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Tuo Z, Lin Y, Zhang Y, Gao L, Yu D, Wang J, Sun C, Sun X, Wang J, Prasad A, Bheesham N, Meng M, Lv Z, Chen X. Prognostic significance and immune landscape of a cell cycle progression-related risk model in bladder cancer. Discov Oncol 2024; 15:160. [PMID: 38735911 PMCID: PMC11089032 DOI: 10.1007/s12672-024-01008-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND A greater emphasis has been placed on the part of cell cycle progression (CCP) in cancer in recent years. Nevertheless, the precise connection between CCP-related genes and bladder cancer (BCa) has remained elusive. This study endeavors to establish and validate a reliable risk model incorporating CCP-related factors, aiming to predict both the prognosis and immune landscape of BCa. METHODS Clinical information and RNA sequencing data were collected from the GEO and TCGA databases. Univariate and multivariate Cox regression analyses were conducted to construct a risk model associated with CCP. The performance of the model was assessed using ROC and Kaplan-Meier survival analyses. Functional enrichment analysis was employed to investigate potential cellular functions and signaling pathways. The immune landscape was characterized using CIBERSORT algorithms. Integration of the risk model with various clinical variables led to the development of a nomogram. RESULTS To build the risk model, three CCP-related genes (RAD54B, KPNA2, and TPM1) were carefully chosen. ROC and Kaplan-Meier survival analysis confirm that our model has good performance. About immunological infiltration, the high-risk group showed decreased levels of regulatory T cells and dendritic cells coupled with increased levels of activated CD4 + memory T cells, M2 macrophages, and neutrophils. Furthermore, the nomogram showed impressive predictive power for OS at 1, 3, and 5 years. CONCLUSION This study provides new insights into the association between the CCP-related risk model and the prognosis of BCa, as well as its impact on the immune landscape.
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Affiliation(s)
- Zhouting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuan Lin
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Zhang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Liang Gao
- Center for Clinical Medicine, Huatuo Institute of Medical Innovation (HTIMI), Berlin, Germany
| | - Dexin Yu
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jiani Wang
- Institute for Social Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin; Berlin Institute of Health, Epidemiology and Health Economics, Berlin, Germany
| | - Chenyu Sun
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xianchao Sun
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jinyou Wang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Apurwa Prasad
- Parkview Regional Medical Center, 11109 Parkview Plaza Dr, Fort Wayne, IN, 46845, USA
| | - Nimarta Bheesham
- Internal Medicine, University of Illinois College of Medicine, One Illini Drive, Peoria, IL, 61605, USA
| | - Muzi Meng
- UK Program Site, American University of the Caribbean School of Medicine, Vernon Building Room 64, Sizer St, Preston, PR1 1JQ, UK
- Bronxcare Health System, 1650 Grand Concourse, The Bronx, NY, 10457, USA
| | - Zhengmei Lv
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Anhui, China.
| | - Xin Chen
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
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Sun L, Tuo Z, Chen X, Wang H, Lyu Z, Li G. Identification of cell differentiation trajectory-related gene signature to reveal the prognostic significance and immune landscape in prostate cancer based on multiomics analysis. Heliyon 2024; 10:e27628. [PMID: 38510027 PMCID: PMC10950568 DOI: 10.1016/j.heliyon.2024.e27628] [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: 01/02/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Background In the context of prostate cancer (PCa), the occurrence of biochemical recurrence (BCR) stands out as a pivotal factor significantly impacting prognosis, potentially leading to metastasis and mortality. However, the early detection of BCR poses a substantial challenge for PCa patients. There is an urgent need to pinpoint hub genes that can serve as predictive indicators for BCR in PCa patients. Methods Our primary goal was to identify cell differentiation trajectory-related gene signature in PCa patients by pseudo-time trajectory analysis. We further explored the functional enrichment of overlapped marker genes and probed clinically relevant modules and BCR-related genes using Weighted Gene Co-expression Network Analysis (WGCNA) in PCa patients. Key genes predicting recurrence-free survival were meticulously identified through univariate and multivariate Cox regression analyses. Subsequently, these genes were utilized to construct a prognostic gene signature, the expression, predictive efficacy, putative functions, and immunological landscape of which were thoroughly validated. Additionally, we employed immunohistochemistry (IHC) and a western blotting assay to quantify the expression of PYCR1 in clinical samples. Results Our single-cell RNA (scRNA) sequencing analysis unveiled three subgroups characterized by distinct differentiation trajectories, and the marker genes associated with these groups were extracted from PCa patients. These marker genes successfully classified the PCa sample into two molecular subtypes, demonstrating a robust correlation with clinical characteristics and recurrence-free survival. Through WGCNA and Lasso analysis, we identified four hub genes (KLK3, CD38, FASN, and PYCR1) to construct a risk profile of prognostic genes linked to BCR. Notably, the high-risk patient group exhibited elevated levels of B cell naive, Macrophage M0, and Macrophage M2 infiltration, while the low-risk group displayed higher levels of T cells CD4 memory activated and monocyte infiltration. Furthermore, IHC and western blotting assays confirmed the heightened expression of PYCR1 in PCa tissues. Conclusion This study leveraged the differentiation trajectory and genetic variability of the microenvironment to uncover crucial prognostic genes associated with BCR in PCa patients. These findings present novel perspectives for tailoring treatment strategies for PCa patients on an individualized basis.
