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Li J, Kong Z, Qi Y, Wang W, Su Q, Huang W, Zhang Z, Li S, Du E. Single-cell and bulk RNA-sequence identified fibroblasts signature and CD8 + T-cell - fibroblast subtype predicting prognosis and immune therapeutic response of bladder cancer, based on machine learning: bioinformatics multi-omics study. Int J Surg 2024; 110:4911-4931. [PMID: 38759695 PMCID: PMC11325897 DOI: 10.1097/js9.0000000000001516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/14/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are found in primary and advanced tumours. They are primarily involved in tumour progression through complex mechanisms with other types of cells in the tumour microenvironment. However, essential fibroblasts-related genes (FRG) in bladder cancer still need to be explored, and there is a shortage of an ideal predictive model or molecular subtype for the progression and immune therapeutic assessment for bladder cancer, especially muscular-invasive bladder cancer based on the FRG. MATERIALS AND METHODS CAF-related genes of bladder cancer were identified by analysing single-cell RNA sequence datasets, and bulk transcriptome datasets and gene signatures were used to characterize them. Then, 10 types of machine learning algorithms were utilised to determine the hallmark FRG and construct the FRG index (FRGI) and subtypes. Further molecular subtypes combined with CD8+ T-cells were established to predict the prognosis and immune therapy response. RESULTS Fifty-four BLCA-related FRG were screened by large-scale scRNA-sequence datasets. The machine learning algorithm established a 3-genes FRGI. High FRGI represented a worse outcome. Then, FRGI combined clinical variables to construct a nomogram, which shows high predictive performance for the prognosis of bladder cancer. Furthermore, the BLCA datasets were separated into two subtypes - fibroblast hot and cold types. In five independent BLCA cohorts, the fibroblast hot type showed worse outcomes than the cold type. Multiple cancer-related hallmark pathways are distinctively enriched in these two types. In addition, high FRGI or fibroblast hot type shows a worse immune therapeutic response. Then, four subtypes called CD8-FRG subtypes were established under the combination of FRG signature and activity of CD8+ T-cells, which turned out to be effective in predicting the prognosis and immune therapeutic response of bladder cancer in multiple independent datasets. Pathway enrichment analysis, multiple gene signatures, and epigenetic alteration characterize the CD8-FRG subtypes and provide a potential combination strategy method against bladder cancer. CONCLUSIONS In summary, the authors established a novel FRGI and CD8-FRG subtype by large-scale datasets and organised analyses, which could accurately predict clinical outcomes and immune therapeutic response of BLCA after surgery.
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Affiliation(s)
- Jingxian Li
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Zheng Kong
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Yuanjiong Qi
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Wei Wang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Qiang Su
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Wei Huang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Zhihong Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
| | - Shuai Li
- Department of Colorectal Surgery, The Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - E Du
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University
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Chang Z, Lu J, Zhang Q, Wu H, Liang Z, Pan X, Li B, Cheng ZJ, Sun B. Clinical biomarker profiles reveals gender differences and mortality factors in sepsis. Front Immunol 2024; 15:1413729. [PMID: 38835774 PMCID: PMC11148215 DOI: 10.3389/fimmu.2024.1413729] [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: 04/07/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Background Sepsis is a major contributor to global morbidity and mortality, affecting millions each year. Notwithstanding the decline in sepsis incidence and mortality over decades, gender disparities in sepsis outcomes persist, with research suggesting higher mortality rates in males. Methods This retrospective study aims to delineate gender-specific clinical biomarker profiles impacting sepsis progression and mortality by examining sepsis cases and related clinical data from the past three years. Propensity score matching was used to select age-matched healthy controls for comparison. Results Among 265 sepsis patients, a significantly higher proportion were male (60.8%, P<0.001). While mortality did not significantly differ by gender, deceased patients were significantly older (mean 69 vs 43 years, P=0.003), more likely to have hypertension (54% vs 25%, P=0.019), and had higher SOFA scores (mean ~10 vs 4, P<0.01) compared to survivors. Principal Component Analysis (PCA) showed clear separation between sepsis patients and healthy controls. 48 serum biomarkers were significantly altered in sepsis, with Triiodothyronine, Apolipoprotein A, and Serum cystatin C having the highest diagnostic value by ROC analysis. Gender-stratified comparisons identified male-specific (e.g. AFP, HDLC) and female-specific (e.g. Rheumatoid factor, Interleukin-6) diagnostic biomarkers. Deceased patients significantly differed from survivors, with 22 differentially expressed markers; Antithrombin, Prealbumin, HDL cholesterol, Urea nitrogen and Hydroxybutyrate had the highest diagnostic efficiency for mortality. Conclusion These findings enhance our understanding of gender disparities in sepsis and may guide future therapeutic strategies. Further research is warranted to validate these biomarker profiles and investigate the molecular mechanisms underlying these gender differences in sepsis outcomes.
