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Cai LQ, Yang DQ, Wang RJ, Huang H, Shi YX. Establishing and clinically validating a machine learning model for predicting unplanned reoperation risk in colorectal cancer. World J Gastroenterol 2024; 30:2991-3004. [PMID: 38946868 PMCID: PMC11212699 DOI: 10.3748/wjg.v30.i23.2991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/07/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Colorectal cancer significantly impacts global health, with unplanned reoperations post-surgery being key determinants of patient outcomes. Existing predictive models for these reoperations lack precision in integrating complex clinical data.
AIM To develop and validate a machine learning model for predicting unplanned reoperation risk in colorectal cancer patients.
METHODS Data of patients treated for colorectal cancer (n = 2044) at the First Affiliated Hospital of Wenzhou Medical University and Wenzhou Central Hospital from March 2020 to March 2022 were retrospectively collected. Patients were divided into an experimental group (n = 60) and a control group (n = 1984) according to unplanned reoperation occurrence. Patients were also divided into a training group and a validation group (7:3 ratio). We used three different machine learning methods to screen characteristic variables. A nomogram was created based on multifactor logistic regression, and the model performance was assessed using receiver operating characteristic curve, calibration curve, Hosmer-Lemeshow test, and decision curve analysis. The risk scores of the two groups were calculated and compared to validate the model.
RESULTS More patients in the experimental group were ≥ 60 years old, male, and had a history of hypertension, laparotomy, and hypoproteinemia, compared to the control group. Multiple logistic regression analysis confirmed the following as independent risk factors for unplanned reoperation (P < 0.05): Prognostic Nutritional Index value, history of laparotomy, hypertension, or stroke, hypoproteinemia, age, tumor-node-metastasis staging, surgical time, gender, and American Society of Anesthesiologists classification. Receiver operating characteristic curve analysis showed that the model had good discrimination and clinical utility.
CONCLUSION This study used a machine learning approach to build a model that accurately predicts the risk of postoperative unplanned reoperation in patients with colorectal cancer, which can improve treatment decisions and prognosis.
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Affiliation(s)
- Li-Qun Cai
- Department of Colorectal and Anal Surgery, Whenzhou Central Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Da-Qing Yang
- Department of Colorectal and Anal Surgery, Whenzhou Central Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Rong-Jian Wang
- Department of Colorectal and Anal Surgery, Whenzhou Central Hospital, Wenzhou 325000, Zhejiang Province, China
| | - He Huang
- Department of Colorectal and Anal Surgery, Whenzhou Central Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Yi-Xiong Shi
- Department of Colorectal and Anorectal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
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Xu X, Lai C, Luo J, Shi J, Guo K, Hu J, Mulati Y, Xiao Y, Kong D, Liu C, Huang J, Xu K. The predictive significance of chromobox family members in prostate cancer in humans. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00929-7. [PMID: 38427207 DOI: 10.1007/s13402-024-00929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE The Chromobox (CBX) family proteins are crucial elements of the epigenetic regulatory machinery and play a significant role in the development and advancement of cancer. Nevertheless, there is limited understanding regarding the role of CBXs in development or progression of prostate cancer (PCa). Our objective is to develop a unique prognostic model associated with CBXs to improve the accuracy of predicting outcomes of patients with PCa. METHODS Data from TCGA and GEO databases were analyzed to assess differential expression, prognostic value, gene pathway enrichment, and immune cell infiltration. COX regression analysis was utilized to identify the independent prognostic factors that impact disease-free survival (DFS). The expression of CBX2 and FOXP3+ cells infiltration was verified by immunohistochemical staining of clinical tissue sections. In vitro proliferation, migration and invasion assay were conducted to examine the function of CBX2. RNA-seq was employed to examine the CBX2 related pathway enrichment. RESULTS CBX2, CBX3, CBX4, and CBX8 were upregulated, while CBX6 and CBX7 were downregulated in PCa tissues. CBXs expression varied by stage and grade. Elevated expression of CBX1, CBX2, CBX3, CBX4 and CBX8 is correlated with poor outcome. CBX2 expression, T stage, and Gleason score were independent prognostic factors. The expression level of CBX2 in PCa tissues was significantly higher than that in adjacent normal tissues. More Treg infiltration was observed in the group with high CBX2 expression. CBX2 expression affected PCa cell growth, migration, and invasion. CONCLUSIONS CBX2 is involved in the development and advancement of PCa, suggesting its potential as a reliable prognostic indicator for PCa patients.
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Affiliation(s)
- Xiaoting Xu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Urology, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Cong Lai
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiawen Luo
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Juanyi Shi
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaixuan Guo
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jintao Hu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yelisudan Mulati
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yunfei Xiao
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Degeng Kong
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng Liu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, China
| | - Jingang Huang
- Medical Research Center, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Kewei Xu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China.
