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Yan B, Chen Y, Wang Z, Li J, Wang R, Pan X, Li B, Li R. Analysis and identification of mRNAsi‑related expression signatures via RNA sequencing in lung cancer. Oncol Lett 2024; 28:549. [PMID: 39319211 PMCID: PMC11420643 DOI: 10.3892/ol.2024.14682] [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: 04/02/2024] [Accepted: 08/15/2024] [Indexed: 09/26/2024] Open
Abstract
High stemness index scores are associated with poor survival in patients with lung cancer. Studies on the mRNA expression-based stemness index (mRNAsi) are typically conducted using tumor tissues; however, mRNAsi-related expression signatures based on cell-free RNA (cfRNA) are yet to be comprehensively investigated. The present study aimed to elucidate the gene expression profiles of tumor stemness in lung cancer tissues and corresponding cfRNAs in blood, and to assess their links with immune infiltration. Tumor tissue, paracancerous tissue, peripheral blood and lymph node samples were collected from patients with stage I-III non-small cell lung cancer and RNA sequencing was performed. The TCGAbiolinks package was used to calculate the mRNAsi for each of these four types of sample. Weighted gene co-expression network analysis and differentially expressed gene analyses were performed to investigate mRNAsi-related genes, and pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology-based annotation system. In addition, the STAR-Fusion tool was used to detect fusion variants, and CIBERSORT was used to analyze the correlations of stemness signatures in tissues and blood with immune cell infiltration. The mRNAsi values in peripheral blood and lymph nodes were found to be higher than those in cancer tissues. 'Hematopoietic cell lineage' was the only KEGG pathway enriched in mRNAsi-related genes in both lung cancer tissues and peripheral blood. In addition, the protein tyrosine phosphatase receptor type C associated protein gene was the only gene commonly associated with the mRNAsi in these two types of sample. The expression of mRNAsi-related genes was increased in the dendritic and Treg cells in tumor tissues, but was elevated in Treg and CD8 cells in the blood. In conclusion, cfRNAs in the blood exhibit unique stemness signatures that have potential for use in the diagnosis of lung cancer.
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Affiliation(s)
- Bo Yan
- Clinical Research Unit, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200050, P.R. China
| | - Yong Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200050, P.R. China
| | - Zhouyu Wang
- Berry Oncology Corporation, Beijing 100102, P.R. China
| | - Jing Li
- Berry Oncology Corporation, Beijing 100102, P.R. China
| | - Ruiru Wang
- Berry Oncology Corporation, Beijing 100102, P.R. China
| | - Xufeng Pan
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200050, P.R. China
| | - Boyi Li
- Kanghui Biotechnology Corporation, Shenyang, Liaoning 110042, P.R. China
| | - Rong Li
- Clinical Research Unit, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200050, P.R. China
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Li J, Zou L, Ma H, Zhao J, Wang C, Li J, Hu G, Yang H, Wang B, Xu D, Xia Y, Jiang Y, Jiang X, Li N. Interpretable machine learning based on CT-derived extracellular volume fraction to predict pathological grading of hepatocellular carcinoma. Abdom Radiol (NY) 2024; 49:3383-3396. [PMID: 38703190 DOI: 10.1007/s00261-024-04313-9] [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: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 05/06/2024]
Abstract
PURPOSE To develop a non-invasive auxiliary assessment method based on CT-derived extracellular volume (ECV) to predict the pathological grading (PG) of hepatocellular carcinoma (HCC). METHODS The study retrospectively analyzed 238 patients who underwent HCC resection surgery between January 2013 and April 2023. Six machine learning algorithms were employed to construct predictive models for HCC PG: logistic regression, extreme gradient boosting, Light Gradient Boosting Machine (LightGBM), random forest, adaptive boosting, and Gaussian naive Bayes. Model performance was evaluated using receiver operating characteristic curve analysis, including area under the curve (AUC), sensitivity, specificity, accuracy, positive predictive value, negative predictive value, and F1 score. Calibration plots were used for visual evaluation of model calibration. Clinical decision curve analysis was performed to assess potential clinical utility by calculating net benefit. RESULTS 166 patients from Hospital A were allocated to the training set, while 72 patients from Hospital B (constituting 30.25% of the total sample) were assigned to the test set. The model achieved an AUC of 1.000 (95%CI: 1.000-1.000) in the training set and 0.927 (95%CI: 0.837-0.999) in the validation set, respectively. Ultimately, the model achieved an AUC of 0.909 (95%CI: 0.837-0.980) in the test set, with an accuracy of 0.778, sensitivity of 0.906, specificity of 0.789, negative predictive value of 0.556, and F1 score of 0.908. CONCLUSION This study successfully developed and validated a non-invasive auxiliary assessment method based on CT-derived ECV to predict the HCC PG, providing important supplementary information for clinical decision-making.
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Affiliation(s)
- Jie Li
- Department of Radiology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Bincheng District, Binzhou, 256600, China
| | - Linxuan Zou
- Department of Radiology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Bincheng District, Binzhou, 256600, China
| | - Heng Ma
- Department of Radiology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, 264000, China
| | - Jifu Zhao
- Department of Radiology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Bincheng District, Binzhou, 256600, China
| | - Chengyan Wang
- Department of Radiology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Bincheng District, Binzhou, 256600, China
| | - Jun Li
- Department of Radiology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264000, China
| | - Guangchao Hu
- School of Medical Imaging, Binzhou Medical University, No. 346 Guanhai Road, Laishan District, Yantai, 264003, China
| | - Haoran Yang
- School of Medical Imaging, Binzhou Medical University, No. 346 Guanhai Road, Laishan District, Yantai, 264003, China
| | - Beizhong Wang
- Department of Radiology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Bincheng District, Binzhou, 256600, China
| | - Donghao Xu
- School of Medical Imaging, Binzhou Medical University, No. 346 Guanhai Road, Laishan District, Yantai, 264003, China
| | - Yuanhao Xia
- Department of Radiology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, 264000, China
- School of Medical Imaging, Binzhou Medical University, No. 346 Guanhai Road, Laishan District, Yantai, 264003, China
| | - Yi Jiang
- Department of Vascular Interventional Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264000, China
| | - Xingyue Jiang
- Department of Radiology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Bincheng District, Binzhou, 256600, China.
| | - Naixuan Li
- Department of Vascular Interventional Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264000, China.
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Wu Y, Wu S, Chen Z, Yang E, Yu H, Zhang G, Lian X, Xu J. Machine learning and single-cell analysis identify the mitophagy-associated gene TOMM22 as a potential diagnostic biomarker for intervertebral disc degeneration. Heliyon 2024; 10:e37378. [PMID: 39296040 PMCID: PMC11407931 DOI: 10.1016/j.heliyon.2024.e37378] [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: 08/19/2024] [Accepted: 09/02/2024] [Indexed: 09/21/2024] Open
Abstract
Background Mitophagy selectively eliminates potentially cytotoxic and damaged mitochondria and effectively prevents excessive cytotoxicity from damaged mitochondria, thereby attenuating inflammatory and oxidative responses. However, the potential role of mitophagy in intervertebral disc degeneration remains to be elucidated. Methods The GSVA method, two machine learning methods (SVM-RFE algorithm and random forest), the CIBERSORT and MCPcounter methods, as well as the consensus clustering method and the WGCNA algorithm were used to analyze the involvement of mitophagy in intervertebral disc degeneration, the diagnostic value of mitophagy-associated genes in intervertebral disc degeneration, and the infiltration of immune cells, and identify the gene modules that were closely related to mitophagy. Single-cell analysis was used to detect mitophagy scores and TOMM22 expression, and pseudo-temporal analysis was used to explore the function of TOMM22 in nucleus pulposus cells. In addition, TOMM22 expression was compared between human normal and degenerated intervertebral disc tissue samples by immunohistochemistry and PCR. Results This study identified that the mitophagy pathway score was elevated in intervertebral disc degeneration compared with the normal condition. A strong link was present between mitophagy genes and immune cells, which may be used to typify intervertebral disc degeneration. The single-cell level showed that mitophagy-associated gene TOMM22 was highly expressed in medullary cells of the disease group. Further investigations indicated the upregulation of TOMM22 expression in late-stage nucleus pulposus cells and its role in cellular communication. In addition, human intervertebral disc tissue samples established that TOMM22 levels were higher in disc degeneration samples than in normal samples. Conclusions Our findings revealed that mitophagy may be used in the diagnosis of intervertebral disc degeneration and its typing, and TOMM22 is a molecule in this regard and may act as a potential diagnostic marker in intervertebral disc degeneration.
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Affiliation(s)
- Yinghao Wu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
| | - Shengting Wu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
| | - Zhiheng Chen
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
| | - Erzhu Yang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
| | - Haiyue Yu
- Bengbu Medical University, Anhui, 233030, PR China
| | - Guowang Zhang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
| | - XiaoFeng Lian
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
| | - JianGuang Xu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, PR China
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Chen R, Liu Y, Xie J. Construction of a pathomics model for predicting mRNAsi in lung adenocarcinoma and exploration of biological mechanism. Heliyon 2024; 10:e37100. [PMID: 39286147 PMCID: PMC11402732 DOI: 10.1016/j.heliyon.2024.e37100] [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: 05/08/2024] [Revised: 08/04/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Objective This study aimed to predict the level of stemness index (mRNAsi) and survival prognosis of lung adenocarcinoma (LUAD) using pathomics model. Methods From The Cancer Genome Atlas (TCGA) database, 327 LUAD patients were randomly assigned to a training set (n = 229) and a validation set (n = 98) for pathomics model development and evaluation. PyRadiomics was used to extract pathomics features, followed by feature selection using the mRMR-RFE algorithm. In the training set, Gradient Boosting Machine (GBM) was utilized to establish a model for predicting mRNAsi in LUAD. The model's predictive performance was evaluated using ROC curves, calibration curves, and decision curve analysis (DCA). Prognostic analysis was conducted using Kaplan-Meier curves and cox regression. Additionally, gene enrichment analysis, tumor microenvironment analysis, and tumor mutational burden (TMB) analysis were performed to explore the biological mechanisms underlying the pathomics prediction model. Results Multivariable cox analysis (HR = 1.488, 95 % CI 1.012-2.187, P = 0.043) identified mRNAsi as a prognostic risk factor for LUAD. A total of 465 pathomics features were extracted from TCGA-LUAD histopathological images, and ultimately, the most representative 8 features were selected to construct the predictive model. ROC curves demonstrated the significant predictive value of the model for mRNAsi in both the training set (AUC = 0.769) and the validation set (AUC = 0.757). Calibration curves and Hosmer-Lemeshow goodness-of-fit test showed good consistency between the model's prediction of mRNAsi levels and the actual values. DCA indicated a good net benefit of the model. The prediction of mRNAsi levels by the pathomics model is represented using the pathomics score (PS). PS was strongly associated with the prognosis of LUAD (HR = 1.496, 95 % CI 1.008-2.222, P = 0.046). Signaling pathways related to DNA replication and damage repair were significantly enriched in the high PS group. Prediction of immune therapy response indicated significantly reduced Dysfunction in the high PS group (P < 0.001). The high PS group exhibited higher TMB values (P < 0.001). Conclusions The predictive model constructed based on pathomics features can forecast the mRNAsi and survival risk of LUAD. This model holds promise to aid clinical practitioners in identifying high-risk patients and devising more optimized treatment plans for patients by jointly employing therapeutic strategies targeting cancer stem cells (CSCs).
