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Yuanyuan Xu
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Huizhi Peng
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Zengwei Chen
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Min Zeng
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China
| | - Rongjun Mao
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, 528300, Guangdong, China.
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