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Affiliation(s)
- Zhenglin Chang
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Jiancai Lu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qitai Zhang
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haojie Wu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhiman Liang
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaocong Pan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bishan Li
- State Key Laboratory of Respiratory Disease, Department of Blood Transfusion, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhangkai J Cheng
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
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Yan Q, Gao C, Li M, Lan R, Wei S, Fan R, Cheng W. TRP Ion Channels in Immune Cells and Their Implications for Inflammation. Int J Mol Sci 2024; 25:2719. [PMID: 38473965 DOI: 10.3390/ijms25052719] [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: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The transient receptor potential (TRP) ion channels act as cellular sensors and mediate a plethora of physiological processes, including somatosensation, proliferation, apoptosis, and metabolism. Under specific conditions, certain TRP channels are involved in inflammation and immune responses. Thus, focusing on the role of TRPs in immune system cells may contribute to resolving inflammation. In this review, we discuss the distribution of five subfamilies of mammalian TRP ion channels in immune system cells and how these ion channels function in inflammatory mechanisms. This review provides an overview of the current understanding of TRP ion channels in mediating inflammation and may offer potential avenues for therapeutic intervention.
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Affiliation(s)
- Qiyue Yan
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Chuanzhou Gao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Mei Li
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Rui Lan
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Shaohan Wei
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Runsong Fan
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wei Cheng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
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Guo C, Li P, Guo X, Wang X, Liu B, Cui L. Identification of bladder cancer subtypes and predictive model for prognosis, immune features, and immunotherapy based on neutrophil extracellular trap-related genes. Sci Rep 2023; 13:20791. [PMID: 38012244 PMCID: PMC10682410 DOI: 10.1038/s41598-023-47824-z] [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: 10/07/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023] Open
Abstract
Bladder cancer is the most common malignant tumor of urinary system, and its morbidity and mortality are increasing rapidly. Although great advances have been made in medical technology in recent years, there is still a lack of effective prognostic and therapeutic methods for bladder cancer. NETs are reticulated DNA structures decorated with various protein substances released extracellularly by neutrophils stimulated by strong signals. Recently, it has been found that NETs are closely related to the growth, metastasis and drug resistance of many types of cancers. However, up to now, the research on the relationship between NETs and bladder cancer is still not enough. In this study, we aimed to conduct a comprehensive analysis of NRGs in bladder cancer tissues to evaluate the relationship between NRGs and prognosis prediction and sensitivity to therapy in patients with bladder cancer. We scored NRGs in each tissue by using ssGSEA, and selected gene sets that were significantly associated with NRGs scores by using the WCGNA algorithm. Based on the expression profiles of NRGs-related genes, NMF clustering analysis was performed to identify different BLCA molecular subtypes. For the differentially expressed genes between subtypes, we used univariate COX regression, LASSO regression and multivariate COX regression to further construct a hierarchical model of BLCA patients containing 10 genes. This model and the nomogram based on this model can accurately predict the prognosis of BLCA patients in multiple datasets. Besides, BLCA patients classified based on this model differ greatly in their sensitivity to immunotherapy and targeted therapies, which providing a reference for individualized treatment of patients with bladder cancer.