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Affiliation(s)
- Rui Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No.1, Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Yuzhen Liu
- Department of Oncology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Junping Xie
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No.1, Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China
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Zhang G, Xiao Y, Liu H, Wu Y, Xue M, Li J. Integrated machine learning screened glutamine metabolism-associated biomarker SLC1A5 to predict immunotherapy response in hepatocellular carcinoma. Immunobiology 2024; 229:152841. [PMID: 39096658 DOI: 10.1016/j.imbio.2024.152841] [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: 06/14/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Hepatocellular carcinoma (HCC) stands as one of the most prevalent malignancies. While PD-1 immune checkpoint inhibitors have demonstrated promising therapeutic efficacy in HCC, not all patients exhibit a favorable response to these treatments. Glutamine is a crucial immune cell regulatory factor, and tumor cells exhibit glutamine dependence. In this study, HCC patients were divided into two subtypes (C1 and C2) based on glutamine metabolism-related genes via consensus clustering. The C1 pattern, in contrast to C2, was associated with a lower survival probability among HCC patients. Additionally, the C1 pattern exhibited higher proportions of patients with advanced tumor stages. The activity of C1 in glutamine metabolism and transport is significantly enhanced, while its oxidative phosphorylation activity is reduced. And, C1 was mainly involved in the progression-related pathway of HCC. Furthermore, C1 exhibited high levels of immunosuppressive cells, cytokine-receptor interactions and immune checkpoint genes, suggesting C1 as an immunosuppressive subtype. After stepwise selection based on integrated four machine learning methods, SLC1A5 was finally identified as the pivotal gene that distinguishes the subtypes. The expression of SLC1A5 was significantly positively correlated with immunosuppressive status. SLC1A5 showed the most significant correlation with macrophage infiltration, and this correlation was confirmed through the RNA-seq data of CLCA project and our cohort. Low-SLC1A5-expression samples had better immunogenicity and responsiveness to immunotherapy. As expected, SubMap and survival analysis indicated that individuals with low SLC1A5 expression were more responsive to anti-PD1 therapy. Collectively, this study categorized HCC patients based on glutamine metabolism-related genes and proposed two subclasses with different clinical traits, biological behavior, and immune status. Machine learning was utilized to identify the hub gene SLC1A5 for HCC classification, which also could predict immunotherapy response.
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Affiliation(s)
- Guixiong Zhang
- Department of Interventional Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province 510080, PR China
| | - Yitai Xiao
- Department of Endoscopy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province 510060, PR China
| | - Hang Liu
- Department of Interventional Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province 510080, PR China
| | - Yanqin Wu
- Department of Interventional Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province 510080, PR China
| | - Miao Xue
- Department of Interventional Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province 510080, PR China
| | - Jiaping Li
- Department of Interventional Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province 510080, PR China.
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Ghosh S, Zhao X, Alim M, Brudno M, Bhat M. Artificial intelligence applied to 'omics data in liver disease: towards a personalised approach for diagnosis, prognosis and treatment. Gut 2024:gutjnl-2023-331740. [PMID: 39174307 DOI: 10.1136/gutjnl-2023-331740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/24/2024] [Indexed: 08/24/2024]
Abstract
Advancements in omics technologies and artificial intelligence (AI) methodologies are fuelling our progress towards personalised diagnosis, prognosis and treatment strategies in hepatology. This review provides a comprehensive overview of the current landscape of AI methods used for analysis of omics data in liver diseases. We present an overview of the prevalence of different omics levels across various liver diseases, as well as categorise the AI methodology used across the studies. Specifically, we highlight the predominance of transcriptomic and genomic profiling and the relatively sparse exploration of other levels such as the proteome and methylome, which represent untapped potential for novel insights. Publicly available database initiatives such as The Cancer Genome Atlas and The International Cancer Genome Consortium have paved the way for advancements in the diagnosis and treatment of hepatocellular carcinoma. However, the same availability of large omics datasets remains limited for other liver diseases. Furthermore, the application of sophisticated AI methods to handle the complexities of multiomics datasets requires substantial data to train and validate the models and faces challenges in achieving bias-free results with clinical utility. Strategies to address the paucity of data and capitalise on opportunities are discussed. Given the substantial global burden of chronic liver diseases, it is imperative that multicentre collaborations be established to generate large-scale omics data for early disease recognition and intervention. Exploring advanced AI methods is also necessary to maximise the potential of these datasets and improve early detection and personalised treatment strategies.
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Affiliation(s)
- Soumita Ghosh
- Transplant AI Initiative, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Xun Zhao
- Transplant AI Initiative, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Mouaid Alim
- Transplant AI Initiative, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Vector Institute of Artificial Intelligence, Toronto, Ontario, Canada
| | - Mamatha Bhat
- Transplant AI Initiative, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
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Chen Y, Han K, Liu Y, Wang Q, Wu Y, Chen S, Yu J, Luo Y, Tan L. Identification of effective diagnostic genes and immune cell infiltration characteristics in small cell lung cancer by integrating bioinformatics analysis and machine learning algorithms. Saudi Med J 2024; 45:771-782. [PMID: 39074893 PMCID: PMC11288485 DOI: 10.15537/smj.2024.45.8.20240170] [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: 03/04/2024] [Accepted: 07/04/2024] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVES To identify potential diagnostic markers for small cell lung cancer (SCLC) and investigate the correlation with immune cell infiltration. METHODS GSE149507 and GSE6044 were used as the training group, while GSE108055 served as validation group A and GSE73160 served as validation group B. Differentially expressed genes (DEGs) were identified and analyzed for functional enrichment. Machine learning (ML) was used to identify candidate diagnostic genes for SCLC. The area under the receiver operating characteristic curves was applied to assess diagnostic efficacy. Immune cell infiltration analyses were carried out. RESULTS There were 181 DEGs identified. The gene ontology analysis showed that DEGs were enriched in 455 functional annotations, some of which were associated with immunity. The kyoto encyclopedia of genes and genomes analysis revealed that there were 9 signaling pathways enriched. The disease ontology analysis indicated that DEGs were related to 116 diseases. The gene set enrichment analysis results displayed multiple items closely related to immunity. ZWINT and NRCAM were screened using ML and further validated as diagnostic genes. Significant differences were observed in SCLC with normal lung tissue samples among immune cell infiltration characteristics. Strong associations were found between the diagnostic genes and immune cell infiltration. CONCLUSION This study identified 2 diagnostic genes, ZWINT and NRCAM, that were related to immune cell infiltration by integrating bioinformatics analysis and ML algorithms. These genes could serve as potential diagnostic biomarkers and provide possible molecular targets for immunotherapy in SCLC.
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Affiliation(s)
- Yinyi Chen
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Kexin Han
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Yanzhao Liu
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Qunxia Wang
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Yang Wu
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Simei Chen
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Jianlin Yu
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Yi Luo
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
| | - Liming Tan
- From the Department of Clinical Laboratory (Chen, Han, Liu, Wang, Wu, Yu, Tan); from the Department of Blood Transfusion (Chen), The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, and from the Department of Clinical Laboratory (Luo), The Second Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Jiangxi, China.
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Wu H, Yang L, Yuan J, Zhang L, Tao Q, Yin L, Yu X, Lin Y. Potential therapeutic targets for pelvic organ prolapse: insights from key genes related to blood vessel development. Front Med (Lausanne) 2024; 11:1435135. [PMID: 39118664 PMCID: PMC11306185 DOI: 10.3389/fmed.2024.1435135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024] Open
Abstract
Objective Pelvic organ prolapse (POP) is a disease in which pelvic floor support structures are dysfunctional due to disruption of the extracellular matrix (ECM). The vascular system is essential for maintaining ECM homeostasis. Therefore, this study explored the potential mechanism of blood vessel development-related genes (BVDRGs) in POP. Methods POP-related datasets and BVDRGs were included in this study. Differentially expressed genes (DEGs) between the POP and control groups were first identified in the GSE12852 and GSE208271 datasets, and DE-BVDRGs were identified by determining the intersection of these DEGs and BVDRGs. Subsequently, the feature genes were evaluated by machine learning. Feature genes with consistent expression trends in the GSE12852 and GSE208271 datasets were considered key genes. Afterward, the overall diagnostic efficacy of key genes in POP was evaluated through receiver operating characteristic (ROC) curve analysis. Based on the key genes, enrichment analysis, immune infiltration analysis and regulatory network construction were performed to elucidate the molecular mechanisms underlying the functions of the key genes in POP. Results A total of 888 DEGs1 and 643 DEGs2 were identified in the GSE12852 and GSE208271 datasets, and 26 candidate genes and 4 DE-BVDRGs were identified. Furthermore, Hyaluronan synthase 2 (HAS2), Matrix metalloproteinase 19 (MMP19) and Plexin Domain Containing 1 (PLXDC1) were identified as key genes in POP and had promising value for diagnosing POP (AUC > 0.8). Additional research revealed that the key genes were predominantly implicated in immune cell activation, chemotaxis, and cytokine release via the chemokine signaling pathway, the Nod-like receptor signaling pathway, and the Toll-like receptor signaling pathway. Analysis of immune cell infiltration confirmed a decrease in the proportion of plasma cells in POP, and MMP19 expression showed a significant negative correlation with plasma cell numbers. In addition, regulatory network analysis revealed that MALAT1 (a lncRNA) targeted hsa-miR-503-5p, hsa-miR-23a-3p and hsa-miR-129-5p to simultaneously regulate three key genes. Conclusion We identified three key BVDRGs (HAS2, MMP19 and PLXDC1) related to the ECM in POP, providing markers for diagnostic studies and investigations of the molecular mechanism of POP.