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, China.
- Sun Yat-sen University School of Medicine, Sun Yat-sen University, Shenzhen, China.
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Ma Q, Chen L, Feng K, Guo W, Huang T, Cai YD. Exploring Prognostic Gene Factors in Breast Cancer via Machine Learning. Biochem Genet 2024:10.1007/s10528-024-10712-w. [PMID: 38383836 DOI: 10.1007/s10528-024-10712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/21/2024] [Indexed: 02/23/2024]
Abstract
Breast cancer remains the most prevalent cancer in women. To date, its underlying molecular mechanisms have not been fully uncovered. The determination of gene factors is important to improve our understanding on breast cancer, which can correlate the specific gene expression and tumor staging. However, the knowledge in this regard is still far from complete. Thus, this study aimed to explore these knowledge gaps by analyzing existing gene expression profile data from 3149 breast cancer samples, where each sample was represented by the expression of 19,644 genes and classified into Nottingham histological grade (NHG) classes (Grade 1, 2, and 3). To this end, a machine learning-based framework was designed. First, the profile data were analyzed by using seven feature ranking algorithms to evaluate the importance of features (genes). Seven feature lists were generated, each of which sorted features in accordance with feature importance evaluated from a special aspect. Then, the incremental feature selection method was applied to each list to determine essential features for classification and building efficient classifiers. Consequently, overlapping genes, such as AURKA, CBX2, and MYBL2, were deemed as potentially related to breast cancer malignancy and prognosis, indicating that such genes were identified to be important by multiple feature ranking algorithms. In addition, the study formulated classification rules to reflect special gene expression patterns for three NHG classes. Some genes and rules were analyzed and supported by recent literature, providing new references for studying breast cancer.
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Affiliation(s)
- QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, 510507, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200030, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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Gurung R, Masood M, Singh P, Jha P, Sinha A, Ajmeriya S, Sharma M, Dohare R, Haque MM. Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach. J Appl Genet 2024:10.1007/s13353-024-00843-6. [PMID: 38358594 DOI: 10.1007/s13353-024-00843-6] [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: 10/16/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infiltration analysis followed by HPA validation. Lastly, we established a 3-node miRNA-TF-mRNA regulatory network and performed protein-protein docking of the highest-degree subnetwork motif between TF and mRNA. Significant upregulation of CBX3/2 and downregulation of AQP3/5/7 correlated with poor overall survival (OS) in HNSC patients. The most significant pathway, GO-BP, GO-MF, and GO-CC terms associated with AQP3 and CBX3 were passive transport by aquaporins, response to vitamin, glycerol channel activity, and condensed chromosome, centromeric region. AQP3 negatively correlated with [Formula: see text] T cells, positively with [Formula: see text] T cells and B cells, and negatively with tumor purity, whereas CBX3 positively correlated with [Formula: see text] T cells, negatively with [Formula: see text] T cells and B cells, and positively with tumor purity. Three-node miRNA-TF-mRNA regulatory network revealed a highest-degree subnetwork motif comprising one TF (SMAD3), one miRNA (miR-423-5p), and one mRNA (AQP3). Protein-protein interaction studies suggested a direct interaction between AQP3 and Smad3 proteins. We concluded that AQP3 and CBX3 hold potential as treatment strategies and individual prognostic biomarkers, while further protein-protein interaction studies of AQP3 could offer insights into its interactions with Smad3 proteins.