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Affiliation(s)
- Changhong Guo
- Department of Urology, Civil Aviation General Hospital, Beijing, China
| | - Peiying Li
- Department of Urology, The Fifth Medical Center of the General Hospital of the People's Liberation Army of China, Beijing, China
| | - Xingkui Guo
- Department of Urology, The Second People's Hospital of Juancheng County, Shandong, China
| | - Xinfen Wang
- Department of Urology, The Second People's Hospital of Juancheng County, Shandong, China
| | - Bo Liu
- Department of Urology, The First People's Hospital of Juancheng County, Shandong, China
| | - Liang Cui
- Department of Urology, Civil Aviation General Hospital, Beijing, China.
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Chang Z, An L, Lei M, Song Z, Deng J, Tang R, Cheng ZJ, Wu W, Sun B. The genetic associations of COVID-19 on genitourinary symptoms. Front Immunol 2023; 14:1216211. [PMID: 37415973 PMCID: PMC10319997 DOI: 10.3389/fimmu.2023.1216211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
Background Recently emerged reports indicated that patients with coronavirus disease 2019 (COVID-19) might experience novo genitourinary symptoms after discharge. Nevertheless, the causal associations and underlying mechanisms remain largely unclear. Methods Genome-wide association study (GWAS) statistics for COVID-19 and 28 genitourinary symptoms with consistent definitions were collected from the COVID-19 Host Genetic Initiative, FinnGen, and UK Biobanks. Mendelian randomization (MR) analyses were applied to explore the causal effects of COVID-19 on genitourinary symptoms by selecting single-nucleotide polymorphisms as instrumental variables. Meta-analyses were conducted to evaluate the combined causal effect. Molecular pathways connecting COVID-19 and its associated disorders were evaluated by weighted gene co-expression network analysis (WGCNA) and enrichment analyses to extract insights into the potential mechanisms underlying the connection. Results The MR and meta-analyses indicated that COVID-19 was causally associated with increased risk for calculus of the lower urinary tract (LUTC, OR: 1.2984 per doubling in odds of COVID-19, 95% CI: 1.0752-1.5680, p = 0.007) and sexual dysfunction (SD, OR: 1.0931, 95% CI: 1.0292-1.1610, p = 0.004). Intriguingly, COVID-19 might exert a slight causal protective effect on the progression of urinary tract infections (UTIs) and bladder cancer (BLCA). These results were robust to sensitivity analyses. Bioinformatic analyses indicated that the inflammatory-immune response module may mediate the links between COVID-19 and its associated disorders at the molecular level. Conclusions In response to post-COVID-19 symptoms, we recommend that COVID-19 patients should strengthen the prevention of LUTC and the monitoring of sexual function. Meanwhile, the positive effects of COVID-19 on UTIs and BLCA should attach equal importance.
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Affiliation(s)
- Zhenglin Chang
- Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Allergy and Clinical Immunology, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Laboratory, Guangzhou Laboratory, Guangzhou, China
| | - Lingyue An
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Min Lei
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhenfeng Song
- Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Allergy and Clinical Immunology, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jian Deng
- Department of General Surgery, Ziyang First People’s Hospital, Ziyang, Sichuan, China
| | - Ruizheng Tang
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhangkai J. Cheng
- Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Allergy and Clinical Immunology, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Laboratory, Guangzhou Laboratory, Guangzhou, China
| | - Wenqi Wu
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Baoqing Sun
- Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Allergy and Clinical Immunology, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Laboratory, Guangzhou Laboratory, Guangzhou, China
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The Application of Single-Cell RNA Sequencing in the Inflammatory Tumor Microenvironment. Biomolecules 2023; 13:biom13020344. [PMID: 36830713 PMCID: PMC9953711 DOI: 10.3390/biom13020344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The initiation and progression of tumors are complex. The cancer evolution-development hypothesis holds that the dysregulation of immune balance is caused by the synergistic effect of immune genetic factors and environmental factors that stimulate and maintain non-resolving inflammation. Throughout the cancer development process, this inflammation creates a microenvironment for the evolution and development of cancer. Research on the inflammatory tumor microenvironment (TME) explains the initiation and progression of cancer and guides anti-cancer immunotherapy. Single-cell RNA sequencing (scRNA-seq) can detect the transcription levels of cells at the single-cell resolution level, reveal the heterogeneity and evolutionary trajectory of infiltrated immune cells and cancer cells, and provide insight into the composition and function of each cell group in the inflammatory TME. This paper summarizes the application of scRNA-seq in inflammatory TME.
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