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Affiliation(s)
- Huaye Wu
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Yang
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiakun Yuan
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ling Zhang
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qin Tao
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Litong Yin
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xia Yu
- Department of Clinical Laboratory, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yonghong Lin
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Li H, Zhou C, Wang C, Li B, Song Y, Yang B, Zhang Y, Li X, Rao M, Zhang J, Su K, He K, Han Y. Lasso-Cox interpretable model of AFP-negative hepatocellular carcinoma. Clin Transl Oncol 2024:10.1007/s12094-024-03588-0. [PMID: 38965191 DOI: 10.1007/s12094-024-03588-0] [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: 05/29/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND In AFP-negative hepatocellular carcinoma patients, markers for predicting tumor progression or prognosis are limited. Therefore, our objective is to establish an optimal predicet model for this subset of patients, utilizing interpretable methods to enhance the accuracy of HCC prognosis prediction. METHODS We recruited a total of 508 AFP-negative HCC patients in this study, modeling with randomly divided training set and validated with validation set. At the same time, 86 patients treated in different time periods were used as internal validation. After comparing the cox model with the random forest model based on Lasso regression, we have chosen the former to build our model. This model has been interpreted with SHAP values and validated using ROC, DCA. Additionally, we have reconfirmed the model's effectiveness by employing an internal validation set of independent periods. Subsequently, we have established a risk stratification system. RESULTS The AUC values of the Lasso-Cox model at 1, 2, and 3 years were 0.807, 0.846, and 0.803, and the AUC values of the Lasso-RSF model at 1, 2, and 3 years were 0.783, 0.829, and 0.776. Lasso-Cox model was finally used to predict the prognosis of AFP-negative HCC patients in this study. And BCLC stage, gamma-glutamyl transferase (GGT), diameter of tumor, lung metastases (LM), albumin (ALB), alkaline phosphatase (ALP), and the number of tumors were included in the model. The validation set and the separate internal validation set both indicate that the model is stable and accurate. Using risk factors to establish risk stratification, we observed that the survival time of the low-risk group, the middle-risk group, and the high-risk group decreased gradually, with significant differences among the three groups. CONCLUSION The Lasso-Cox model based on AFP-negative HCC showed good predictive performance for liver cancer. SHAP explained the model for further clinical application.
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Affiliation(s)
- Han Li
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
| | - Chengyuan Zhou
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
| | - Chenjie Wang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
| | - Bo Li
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Yanqiong Song
- School of Medicine, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
| | - Yan Zhang
- Department of Oncology, Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, China
| | - Xueting Li
- Department of Oncology, 363 Hospital, Chengdu, China
| | - Mingyue Rao
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
| | - Jianwen Zhang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
| | - Ke Su
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China
- Department of Radiation Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kun He
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China.
| | - Yunwei Han
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Taiping Street, Luzhou, 646000, Sichuan Province, China.
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10
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Chen Y, Li X, Sun R, Yang F, Tian W, Huang Q. Screening and experimental validation of diagnostic gene in ulcerative colitis with anti-TNF-α therapy. IUBMB Life 2024; 76:451-463. [PMID: 38269750 DOI: 10.1002/iub.2807] [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: 07/13/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
In clinical practice, the diagnosis of ulcerative colitis (UC) mainly relies on a comprehensive analysis of a series of signs and symptoms of patients. The current biomarkers for diagnosis of UC and prognostic prediction of anti-TNF-α therapy are inaccurate. The present study aimed to perform an integrative analysis of gene expression profiles in patients with UC. A total of seven datasets from the GEO database that met our strict inclusion criteria were included. After identifying differentially expressed genes (DEGs) between UC patients and healthy individuals, the diagnostic and prognostic utility of the DEGs were then analyzed via least absolute shrinkage and selection operator and support-vector machine recursive feature elimination. Subgroup analyses of the treated and untreated groups, as well as the treatment-response group and non-response group, were also performed. Furthermore, the relationship between the expressions of UC-related genes and infiltration of immune cells in the course of treatment was also investigated. Immunohistochemical (IHC) assay was used to verify the gene expression in inflamed UC tissues. When considering all the applied methods, DUOX2, PI3, S100P, MMP7, and S100A8 had priority to be defined as the characteristic genes among DEGs. The area under curve (AUC) of the five genes, which were all consistently over-expressed, based on an external validation dataset, were all above 0.94 for UC diagnosis. Four of the five genes (DUOX2, PI3, MMP7, and S100A8) were down-regulated between treatment-responsive and nonresponsive patients. A significant difference was also observed concerning the infiltration of immune cells, including macrophage and neutrophil, between the two groups (treatment responsive and nonresponsive). The changes in the expression of DUOX2 and MMP7 based on the IHC assay were highly consistent with the results obtained in the current study. This confirmed the mild to moderate diagnostic and predictive value of DUOX2 and MMP7 in patients with UC. The conducted analyses showed that the expression profile of the five identified biomarkers accurately detects UC, whereas four of the five genes evidently predicted the response to anti-TNF-α therapy.
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Affiliation(s)
- Yuan Chen
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Xinfang Li
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Ran Sun
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Fan Yang
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Weiliang Tian
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Qian Huang
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
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11
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Yan X, Hu Z, Li X, Liang J, Zheng J, Gong J, Hu K, Sui X, Li R. Systemic analysis of the prognostic significance and interaction network of miR-26b-3p in cholangiocarcinoma. Appl Biochem Biotechnol 2024; 196:4166-4187. [PMID: 37914963 DOI: 10.1007/s12010-023-04753-x] [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] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
MicroRNAs (miRNAs) reportedly play significant roles in the progression of various cancers and hold huge potential as both diagnostic tools and therapeutic targets. Given the ongoing uncertainty surrounding the precise functions of several miRNAs in cholangiocarcinoma (CCA), this research undertakes a comprehensive analysis of CCA data sourced from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The present study identified a novel miRNA, specifically miR-26b-3p, which exhibited prognostic value for individuals with CCA. Notably, miR-26b-3p was upregulated within CCA samples, with an inverse correlation established with patient prognosis (Hazard Ratio = 8.19, p = 0.018). Through a combination of functional enrichment analysis, analysis of the LncRNA-miR-26b-3p-mRNA interaction network, and validation by qRT PCR and western blotting, this study uncovered the potential of miR-26b-3p in potentiating the malignant progression of CCA via regulation of essential genes (including PSMD14, XAB2, SLC4A4) implicated in processes such as endoplasmic reticulum (ER) stress and responses to misfolded proteins. Our findings introduce novel and valuable insights that position miR-26b-3p-associated genes as promising biomarkers for the diagnosis and treatment of CCA.
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Affiliation(s)
- Xijing Yan
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
- Department of Breast and Thyroid Surgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Zhongying Hu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xuejiao Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jinliang Liang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jun Zheng
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jiao Gong
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Kunpeng Hu
- Department of Breast and Thyroid Surgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Xin Sui
- Surgical ICU, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Rong Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
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Wu Q, Lu M, Ouyang H, Zhou T, Lei J, Wang P, Wang W. CDKL3 is a promising biomarker for diagnosis and prognosis prediction in patients with hepatocellular carcinoma. Exp Biol Med (Maywood) 2024; 249:10106. [PMID: 38993199 PMCID: PMC11237920 DOI: 10.3389/ebm.2024.10106] [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: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 07/13/2024] Open
Abstract
Cyclin-dependent kinase-like 3 (CDKL3) has been identified as an oncogene in certain types of tumors. Nonetheless, its function in hepatocellular carcinoma (HCC) is poorly understood. In this study, we conducted a comprehensive analysis of CDKL3 based on data from the HCC cohort of The Cancer Genome Atlas (TCGA). Our analysis included gene expression, diagnosis, prognosis, functional enrichment, tumor microenvironment and metabolic characteristics, tumor burden, mRNA expression-based stemness, alternative splicing, and prediction of therapy response. Additionally, we performed a cell counting kit-8 assay, TdT-mediated dUTP nick-end Labeling staining, migration assay, wound healing assay, colony formation assay, and nude mouse experiments to confirm the functional relevance of CDKL3 in HCC. Our findings showed that CDKL3 was significantly upregulated in HCC patients compared to controls. Various bioinformatic analyses suggested that CDKL3 could serve as a potential marker for HCC diagnosis and prognosis. Furthermore, CDKL3 was found to be involved in various mechanisms linked to the development of HCC, including copy number variation, tumor burden, genomic heterogeneity, cancer stemness, and alternative splicing of CDKL3. Notably, CDKL3 was also closely correlated with tumor immune cell infiltration and the expression of immune checkpoint markers. Additionally, CDKL3 was shown to independently function as a risk predictor for overall survival in HCC patients by multivariate Cox regression analysis. Furthermore, the knockdown of CDKL3 significantly inhibited cell proliferation in vitro and in vivo, indicating its role as an oncogene in HCC. Taken together, our findings suggest that CDKL3 shows promise as a biomarker for the detection and treatment outcome prediction of HCC patients.