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Affiliation(s)
- Rishabh Gurung
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohammad Masood
- Department of Biotechnology, Faculty of Life Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, 110007, India
| | - Anuradha Sinha
- Department of Preventive Oncology, Homi Bhabha Cancer Hospital and Research Centre, Muzaffarpur, 842004, India
| | - Swati Ajmeriya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Milin Sharma
- Department of Biotechnology, Faculty of Life Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Mohammad Mahfuzul Haque
- Department of Biotechnology, Faculty of Life Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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Pan C, Zhang C, Lin Z, Liang Z, Cui Y, Shang Z, Wei Y, Chen F. Disulfidptosis-related Protein RPN1 may be a Novel Anti-osteoporosis Target of Kaempferol. Comb Chem High Throughput Screen 2024; 27:1611-1628. [PMID: 38213143 DOI: 10.2174/0113862073273655231213070619] [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: 07/23/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Osteoporosis (OP) is an age-related skeletal disease. Kaempferol can regulate bone mesenchymal stem cells (BMSCs) osteogenesis to improve OP, but its mechanism related to disulfidptosis, a newly discovered cell death mechanism, remains unclear. OBJECTIVE The study aimed to investigate the biological function and immune mechanism of disulfidptosis- related ribophorin I (RPN1) in OP and to experimentally confirm that RPN1 is the target for the treatment of OP with kaempferol. METHODS Differential expression analysis was conducted on disulfide-related genes extracted from the GSE56815 and GSE7158 datasets. Four machine learning algorithms identified disease signature genes, with RPN1 identified as a significant risk factor for OP through the nomogram. Validation of RPN1 differential expression in OP patients was performed using the GSE56116 dataset. The impact of RPN1 on immune alterations and biological processes was explored. Predictive ceRNA regulatory networks associated with RPN1 were generated via miRanda, miRDB, and TargetScan databases. Molecular docking estimated the binding model between kaempferol and RPN1. The targeting mechanism of kaempferol on RPN1 was confirmed through pathological HE staining and immunohistochemistry in ovariectomized (OVX) rats. RESULTS RPN1 was abnormally overexpressed in the OP cohort, associated with TNF signaling, hematopoietic cell lineage, and NF-kappa B pathway. Immune infiltration analysis showed a positive correlation between RPN1 expression and CD8+ T cells and resting NK cells, while a negative correlation with CD4+ naive T cells, macrophage M1, T cell gamma delta, T cell follicular helper cells, activated mast cells, NK cells, and dendritic cells, was found. Four miRNAs and 17 lncRNAs associated with RPN1 were identified. Kaempferol exhibited high binding affinity (-7.2 kcal/mol) and good stability towards the RPN1. The experimental results verified that kaempferol could improve bone microstructure destruction and reverse the abnormally high expression of RPN1 in the femur of ovariectomized rats. CONCLUSION RPN1 may be a new diagnostic biomarker in patients with OP, and may serve as a new target for kaempferol to improve OP.
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Affiliation(s)
- Chengzhen Pan
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Chi Zhang
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zonghan Lin
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zhou Liang
- Yulin Orthopedic Hospital of Integrated Traditional Chinese and Western Medicine, Yulin, Guangxi, China
| | - Yinhang Cui
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zhihao Shang
- Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuanxun Wei
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Feng Chen
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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Huang L, Shu Y, Liu X, Li L, Long T, Zeng L, Liu Y, Deng Y, Li H, Peng D. Abnormal dynamic functional connectivity in the hippocampal subregions of patients with untreated moderate-to-severe obstructive sleep apnea. Sleep Med 2023; 112:273-281. [PMID: 37939546 DOI: 10.1016/j.sleep.2023.10.037] [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: 08/29/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
OBJECTIVE To investigate the dynamic change characteristics of dynamic functional connectivity (dFC) between the hippocampal subregions (anterior and posterior) and other brain regions in obstructive sleep apnoea (OSA) and its relationship with cognitive function, and to explore whether these characteristics can be used to distinguish OSA from healthy controls (HCs). METHODS Eighty-five patients with newly diagnosed moderate-to-severe OSA and 85 HCs were enrolled. All participants underwent resting-state functional magnetic resonance imaging (fMRI). The difference between dFC values between the hippocampal subregions and other brain regions in OSA patients and HCs was compared using the two-sample t tests. Correlation analyses were used to assess the relationship between dFC, clinical data, and cognitive functions in OSA patients. dFC values from different brain regions were used as classification features to distinguish between the two groups using a support vector machine. RESULTS Compared with HCs, the dFC values between the left anterior hippocampus and right culmen of the cerebellum anterior lobe, right anterior hippocampus and left lingual gyrus, and left posterior hippocampus and left precentral gyrus were significantly lower, and the dFC values between the left posterior hippocampus and precuneus were significantly higher in OSA patients. The dFC values between the left posterior hippocampus and the precuneus of OSA patients were associated with sleep-related indicators and Montreal Cognitive Assessment scores. Support vector machine analysis results showed that dFC values in different brain regions could distinguish OSA patients from HCs. CONCLUSION dFC patterns between the hippocampal subregions and other brain regions were altered in patients with OSA, including the cerebellum, default mode networks, sensorimotor networks, and visual function networks, which is possibly associated with cognitive decline. In addition, the dFC values of different brain regions could effectively distinguish OSA patients from HCs. These findings provide new perspectives on neurocognition in these patients.
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Affiliation(s)
- Ling Huang
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yongqiang Shu
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiang Liu
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lifeng Li
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ting Long
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Li Zeng
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yumeng Liu
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yingke Deng
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Haijun Li
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China; PET Center, The First Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Dechang Peng
- Medical Imaging Center, The First Affiliated Hospital of Nanchang University, Nanchang, China; PET Center, The First Affiliated Hospital of Nanchang University, Nanchang, China.