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Affiliation(s)
- Liangxue Sun
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Public Health Clinical Center, Hefei, China
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Zhouting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xin Chen
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huming Wang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhaojie Lyu
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Guangyuan Li
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Public Health Clinical Center, Hefei, China
- The Lu’ an Hospital Affiliated to Anhui Medical University, Lu’ an, China
- The Lu’ an People’s Hospital, Lu’ an, China
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Wei J, Ge X, Qian Y, Jiang K, Chen X, Lu W, Yang H, Fu D, Fang Y, Zhou X, Xiao Q, Tang Y, Ding K. Development and verification of a combined immune- and cancer-associated fibroblast related prognostic signature for colon adenocarcinoma. Front Immunol 2024; 15:1291938. [PMID: 38312843 PMCID: PMC10834644 DOI: 10.3389/fimmu.2024.1291938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
Introduction To better understand the role of immune escape and cancer-associated fibroblasts (CAFs) in colon adenocarcinoma (COAD), an integrative analysis of the tumor microenvironment was performed using a set of 12 immune- and CAF-related genes (ICRGs). Methods Univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses were used to establish a prognostic signature based on the expression of these 12 genes (S1PR5, AEN, IL20RB, FGF9, OSBPL1A, HSF4, PCAT6, FABP4, KIF15, ZNF792, CD1B and GLP2R). This signature was validated in both internal and external cohorts and was found to have a higher C-index than previous COAD signatures, confirming its robustness and reliability. To make use of this signature in clinical settings, a nomogram incorporating ICRG signatures and key clinical parameters, such as age and T stage, was developed. Finally, the role of S1PR5 in the immune response of COAD was validated through in vitro cytotoxicity experiments. Results The developed nomogram exhibited slightly improved predictive accuracy compared to the ICRG signature alone, as indicated by the areas under the receiver operating characteristic curves (AUC, nomogram:0.838; ICRGs:0.807). The study also evaluated the relationships between risk scores (RS) based on the expression of the ICRGs and other key immunotherapy variables, including immune checkpoint expression, immunophenoscore (IPS), and microsatellite instability (MSI). Integration of these variables led to more precise prediction of treatment efficacy, enabling personalized immunotherapy for COAD patients. Knocking down S1PR5 can enhance the efficacy of PD-1 monoclonal antibody, promoting the cytotoxicity of T cells against HCT116 cells ((p<0.05). Discussion These findings indicate that the ICRG signature may be a valuable tool for predicting prognostic risk, evaluating the efficacy of immunotherapy, and tailoring personalized treatment options for patients with COAD.
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Affiliation(s)
- Jingsun Wei
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoxu Ge
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Yucheng Qian
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Kai Jiang
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin Chen
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Lu
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Hang Yang
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Dongliang Fu
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Yimin Fang
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyi Zhou
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Qian Xiao
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Yang Tang
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Kefeng Ding
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Department of Colorectal Surgery and Oncology, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
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Zou M, Li H, Su D, Xiong Y, Wei H, Wang S, Sun H, Wang T, Xi Q, Zuo Y, Yang L. Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes. Brief Bioinform 2023; 25:bbad430. [PMID: 38040491 PMCID: PMC10783866 DOI: 10.1093/bib/bbad430] [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: 08/16/2023] [Revised: 09/29/2023] [Accepted: 11/05/2023] [Indexed: 12/03/2023] Open
Abstract
Pancreatic cancer is a globally recognized highly aggressive malignancy, posing a significant threat to human health and characterized by pronounced heterogeneity. In recent years, researchers have uncovered that the development and progression of cancer are often attributed to the accumulation of somatic mutations within cells. However, cancer somatic mutation data exhibit characteristics such as high dimensionality and sparsity, which pose new challenges in utilizing these data effectively. In this study, we propagated the discrete somatic mutation data of pancreatic cancer through a network propagation model based on protein-protein interaction networks. This resulted in smoothed somatic mutation profile data that incorporate protein network information. Based on this smoothed mutation profile data, we obtained the activity levels of different metabolic pathways in pancreatic cancer patients. Subsequently, using the activity levels of various metabolic pathways in cancer patients, we employed a deep clustering algorithm to establish biologically and clinically relevant metabolic subtypes of pancreatic cancer. Our study holds scientific significance in classifying pancreatic cancer based on somatic mutation data and may provide a crucial theoretical basis for the diagnosis and immunotherapy of pancreatic cancer patients.
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Affiliation(s)
- Min Zou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Honghao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Dongqing Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuqiang Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haodong Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongmei Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qilemuge Xi
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd. Hohhot 010010, China
- Inner Mongolia International Mongolian Hospital, Hohhot 010065, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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