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Affiliation(s)
- Qingsi Wu
- Department of Blood Transfusion, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Microbiology and Parasitology, Hefei, Anhui, China
| | - Mengran Lu
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Huijuan Ouyang
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Tingting Zhou
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Jingyuan Lei
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Panpan Wang
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Wei Wang
- Department of Gastroenterology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
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13
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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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Zhang X, Zheng P, Meng B, Zhuang H, Lu B, Yao J, Han F, Luo S. Histamine-related genes participate in the establishment of an immunosuppressive microenvironment and impact the immunotherapy response in hepatocellular carcinoma. Clin Exp Med 2024; 24:129. [PMID: 38884870 PMCID: PMC11182831 DOI: 10.1007/s10238-024-01399-9] [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: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Chronic inflammation is pivotal in the pathogenesis of hepatocellular carcinoma (HCC). Histamine is a biologically active substance that amplifies the inflammatory and immune response and serves as a neurotransmitter. However, knowledge of histamine's role in HCC and its effects on immunotherapy remains lacking. We focused on histamine-related genes to investigate their potential role in HCC. The RNA-seq data and clinical information regarding HCC were obtained from The Cancer Genome Atlas (TCGA). After identifying the differentially expressed genes, we constructed a signature using the univariate Cox proportional hazard regression and least absolute shrinkage and selection operator (LASSO) analyses. The signature's predictive performance was evaluated using a receiver operating characteristic curve (ROC) analysis. Furthermore, drug sensitivity, immunotherapy effects, and enrichment analyses were conducted. Histamine-related gene expression in HCC was confirmed using quantitative real-time polymerase chain reaction (qRT-PCR). A histamine-related gene prognostic signature (HRGPS) was developed in TCGA. Time-dependent ROC and Kaplan-Meier survival analyses demonstrated the signature's strong predictive power. Importantly, patients in high-risk groups exhibited a higher frequency of TP53 mutations, elevated immune checkpoint-related gene expression, and increased infiltration of immunosuppressive cells-indicating a potentially favorable response to immunotherapy. In addition, drug sensitivity analysis revealed that the signature could effectively predict chemotherapy efficacy and sensitivity. qRT-PCR results validated histamine-related gene overexpression in HCC. Our findings demonstrate that inhibiting histamine-related genes and signaling pathways can impact the therapeutic effect of anti-PD-1/PD-L1. The precise predictive ability of our signature in determining the response to different therapeutic options highlights its potential clinical significance.
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Affiliation(s)
- Xianzhou Zhang
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Peng Zheng
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Bo Meng
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Hao Zhuang
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Bing Lu
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Jun Yao
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Feng Han
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China.
| | - Suxia Luo
- Department of Hepatic Biliary Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008, China.
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Liu Z, Yang L, Liu C, Wang Z, Xu W, Lu J, Wang C, Xu X. Identification and validation of immune-related gene signature models for predicting prognosis and immunotherapy response in hepatocellular carcinoma. Front Immunol 2024; 15:1371829. [PMID: 38933262 PMCID: PMC11199539 DOI: 10.3389/fimmu.2024.1371829] [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: 01/17/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Background This study seeks to enhance the accuracy and efficiency of clinical diagnosis and therapeutic decision-making in hepatocellular carcinoma (HCC), as well as to optimize the assessment of immunotherapy response. Methods A training set comprising 305 HCC cases was obtained from The Cancer Genome Atlas (TCGA) database. Initially, a screening process was undertaken to identify prognostically significant immune-related genes (IRGs), followed by the application of logistic regression and least absolute shrinkage and selection operator (LASSO) regression methods for gene modeling. Subsequently, the final model was constructed using support vector machines-recursive feature elimination (SVM-RFE). Following model evaluation, quantitative polymerase chain reaction (qPCR) was employed to examine the gene expression profiles in tissue samples obtained from our cohort of 54 patients with HCC and an independent cohort of 231 patients, and the prognostic relevance of the model was substantiated. Thereafter, the association of the model with the immune responses was examined, and its predictive value regarding the efficacy of immunotherapy was corroborated through studies involving three cohorts undergoing immunotherapy. Finally, the study uncovered the potential mechanism by which the model contributed to prognosticating HCC outcomes and assessing immunotherapy effectiveness. Results SVM-RFE modeling was applied to develop an OS prognostic model based on six IRGs (CMTM7, HDAC1, HRAS, PSMD1, RAET1E, and TXLNA). The performance of the model was assessed by AUC values on the ROC curves, resulting in values of 0.83, 0.73, and 0.75 for the predictions at 1, 3, and 5 years, respectively. A marked difference in OS outcomes was noted when comparing the high-risk group (HRG) with the low-risk group (LRG), as demonstrated in both the initial training set (P <0.0001) and the subsequent validation cohort (P <0.0001). Additionally, the SVMRS in the HRG demonstrated a notable positive correlation with key immune checkpoint genes (CTLA-4, PD-1, and PD-L1). The results obtained from the examination of three cohorts undergoing immunotherapy affirmed the potential capability of this model in predicting immunotherapy effectiveness. Conclusions The HCC predictive model developed in this study, comprising six genes, demonstrates a robust capability to predict the OS of patients with HCC and immunotherapy effectiveness in tumor management.
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Affiliation(s)
- Zhiqiang Liu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lingge Yang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chun Liu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zicheng Wang
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wendi Xu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jueliang Lu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chunmeng Wang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xundi Xu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of General Surgery, South China Hospital of Shenzhen University, Shenzhen, China
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Jiang W, Jiang L, Zhao X, Liu Y, Sun H, Zhou X, Liu Y, Huang S. Bioinformatics Analysis Reveals HIST1H2BH as a Novel Diagnostic Biomarker for Atrial Fibrillation-Related Cardiogenic Thromboembolic Stroke. Mol Biotechnol 2024:10.1007/s12033-024-01187-6. [PMID: 38825608 DOI: 10.1007/s12033-024-01187-6] [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: 10/27/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
Atrial fibrillation (AF) is a significant precursor to cerebral embolism. Our study sought to unearth new diagnostic biomarkers for atrial fibrillation-related cerebral embolism (AF-CE) by meticulously examining multiple GEO datasets and meta-analysis. The gene expression omnibus (GEO) database provided RNA sequencing data associated with AF and stroke. We began by pinpointing genes with varied expressions in AF-CE patient blood samples. A meta-analysis was subsequently undertaken using several RNA sequencing datasets to verify these genes. LASSO regression discerned key genes for AF-CE, with their diagnostic prowess verified through ROC curve examination. Active signaling pathways within stroke patients were discerned via GO and KEGG enrichment, with PPI interactions detailing gene interplay. Differential gene analysis revealed an upregulation of sixteen genes and a downregulation of four in stroke patient blood samples. Eight genes showcased varied expression in the meta-analysis. LASSO regression zeroed in on five of these, culminating in HIST1H2BH's identification as a characteristic gene. HIST1H2BH's prowess in predicting AF-CE was confirmed through ROC. Integrin signaling, platelet activation, ECM interactions, and the PI3K-Akt pathway were found active in stroke victims. HIST1H2BH's interaction with the notably upregulated ITGA2B was spotlighted by PPI. Additionally, HIST1H2BH exhibited links with NK cells and eosinophils. HIST1H2BH emerges as an insightful diagnostic beacon for AF-CE. Its presence, post AF, potentially modulates pathways, accentuating platelet activation and consequent thrombus generation, leading to cerebral embolism.
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Affiliation(s)
- Wenbing Jiang
- Department of Cardiology, Wenzhou Integrated Traditional Chinese and Western Medicine Hospital, No.75 Jinxiu Road, Lucheng District, Wenzhou, 325000, Zhejiang Province, People's Republic of China.
| | - Lelin Jiang
- Second Clinical College of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Xiaoli Zhao
- Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Yiying Liu
- Postgraduate Training Base Allianceof Wenzhou Medical University (Wenzhou Central Hosptial), Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Huanghui Sun
- The Dingli Clinical College of Wenzhou Medical University, Heart Function Examination Room, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Xinlang Zhou
- Department of Cardiology, Wenzhou Integrated Traditional Chinese and Western Medicine Hospital, No.75 Jinxiu Road, Lucheng District, Wenzhou, 325000, Zhejiang Province, People's Republic of China
| | - Yin Liu
- Department of Cardiology, Wenzhou Integrated Traditional Chinese and Western Medicine Hospital, No.75 Jinxiu Road, Lucheng District, Wenzhou, 325000, Zhejiang Province, People's Republic of China
| | - Shu'se Huang
- Department of Cardiology, Wenzhou Integrated Traditional Chinese and Western Medicine Hospital, No.75 Jinxiu Road, Lucheng District, Wenzhou, 325000, Zhejiang Province, People's Republic of China
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Mohr R, Tacke F, Roderburg C. Letter: Presence of progression or absence of response? Alternative trial designs for immunotherapy of advanced hepatocellular carcinoma. Authors' reply. Aliment Pharmacol Ther 2024; 59:1465-1466. [PMID: 38711357 DOI: 10.1111/apt.18008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
LINKED CONTENTThis article is linked to Jost‐Brinkmann et al papers. To view these articles, visit https://doi.org/10.1111/apt.17441 and https://doi.org/10.1111/apt.17985
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Affiliation(s)
- Raphael Mohr
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Roderburg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Karimi-Fard A, Saidi A, TohidFar M, Emami SN. Novel candidate genes for environmental stresses response in Synechocystis sp. PCC 6803 revealed by machine learning algorithms. Braz J Microbiol 2024; 55:1219-1229. [PMID: 38705959 PMCID: PMC11153407 DOI: 10.1007/s42770-024-01338-6] [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: 10/18/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Cyanobacteria have developed acclimation strategies to adapt to harsh environments, making them a model organism. Understanding the molecular mechanisms of tolerance to abiotic stresses can help elucidate how cells change their gene expression patterns in response to stress. Recent advances in sequencing techniques and bioinformatics analysis methods have led to the discovery of many genes involved in stress response in organisms. The Synechocystis sp. PCC 6803 is a suitable microorganism for studying transcriptome response under environmental stress. Therefore, for the first time, we employed two effective feature selection techniques namely and support vector machine recursive feature elimination (SVM-RFE) and LASSO (Least Absolute Shrinkage Selector Operator) to pinpoint the crucial genes responsive to environmental stresses in Synechocystis sp. PCC 6803. We applied these algorithms of machine learning to analyze the transcriptomic data of Synechocystis sp. PCC 6803 under distinct conditions, encompassing light, salt and iron stress conditions. Seven candidate genes namely sll1862, slr0650, sll0760, slr0091, ssl3044, slr1285, and slr1687 were selected by both LASSO and SVM-RFE algorithms. RNA-seq analysis was performed to validate the efficiency of our feature selection approach in selecting the most important genes. The RNA-seq analysis revealed significantly high expression for five genes namely sll1862, slr1687, ssl3044, slr1285, and slr0650 under ion stress condition. Among these five genes, ssl3044 and slr0650 could be introduced as new potential candidate genes for further confirmatory genetic studies, to determine their roles in their response to abiotic stresses.