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Chen F, Hou W, Yu X, Wu J, Li Z, Xu J, Deng Z, Chen G, Liu B, Yin X, Yu W, Zhang L, Xu G, Ji H, Liang C, Wang Z. CBX4 deletion promotes tumorigenesis under Kras G12D background by inducing genomic instability. Signal Transduct Target Ther 2023; 8:343. [PMID: 37696812 PMCID: PMC10495400 DOI: 10.1038/s41392-023-01623-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 08/03/2023] [Accepted: 08/22/2023] [Indexed: 09/13/2023] Open
Abstract
Chromobox protein homolog 4 (CBX4) is a component of the Polycomb group (PcG) multiprotein Polycomb repressive complexes 1 (PRC1), which is participated in several processes including growth, senescence, immunity, and tissue repair. CBX4 has been shown to have diverse, even opposite functions in different types of tissue and malignancy in previous studies. In this study, we found that CBX4 deletion promoted lung adenocarcinoma (LUAD) proliferation and progression in KrasG12D mutated background. In vitro, over 50% Cbx4L/L, KrasG12D mouse embryonic fibroblasts (MEFs) underwent apoptosis in the initial period after Adeno-Cre virus treatment, while a small portion of survival cells got increased proliferation and transformation abilities, which we called selected Cbx4-/-, KrasG12D cells. Karyotype analysis and RNA-seq data revealed chromosome instability and genome changes in selected Cbx4-/-, KrasG12D cells compared with KrasG12D cells. Further study showed that P15, P16 and other apoptosis-related genes were upregulated in the primary Cbx4-/-, KrasG12D cells due to chromosome instability, which led to the large population of cell apoptosis. In addition, multiple pathways including Hippo pathway and basal cell cancer-related signatures were altered in selected Cbx4-/-, KrasG12D cells, ultimately leading to cancer. We also found that low expression of CBX4 in LUAD was associated with poorer prognosis under Kras mutation background from the human clinical data. To sum up, CBX4 deletion causes genomic instability to induce tumorigenesis under KrasG12D background. Our study demonstrates that CBX4 plays an emerging role in tumorigenesis, which is of great importance in guiding the clinical treatment of lung adenocarcinoma.
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Affiliation(s)
- Fangzhen Chen
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Shanghai Medical College, Fudan University, Shanghai, 200030, China
| | - Wulei Hou
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China
| | - Xiangtian Yu
- Clinical Research Center, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jing Wu
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Shanghai Medical College, Fudan University, Shanghai, 200030, China
| | - Zhengda Li
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Shanghai Medical College, Fudan University, Shanghai, 200030, China
| | - Jietian Xu
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Shanghai Medical College, Fudan University, Shanghai, 200030, China
| | - Zimu Deng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Gaobin Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxing Yin
- Department of General Surgery, Jing'an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Wei Yu
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Guoliang Xu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chunmin Liang
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Shanghai Medical College, Fudan University, Shanghai, 200030, China.
| | - Zuoyun Wang
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Shanghai Medical College, Fudan University, Shanghai, 200030, China.
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Nguyen MT, Hoang MT, Bui HTT. Pan-Cancer Analysis of the Expression and Prognostic Value of S-Phase Kinase-Associated Protein 2. Open Access Maced J Med Sci 2023. [DOI: 10.3889/oamjms.2023.11212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND: S-Phase Kinase-Associated Protein 2 (SKP2) is essential in modulating metabolism processes, cell proliferation, and carcinogenesis DUE to its capacity to ubiquitinate and degrade various tumor-suppressive substrates. However, the actual biological and mechanism significance of SKP2 in the development of tumors and as a possible therapeutic target remains to be completely understood.
AIM: This study aimed to explore the potential roles of the SKP2 gene in the oncologic pathogenesis of various cancers through an in-depth pan-cancer analysis including gene expression assessment, survival analysis, genetic alteration, and enrichment analysis.
METHODS: Public databases including the Cancer Genome Atlas database, Genotype-Tissue Expression Project database, cBioPortal database, Gene Expression Profiling Interactive Analysis 2 database, Tumor Immune Estimation Resource version 2.0 database, and STRING database were used to detect the SKP2 expression, molecular mechanism, and its association with the prognosis across pan-cancer.
RESULTS: SKP2 was significantly highly expressed in most types of cancers and was substantially correlated to the poor survival of patients with specific cancers based on the log-rank test. SKP2 had the highest frequency of alteration in lung cancer and amplification was the most common genetic alteration type. Finally, SKP2-related genes were identified and enrichment analyses were conducted.
CONCLUSION: This study presented the first demonstration of the pan-cancer landscape of abnormal SKP2 expression, it could potentially serve as a predictive indicator and prospective therapeutic target.
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