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Affiliation(s)
- Abbas Karimi-Fard
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Masoud TohidFar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Seyedeh Noushin Emami
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Shen H, Chen Y, Xu M, Zhou J, Huang C, Wang Z, Shao Y, Zhang H, Lu Y, Li S, Fu Z. Cellular senescence gene TACC3 associated with colorectal cancer risk via genetic and DNA methylated alteration. Arch Toxicol 2024; 98:1499-1513. [PMID: 38480537 DOI: 10.1007/s00204-024-03702-9] [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: 11/19/2023] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
Cell senescence genes play a vital role in the pathogenesis of colorectal cancer, a process that may involve the triggering of genetic variations and reversible phenotypes caused by epigenetic modifications. However, the specific regulatory mechanisms remain unclear. Using CellAge and The Cancer Genome Atlas databases and in-house RNA-seq data, DNA methylation-modified cellular senescence genes (DMCSGs) were validated by Support Vector Machine and correlation analyses. In 1150 cases and 1342 controls, we identified colorectal cancer risk variants in DMCSGs. The regulatory effects of gene, variant, and DNA methylation were explored through dual-luciferase and 5-azacytidine treatment experiments, complemented by multiple database analyses. Biological functions of key gene were evaluated via cell proliferation assays, SA-β-gal staining, senescence marker detection, and immune infiltration analyses. The genetic variant rs4558926 in the downstream of TACC3 was significantly associated with colorectal cancer risk (OR = 1.35, P = 3.22 × 10-4). TACC3 mRNA expression increased due to rs4558926 C > G and decreased DNA methylation levels. The CpG sites in the TACC3 promoter region were regulated by rs4558926. TACC3 knockdown decreased proliferation and senescence in colorectal cancer cells. In addition, subjects with high-TACC3 expression presented an immunosuppressive microenvironment. These findings provide insights into the involvement of genetic variants of cellular senescence genes in the development and progression of colorectal cancer.
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Affiliation(s)
- Hengyang Shen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Menghuan Xu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jieyu Zhou
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changzhi Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenling Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Shao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongqiang Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Lu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shuwei Li
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
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20
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Zhang W, Song LN, You YF, Qi FN, Cui XH, Yi MX, Zhu G, Chang RA, Zhang HJ. Application of artificial intelligence in the prediction of immunotherapy efficacy in hepatocellular carcinoma: Current status and prospects. Artif Intell Gastroenterol 2024; 5:90096. [DOI: 10.35712/aig.v5.i1.90096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/28/2024] [Accepted: 03/12/2024] [Indexed: 04/29/2024] Open
Abstract
Artificial Intelligence (AI) has increased as a potent tool in medicine, with promising oncology applications. The emergence of immunotherapy has transformed the treatment terrain for hepatocellular carcinoma (HCC), offering new hope to patients with this challenging malignancy. This article examines the role and future of AI in forecasting the effectiveness of immunotherapy in HCC. We highlight the potential of AI to revolutionize the prediction of therapy response, thus improving patient selection and clinical outcomes. The article further outlines the challenges and future research directions in this emerging field.
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Affiliation(s)
- Wei Zhang
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Li-Ning Song
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Yun-Fei You
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Feng-Nan Qi
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Xiao-Hong Cui
- Department of General Surgery, Shanghai Electric Power Hospital, Shanghai 200050, China
| | - Ming-Xun Yi
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ren-An Chang
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Hai-Jian Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Research Center of Clinical Medicine, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
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21
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Gao W, Zhou J, Huang J, Zhang Z, Chen W, Zhang R, Kang T, Liao D, Zhong L. Up-regulation of RAN by MYBL2 maintains osteosarcoma cancer stem-like cells population during heterogeneous tumor generation. Cancer Lett 2024; 586:216708. [PMID: 38336287 DOI: 10.1016/j.canlet.2024.216708] [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: 12/04/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Intratumor heterogeneity is one of the major features of cancers, leading to aggressive disease and treatment failure. Cancer stem-like cells (CSCs) are believed to give rise to the heterogeneous cell types within tumors. Hence, understanding the regulatory mechanism underlying the recurrence process of heterogeneous tumor by CSCs could facilitate the development of CSC-targeted therapies. Here, utilizing single-cell transcriptomics, we present the molecular profile of osteosarcoma CSCs-derived heterogeneous tumors consisting of CSC clusters, osteoprogenitor and differentiated cell types, such as pre-osteoblasts, osteoblasts and chondroblasts. Furthermore, by constructing the comprehensive map of modulated genes during CSCs self-renewal and differentiation, we identify RAN exhibiting specific peak expression in osteosarcoma CSCs clusters which is transcriptionally up-regulated by MYBL2. Functionality, MYBL2-RAN pathway promotes the CSCs self-renewal by enhancing the nuclear accumulation of MYC protein, which in turn boosts the overexpression of RAN as a positive feedback. Importantly, blockage of MYBL2-RAN pathway sensitizes CSCs to cisplatin treatment and synergistically enhanced the cisplatin-induced cytotoxicity. Both MYBL2 and RAN are highly expressed in clinical osteosarcoma tissues which indicate poor prognosis. Collectively, our study provides advanced insights into the regeneration process of heterogeneous tumor originating from CSCs and highlights the MYBL2-RAN pathway as a promising target for CSC-based therapy in osteosarcoma.
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Affiliation(s)
- Weijie Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, PR China
| | - Jing Zhou
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, School of Medicine, Hubei Polytechnic University, Huangshi, PR China
| | - Jintao Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Zhiguang Zhang
- Sun Yat-sen University School of Medicine, Shenzhen, PR China
| | - Wanqi Chen
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, PR China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Dan Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Li Zhong
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, PR China.
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22
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Wang W, Wang W, Zhang D, Zeng P, Wang Y, Lei M, Hong Y, Cai C. Creation of a machine learning-based prognostic prediction model for various subtypes of laryngeal cancer. Sci Rep 2024; 14:6484. [PMID: 38499632 PMCID: PMC10948902 DOI: 10.1038/s41598-024-56687-x] [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: 09/27/2023] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
Depending on the source of the blastophore, there are various subtypes of laryngeal cancer, each with a unique metastatic risk and prognosis. The forecasting of their prognosis is a pressing issue that needs to be resolved. This study comprised 5953 patients with glottic carcinoma and 4465 individuals with non-glottic type (supraglottic and subglottic). Five clinicopathological characteristics of glottic and non-glottic carcinoma were screened using univariate and multivariate regression for CoxPH (Cox proportional hazards); for other models, 10 (glottic) and 11 (non-glottic) clinicopathological characteristics were selected using least absolute shrinkage and selection operator (LASSO) regression analysis, respectively; the corresponding survival models were established; and the best model was evaluated. We discovered that RSF (Random survival forest) was a superior model for both glottic and non-glottic carcinoma, with a projected concordance index (C-index) of 0.687 for glottic and 0.657 for non-glottic, respectively. The integrated Brier score (IBS) of their 1-year, 3-year, and 5-year time points is, respectively, 0.116, 0.182, 0.195 (glottic), and 0.130, 0.215, 0.220 (non-glottic), demonstrating the model's effective correction. We represented significant variables in a Shapley Additive Explanations (SHAP) plot. The two models are then combined to predict the prognosis for two distinct individuals, which has some effectiveness in predicting prognosis. For our investigation, we established separate models for glottic carcinoma and non-glottic carcinoma that were most effective at predicting survival. RSF is used to evaluate both glottic and non-glottic cancer, and it has a considerable impact on patient prognosis and risk factor prediction.
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Affiliation(s)
- Wei Wang
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- School of Medicine, Xiamen University, Xiamen, China
| | - Wenhui Wang
- School of Medicine, Xiamen University, Xiamen, China
| | | | - Peiji Zeng
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yue Wang
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Min Lei
- School of Medicine, Xiamen University, Xiamen, China
| | - Yongjun Hong
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chengfu Cai
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
- School of Medicine, Xiamen University, Xiamen, China.
- Otorhinolaryngology Head and Neck Surgery, Xiamen Medical College Affiliated Haicang Hospital, Xiamen, China.
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Li J, Jiang H, Zhu Y, Ma Z, Li B, Dong J, Xiao C, Hu A. Fine particulate matter (PM 2.5) induces the stem cell-like properties of hepatocellular carcinoma by activating ROS/Nrf2/Keap1-mediated autophagy. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116052. [PMID: 38325274 DOI: 10.1016/j.ecoenv.2024.116052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
Exposure to fine particulate matter (PM2.5) has been linked to an increased incidence and mortality of hepatocellular carcinoma (HCC). However, the impact of PM2.5 exposure on HCC progression and the underlying mechanisms remain largely unknown. This study aimed to investigate the effects of PM2.5 exposure on the stem cell-like properties of HCC cells. Our findings indicate that PM2.5 exposure significantly enhances the stemness of HCC cells (p < 0.01). Subsequently, male nude mice were divided into two groups (n = 8/group for tumor-bearing assay, n = 5/group for metastasis assay) for control and PM2.5 exposure. In vivo assays revealed that exposure to PM2.5 promoted the growth, metastasis, and epithelial-mesenchymal transition (EMT) of HCC cells (p < 0.01). Further exploration demonstrated that PM2.5 enhances the stemness of HCC cells by inducing cellular reactive oxygen species (ROS) generation (p < 0.05). Mechanistic investigation indicated that elevated intracellular ROS inhibited kelch-like ECH-associated protein 1 (Keap1) levels, promoting the upregulation and nucleus translocation of NFE2-like bZIP transcription factor 2 (Nrf2). This, in turn, induced autophagy activation, thereby promoting the stemness of HCC cells (p < 0.01). Our present study demonstrates the adverse effects of PM2.5 exposure on HCC development and highlights the mechanism of ROS/Nrf2/Keap1-mediated autophagy. For the first time, we reveal the impact of PM2.5 exposure on the poor prognosis-associated cellular phenotype of HCC and its underlying mechanism, which is expected to provide new theoretical basis for the improvement of public health.
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Affiliation(s)
- Jiujiu Li
- Hefei Center for Disease Control and Prevention, Hefei 230032, China
| | - Haoqi Jiang
- School of Public Health, Anhui Medical University, Hefei 230032, China
| | - Yu Zhu
- Hefei Center for Disease Control and Prevention, Hefei 230032, China
| | - Zijian Ma
- Hefei Center for Disease Control and Prevention, Hefei 230032, China
| | - Bin Li
- School of Public Health, Anhui Medical University, Hefei 230032, China
| | - Jun Dong
- Hefei Center for Disease Control and Prevention, Hefei 230032, China
| | - Changchun Xiao
- Hefei Center for Disease Control and Prevention, Hefei 230032, China.
| | - Anla Hu
- School of Public Health, Anhui Medical University, Hefei 230032, China.
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Guo B, Zheng Q, Jiang Y, Zhan Y, Huang W, Chen Z. Long non-coding RNAFOXD1-AS1 modulated CTCs epithelial-mesenchymal transition and immune escape in hepatocellular carcinoma in vitro by sponging miR-615-3p. Cancer Rep (Hoboken) 2024; 7:e2050. [PMID: 38517478 PMCID: PMC10959247 DOI: 10.1002/cnr2.2050] [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: 11/15/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is widely recognized as a globally prevalent malignancy. Immunotherapy is a promising therapy for HCC patients. Increasing evidence suggests that lncRNAs are involved in HCC progression and immunotherapy. AIM The study reveals the mechanistic role of long non-coding RNA (lncRNA) FOXD1-AS1 in regulating migration, invasion, circulating tumor cells (CTCs), epithelial-mesenchymal transition (EMT), and immune escape in HCC in vitro. METHODS This study employed real-time PCR (RT-qPCR) to measure FOXD1-AS1, miR-615-3p, and programmed death-ligand 1 (PD-L1). The interactions of FOXD1-AS1, miR-615-3p, and PD-L1 were validated via dual-luciferase reporter gene and ribonucleoprotein immunoprecipitation (RIP) assay. In vivo experimentation involves BALB/c mice and BALB/c nude mice to investigate the impact of HCC metastasis. RESULTS The upregulation of lncRNA FOXD1-AS1 in malignant tissues significantly correlates with poor prognosis. The investigation was implemented on the impact of lncRNA FOXD1-AS1 on the migratory, invasive, and EMT of HCC cells. It has been observed that the lncRNA FOXD1-AS1 significantly influences the generation and metastasis of MCTC in vivo analysis. In mechanistic analysis, lncRNA FOXD1-AS1 enhanced immune escape in HCC via upregulation of PD-L1, which acted as a ceRNA by sequestering miR-615-3p. Additionally, lncRNA FOXD1-AS1 was found to modulate the EMT of CTCs through the activation of the PI3K/AKT pathway. CONCLUSION This study presents compelling evidence supporting the role of lncRNA FOXD1-AS1 as a miRNA sponge that sequesters miR-655-3p and protects PD-L1 from suppression.
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Affiliation(s)
- Bao‐ling Guo
- Department of OncologyLongyan First Affiliated Hospital of Fujian Medical UniversityLongyanFujianPeople's Republic of China
| | - Qiu‐xiang Zheng
- Department of OncologyLongyan First Affiliated Hospital of Fujian Medical UniversityLongyanFujianPeople's Republic of China
| | - Yun‐shan Jiang
- Department of OncologyLongyan First Affiliated Hospital of Fujian Medical UniversityLongyanFujianPeople's Republic of China
| | - Ying Zhan
- Department of OncologyLongyan First Affiliated Hospital of Fujian Medical UniversityLongyanFujianPeople's Republic of China
| | - Wen‐jin Huang
- Department of OncologyLongyan First Affiliated Hospital of Fujian Medical UniversityLongyanFujianPeople's Republic of China
| | - Zhi‐yong Chen
- Department of OncologyLongyan First Affiliated Hospital of Fujian Medical UniversityLongyanFujianPeople's Republic of China
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25
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Zhou B, Zhou N, Liu Y, Dong E, Peng L, Wang Y, Yang L, Suo H, Tao J. Identification and validation of CCR5 linking keloid with atopic dermatitis through comprehensive bioinformatics analysis and machine learning. Front Immunol 2024; 15:1309992. [PMID: 38476235 PMCID: PMC10927814 DOI: 10.3389/fimmu.2024.1309992] [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: 10/09/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
There is sufficient evidence indicating that keloid is strongly associated with atopic dermatitis (AD) across ethnic groups. However, the molecular mechanism underlying the association is not fully understood. The aim of this study is to discover the underlying mechanism of the association between keloid and AD by integrating comprehensive bioinformatics techniques and machine learning methods. The gene expression profiles of keloid and AD were downloaded from the Gene Expression Omnibus (GEO) database. A total of 449 differentially expressed genes (DEGs) were found to be shared in keloid and AD using the training datasets of GEO (GSE158395 and GSE121212). The hub genes were identified using the protein-protein interaction network and Cytoscape software. 20 of the most significant hub genes were selected, which were mainly involved in the regulation of the inflammatory and immune response. Through two machine learning algorithms of LASSO and SVM-RFE, CCR5 was identified as the most important key gene. Subsequently, upregulated CCR5 gene expression was confirmed in validation GEO datasets (GSE188952 and GSE32924) and clinical samples of keloid and AD. Immune infiltration analysis showed that T helper (Th) 1, 2 and 17 cells were significantly enriched in the microenvironment of both keloid and AD. Positive correlations were found between CCR5 and Th1, Th2 and Th17 cells. Finally, two TFs of CCR5, NR3C2 and YY1, were identified, both of which were downregulated in keloid and AD tissues. Our study firstly reveals that keloid and AD shared common inflammatory and immune pathways. Moreover, CCR5 plays a key role in the pathogenesis association between keloid and AD. The common pathways and key genes may shed light on further mechanism research and targeted therapy, and may provide therapeutic interventions of keloid with AD.
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Affiliation(s)
- Bin Zhou
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Nuoya Zhou
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Yan Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Enzhu Dong
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Lianqi Peng
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Yifei Wang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Liu Yang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Huinan Suo
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Juan Tao
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
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26
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Zhang X, Xiao Z, Zhang X, Li N, Sun T, Zhang J, Kang C, Fan S, Dai L, Liu X. Signature construction and molecular subtype identification based on liver-specific genes for prediction of prognosis, immune activity, and anti-cancer drug sensitivity in hepatocellular carcinoma. Cancer Cell Int 2024; 24:78. [PMID: 38374122 PMCID: PMC10875877 DOI: 10.1186/s12935-024-03242-3] [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: 05/07/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Liver specific genes (LSGs) are crucial for hepatocyte differentiation and maintaining normal liver function. A deep understanding of LSGs and their heterogeneity in hepatocellular carcinoma (HCC) is necessary to provide clues for HCC diagnosis, prognosis, and treatment. METHODS The bulk and single-cell RNA-seq data of HCC were downloaded from TCGA, ICGC, and GEO databases. Through unsupervised cluster analysis, LSGs-based HCC subtypes were identified in TCGA-HCC samples. The prognostic effects of the subtypes were investigated with survival analyses. With GSVA and Wilcoxon test, the LSGs score, stemness score, aging score, immune score and stromal score of the samples were estimated and compared. The HCC subtype-specific genes were identified. The subtypes and their differences were validated in ICGC-HCC samples. LASSO regression analysis was used for key gene selection and risk model construction for HCC overall survival. The model performance was estimated and validated. The key genes were validated for their heterogeneities in HCC cell lines with quantitative real-time PCR and at single-cell level. Their dysregulations were investigated at protein level. Their correlations with HCC response to anti-cancer drugs were estimated in HCC cell lines. RESULTS We identified three LSGs-based HCC subtypes with different prognosis, tumor stemness, and aging level. The C1 subtype with low LSGs score and high immune score presented a poor survival, while the C2 subtype with high LSGs score and immune score indicated an enduring survival. Although no significant survival difference between C2 and C3 HCCs was shown, the C2 HCCs presented higher immune score and stroma score. The HCC subtypes and their differences were confirmed in ICGC-HCC dataset. A five-gene prognostic signature for HCC survival was constructed. Its good performance was shown in both the training and validation datasets. The five genes presented significant heterogeneities in different HCC cell lines and hepatocyte subclusters. Their dysregulations were confirmed at protein level. Furthermore, their significant associations with HCC sensitivities to anti-cancer drugs were shown. CONCLUSIONS LSGs-based HCC subtype classification and the five-gene risk model might provide useful clues not only for HCC stratification and risk prediction, but also for the development of more personalized therapies for effective HCC treatment.
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Affiliation(s)
- Xiuzhi Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, 451191, Henan, China
| | - Zhefeng Xiao
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xia Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, 451191, Henan, China
| | - Ningning Li
- Department of Pathology, Henan Medical College, Zhengzhou, 451191, Henan, China
| | - Tao Sun
- Department of Pathology, Henan Medical College, Zhengzhou, 451191, Henan, China
| | - JinZhong Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, 451191, Henan, China
| | - Chunyan Kang
- Department of Pathology, Henan Medical College, Zhengzhou, 451191, Henan, China
| | - Shasha Fan
- Oncology Department, Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Hunan Normal University, Changsha, 410000, Hunan, China.
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052, China.
| | - Xiaoli Liu
- Laboratory Department, Henan Provincial People's Hospital, Zhengzhou, 450003, China.
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Martínez-Blanco P, Suárez M, Gil-Rojas S, Torres AM, Martínez-García N, Blasco P, Torralba M, Mateo J. Prognostic Factors for Mortality in Hepatocellular Carcinoma at Diagnosis: Development of a Predictive Model Using Artificial Intelligence. Diagnostics (Basel) 2024; 14:406. [PMID: 38396445 PMCID: PMC10888215 DOI: 10.3390/diagnostics14040406] [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: 12/31/2023] [Revised: 01/24/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) accounts for 75% of primary liver tumors. Controlling risk factors associated with its development and implementing screenings in risk populations does not seem sufficient to improve the prognosis of these patients at diagnosis. The development of a predictive prognostic model for mortality at the diagnosis of HCC is proposed. METHODS In this retrospective multicenter study, the analysis of data from 191 HCC patients was conducted using machine learning (ML) techniques to analyze the prognostic factors of mortality that are significant at the time of diagnosis. Clinical and analytical data of interest in patients with HCC were gathered. RESULTS Meeting Milan criteria, Barcelona Clinic Liver Cancer (BCLC) classification and albumin levels were the variables with the greatest impact on the prognosis of HCC patients. The ML algorithm that achieved the best results was random forest (RF). CONCLUSIONS The development of a predictive prognostic model at the diagnosis is a valuable tool for patients with HCC and for application in clinical practice. RF is useful and reliable in the analysis of prognostic factors in the diagnosis of HCC. The search for new prognostic factors is still necessary in patients with HCC.
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Affiliation(s)
| | - Miguel Suárez
- Gastroenterology Department, Virgen de la Luz Hospital, 16002 Cuenca, Spain
- Medical Analysis Expert Group, Institute of Technology, Universidad de Castilla-La Mancha, 16071 Cuenca, Spain
- Medical Analysis Expert Group, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| | - Sergio Gil-Rojas
- Gastroenterology Department, Virgen de la Luz Hospital, 16002 Cuenca, Spain
| | - Ana María Torres
- Medical Analysis Expert Group, Institute of Technology, Universidad de Castilla-La Mancha, 16071 Cuenca, Spain
- Medical Analysis Expert Group, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| | | | - Pilar Blasco
- Department of Pharmacy, General University Hospital, 46014 Valencia, Spain
| | - Miguel Torralba
- Internal Medicine Unit, Guadalajara University Hospital, 19002 Guadalajara, Spain (M.T.)
- Faculty of Medicine, Universidad de Alcalá de Henares, 28801 Alcalá de Henares, Spain
- Translational Research Group in Cellular Immunology (GITIC), Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| | - Jorge Mateo
- Medical Analysis Expert Group, Institute of Technology, Universidad de Castilla-La Mancha, 16071 Cuenca, Spain
- Medical Analysis Expert Group, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
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Yan S, Zhao J, Gao P, Li Z, Li Z, Liu X, Wang P. Diagnostic potential of NRG1 in benign nerve sheath tumors and its influence on the PI3K-Akt signaling and tumor immunity. Diagn Pathol 2024; 19:28. [PMID: 38331905 PMCID: PMC10851500 DOI: 10.1186/s13000-024-01438-9] [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: 11/06/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
OBJECTIVE Benign nerve sheath tumors (BNSTs) present diagnostic challenges due to their heterogeneous nature. This study aimed to determine the significance of NRG1 as a novel diagnostic biomarker in BNST, emphasizing its involvement in the PI3K-Akt pathway and tumor immune regulation. METHODS Differential genes related to BNST were identified from the GEO database. Gene co-expression networks, protein-protein interaction networks, and LASSO regression were utilized to pinpoint key genes. The CIBERSORT algorithm assessed immune cell infiltration differences, and functional enrichment analyses explored BNST signaling pathways. Clinical samples helped establish PDX models, and in vitro cell lines to validate NRG1's role via the PI3K-Akt pathway. RESULTS Nine hundred eighty-two genes were upregulated, and 375 downregulated in BNST samples. WGCNA revealed the brown module with the most significant difference. Top hub genes included NRG1, which was also determined as a pivotal gene in disease characterization. Immune infiltration showed significant variances in neutrophils and M2 macrophages, with NRG1 playing a central role. Functional analyses confirmed NRG1's involvement in key pathways. Validation experiments using PDX models and cell lines further solidified NRG1's role in BNST. CONCLUSION NRG1 emerges as a potential diagnostic biomarker for BNST, influencing the PI3K-Akt pathway, and shaping the tumor immune microenvironment.
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Affiliation(s)
- Suwei Yan
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China
| | - Jingnan Zhao
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China
| | - Pengyang Gao
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China
| | - Zhaoxu Li
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China
| | - Zhao Li
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China
| | - Xiaobing Liu
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China
| | - Pengfei Wang
- Department of Neurosurgery, The Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, P. R. China.
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Dou H, Song C, Wang X, Feng Z, Su Y, Wang H. Integrated bioinformatics analysis of SEMA3C in tongue squamous cell carcinoma using machine-learning strategies. Cancer Cell Int 2024; 24:58. [PMID: 38321460 PMCID: PMC10845809 DOI: 10.1186/s12935-024-03247-y] [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: 11/26/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
Tongue squamous cell carcinoma (TSCC) is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. We aim to identify and verify potential biomarkers for TSCC using bioinformatics analysis. To begin with, we examined clinical and RNA expression information of individuals with TSCC from the Gene Expression Omnibus (GEO) database. Differential expression analysis and functional analysis were conducted. Multiple machine-learning strategies were next employed to screen and determine the hub gene, and receiver operating characteristic (ROC) analysis was used to assess diagnostic value. Semaphorin3C (SEMA3C) was identified as a critical biomarker, presenting high diagnostic accuracy for TSCC. In the validation cohorts, SEMA3C exhibited high expression levels in TSCC. The high expression of SEMA3C was a poor prognostic factor in TSCC by the Kaplan-Meier curve. Based on the Gene Ontology (GO) analysis, SEMA3C was mapped in terms related to cell adhesion, positive regulation of JAK-STAT, positive regulation of stem cell maintenance, and positive regulation of NF-κB activity. Single-cell RNA sequencing (ScRNA-seq) analysis showed cells expressing SEMA3C were predominantly tumor cells. Then, we further verified that SEMA3C had high expression in TSCC clinical samples. In addition, the knockdown of SEMA3C suppressed the proliferation, migration, and invasion of TSCC cells in vitro. This study is the first to report the involvement of SEMA3C in TSCC, suggesting that upregulated SEMA3C could be a novel and critical potential biomarker for future predictive diagnostics, prevention, prognostic assessment, and personalized medical services in TSCC.
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Affiliation(s)
- Huixin Dou
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Can Song
- Research and Development Department, Allife Medicine Inc., Beijing, China
| | - Xiaoyan Wang
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University, Beijing, China
| | - Zhien Feng
- Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Yingying Su
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
| | - Hao Wang
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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Xia Y, Wang C, Li X, Gao M, Hogg HDJ, Tunthanathip T, Hulsen T, Tian X, Zhao Q. Development and validation of a novel stemness-related prognostic model for neuroblastoma using integrated machine learning and bioinformatics analyses. Transl Pediatr 2024; 13:91-109. [PMID: 38323183 PMCID: PMC10839279 DOI: 10.21037/tp-23-582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024] Open
Abstract
Background Neuroblastoma (NB) is a common solid tumor in children, with a dismal prognosis in high-risk cases. Despite advancements in NB treatment, the clinical need for precise prognostic models remains critical, particularly to address the heterogeneity of cancer stemness which plays a pivotal role in tumor aggressiveness and patient outcomes. By utilizing machine learning (ML) techniques, we aimed to explore the cancer stemness features in NB and identify stemness-related hub genes for future investigation and potential targeted therapy. Methods The public dataset GSE49710 was employed as the training set for acquire gene expression data and NB sample information, including age, stage, and MYCN amplification status and survival. The messenger RNA (mRNA) expression-based stemness index (mRNAsi) was calculated and patients were grouped according to their mRNAsi value. Stemness-related hub genes were identified from the differentially expressed genes (DEGs) to construct a gene signature. This was followed by evaluating the relationship between cancer stemness and the NB immune microenvironment, and the development of a predictive nomogram. We assessed the prognostic outcomes including overall survival (OS) and event-free survival, employing machine learning methods to measure predictive accuracy through concordance indices and validation in an independent cohort E-MTAB-8248. Results Based on mRNAsi, we categorized NB patients into two groups to explore the association between varying levels of stemness and their clinical outcomes. High mRNAsi was linked to the advanced International Neuroblastoma Staging System (INSS) stage, amplified MYCN, and elder age. High mRNAsi patients had a significantly poorer prognosis than low mRNAsi cases. According to the multivariate Cox analysis, the mRNAsi was an independent risk factor of prognosis in NB patients. After least absolute shrinkage and selection operator (LASSO) regression analysis, four key genes (ERCC6L, DUXAP10, NCAN, DIRAS3) most related to mRNAsi scores were discovered and a risk model was built. Our model demonstrated a significant prognostic capacity with hazard ratios (HR) ranging from 18.96 to 41.20, P values below 0.0001, and area under the receiver operating characteristic curve (AUC) values of 0.918 in the training set, suggesting high predictive accuracy which was further confirmed by external verification. Individuals with a low four-gene signature score had a favorable outcome and better immune responses. Finally, a nomogram for clinical practice was constructed by integrating the four-gene signature and INSS stage. Conclusions Our findings confirm the influence of CSC features in NB prognosis. The newly developed NB stemness-related four-gene signature prognostic signature could facilitate the prognostic prediction, and the identified hub genes may serve as promising targets for individualized treatments.
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Affiliation(s)
- Yuren Xia
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Department of General Surgery, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
| | - Chaoyu Wang
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Xin Li
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Department of Pathology, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
| | - Mingyou Gao
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Henry David Jeffry Hogg
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Thara Tunthanathip
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Tim Hulsen
- Data Science & AI Engineering, Philips, Eindhoven, The Netherlands
| | - Xiangdong Tian
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Qiang Zhao
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
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Thi HV, Hoang TN, Le NQK, Chu DT. Application of data science and bioinformatics in RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:83-97. [PMID: 38360007 DOI: 10.1016/bs.pmbts.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nowadays, information technology (IT) has been holding a significant role in daily life worldwide. The trajectory of data science and bioinformatics promises pioneering personalized therapies, reshaping medical landscapes and patient care. For RNA therapy to reach more patients, a comprehensive understanding of the application of data science and bioinformatics to this therapy is essential. Thus, this chapter has summarized the application of data science and bioinformatics in RNA therapeutics. Data science applications in RNA therapy, such as data integration and analytics, machine learning, and drug development, have been discussed. In addition, aspects of bioinformatics such as RNA design and evaluation, drug delivery system simulation, and databases for personalized medicine have also been covered in this chapter. These insights have shed light on existing evidence and opened potential future directions. From there, scientists can elevate RNA-based therapeutics into an era of tailored treatments and revolutionary healthcare.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Nhat Hoang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, Taiwan
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Mondello A, Dal Bo M, Toffoli G, Polano M. Machine learning in onco-pharmacogenomics: a path to precision medicine with many challenges. Front Pharmacol 2024; 14:1260276. [PMID: 38264526 PMCID: PMC10803549 DOI: 10.3389/fphar.2023.1260276] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Over the past two decades, Next-Generation Sequencing (NGS) has revolutionized the approach to cancer research. Applications of NGS include the identification of tumor specific alterations that can influence tumor pathobiology and also impact diagnosis, prognosis and therapeutic options. Pharmacogenomics (PGx) studies the role of inheritance of individual genetic patterns in drug response and has taken advantage of NGS technology as it provides access to high-throughput data that can, however, be difficult to manage. Machine learning (ML) has recently been used in the life sciences to discover hidden patterns from complex NGS data and to solve various PGx problems. In this review, we provide a comprehensive overview of the NGS approaches that can be employed and the different PGx studies implicating the use of NGS data. We also provide an excursus of the ML algorithms that can exert a role as fundamental strategies in the PGx field to improve personalized medicine in cancer.
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Affiliation(s)
| | | | | | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
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Padovan M, Cosci B, Petillo A, Nerli G, Porciatti F, Scarinci S, Carlucci F, Dell’Amico L, Meliani N, Necciari G, Lucisano VC, Marino R, Foddis R, Palla A. ChatGPT in Occupational Medicine: A Comparative Study with Human Experts. Bioengineering (Basel) 2024; 11:57. [PMID: 38247934 PMCID: PMC10813435 DOI: 10.3390/bioengineering11010057] [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: 12/07/2023] [Revised: 01/01/2024] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The objective of this study is to evaluate ChatGPT's accuracy and reliability in answering complex medical questions related to occupational health and explore the implications and limitations of AI in occupational health medicine. The study also provides recommendations for future research in this area and informs decision-makers about AI's impact on healthcare. A group of physicians was enlisted to create a dataset of questions and answers on Italian occupational medicine legislation. The physicians were divided into two teams, and each team member was assigned a different subject area. ChatGPT was used to generate answers for each question, with/without legislative context. The two teams then evaluated human and AI-generated answers blind, with each group reviewing the other group's work. Occupational physicians outperformed ChatGPT in generating accurate questions on a 5-point Likert score, while the answers provided by ChatGPT with access to legislative texts were comparable to those of professional doctors. Still, we found that users tend to prefer answers generated by humans, indicating that while ChatGPT is useful, users still value the opinions of occupational medicine professionals.
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Affiliation(s)
- Martina Padovan
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Bianca Cosci
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Armando Petillo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Gianluca Nerli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Francesco Porciatti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Sergio Scarinci
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Francesco Carlucci
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Letizia Dell’Amico
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Niccolò Meliani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Gabriele Necciari
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Vincenzo Carmelo Lucisano
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Riccardo Marino
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
| | - Rudy Foddis
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (B.C.); (A.P.); (G.N.); (F.P.); (S.S.); (F.C.); (L.D.); (N.M.); (G.N.); (R.M.)
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Teng X, Wang Z. Online COVID-19 diagnosis prediction using complete blood count: an innovative tool for public health. BMC Public Health 2023; 23:2536. [PMID: 38114942 PMCID: PMC10729447 DOI: 10.1186/s12889-023-17477-8] [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: 07/07/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND COVID-19, caused by SARS-CoV-2, presents distinct diagnostic challenges due to its wide range of clinical manifestations and the overlapping symptoms with other common respiratory diseases. This study focuses on addressing these difficulties by employing machine learning (ML) methodologies, particularly the XGBoost algorithm, to utilize Complete Blood Count (CBC) parameters for predictive analysis. METHODS We performed a retrospective study involving 2114 COVID-19 patients treated between December 2022 and January 2023 at our healthcare facility. These patients were classified into fever (1057 patients) and pneumonia groups (1057 patients), based on their clinical symptoms. The CBC data were utilized to create predictive models, with model performance evaluated through metrics like Area Under the Receiver Operating Characteristics Curve (AUC), accuracy, sensitivity, specificity, and precision. We selected the top 10 predictive variables based on their significance in disease prediction. The data were then split into a training set (70% of patients) and a validation set (30% of patients) for model validation. RESULTS We identified 31 indicators with significant disparities. The XGBoost model outperformed others, with an AUC of 0.920 and high precision, sensitivity, specificity, and accuracy. The top 10 features (Age, Monocyte%, Mean Platelet Volume, Lymphocyte%, SIRI, Eosinophil count, Platelet count, Hemoglobin, Platelet Distribution Width, and Neutrophil count.) were crucial in constructing a more precise predictive model. The model demonstrated strong performance on both training (AUC = 0.977) and validation (AUC = 0.912) datasets, validated by decision curve analysis and calibration curve. CONCLUSION ML models that incorporate CBC parameters offer an innovative and effective tool for data analysis in COVID-19. They potentially enhance diagnostic accuracy and the efficacy of therapeutic interventions, ultimately contributing to a reduction in the mortality rate of this infectious disease.
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Affiliation(s)
- Xiaojing Teng
- Department of Clinical Laboratory, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, 310000, China
| | - Zhiyi Wang
- Department of Clinical Laboratory, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), No. 369, Kunpeng Road, Shangcheng District Hangzhou, Hangzhou, Zhejiang, 310008, China.
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Lv JH, Hou AJ, Zhang SH, Dong JJ, Kuang HX, Yang L, Jiang H. WGCNA combined with machine learning to find potential biomarkers of liver cancer. Medicine (Baltimore) 2023; 102:e36536. [PMID: 38115320 PMCID: PMC10727608 DOI: 10.1097/md.0000000000036536] [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: 10/20/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
The incidence of hepatocellular carcinoma (HCC) has been increasing in recent years. With the development of various detection technologies, machine learning is an effective method to screen disease characteristic genes. In this study, weighted gene co-expression network analysis (WGCNA) and machine learning are combined to find potential biomarkers of liver cancer, which provides a new idea for future prediction, prevention, and personalized treatment. In this study, the "limma" software package was used. P < .05 and log2 |fold-change| > 1 is the standard screening differential genes, and then the module genes obtained by WGCNA analysis are crossed to obtain the key module genes. Gene Ontology and Kyoto Gene and Genome Encyclopedia analysis was performed on key module genes, and 3 machine learning methods including lasso, support vector machine-recursive feature elimination, and RandomForest were used to screen feature genes. Finally, the validation set was used to verify the feature genes, the GeneMANIA (http://www.genemania.org) database was used to perform protein-protein interaction networks analysis on the feature genes, and the SPIED3 database was used to find potential small molecule drugs. In this study, 187 genes associated with HCC were screened by using the "limma" software package and WGCNA. After that, 6 feature genes (AADAT, APOF, GPC3, LPA, MASP1, and NAT2) were selected by RandomForest, Absolute Shrinkage and Selection Operator, and support vector machine-recursive feature elimination machine learning algorithms. These genes are also significantly different on the external dataset and follow the same trend as the training set. Finally, our findings may provide new insights into targets for diagnosis, prevention, and treatment of HCC. AADAT, APOF, GPC3, LPA, MASP1, and NAT2 may be potential genes for the prediction, prevention, and treatment of liver cancer in the future.
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Affiliation(s)
- Jia-Hao Lv
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - A-Jiao Hou
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Shi-Hao Zhang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Jiao-Jiao Dong
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Hai-Xue Kuang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Liu Yang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Hai Jiang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
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Sun Q, Shen M, Zhu S, Liao Y, Zhang D, Sun J, Guo Z, Wu L, Xiao L, Liu L. Targeting NAD + metabolism of hepatocellular carcinoma cells by lenvatinib promotes M2 macrophages reverse polarization, suppressing the HCC progression. Hepatol Int 2023; 17:1444-1460. [PMID: 37204655 DOI: 10.1007/s12072-023-10544-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/22/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Lowered nicotinamide adenine dinucleotide (NAD+) levels in tumor cells drive tumor hyperprogression during immunotherapy, and its restoration activates immune cells. However, the effect of lenvatinib, a first-line treatment for unresectable hepatocellular carcinoma (HCC), on NAD+ metabolism in HCC cells, and the metabolite crosstalk between HCC and immune cells after targeting NAD+ metabolism of HCC cells remain unelucidated. METHODS Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and ultra-high-performance liquid chromatography multiple reaction monitoring-mass spectrometry (UHPLC-MRM-MS) were used to detect and validate differential metabolites. RNA sequencing was used to explore mRNA expression in macrophages and HCC cells. HCC mouse models were used to validate the effects of lenvatinib on immune cells and NAD+ metabolism. The macrophage properties were elucidated using cell proliferation, apoptosis, and co-culture assays. In silico structural analysis and interaction assays were used to determine whether lenvatinib targets tet methylcytosine dioxygenase 2 (TET2). Flow cytometry was performed to assess changes in immune cells. RESULTS Lenvatinib targeted TET2 to synthesize and increase NAD+ levels, thereby inhibiting decomposition in HCC cells. NAD+ salvage increased lenvatinib-induced apoptosis of HCC cells. Lenvatinib also induced CD8+ T cells and M1 macrophages infiltration in vivo. And lenvatinib suppressed niacinamide, 5-Hydroxy-L-tryptophan and quinoline secretion of HCC cells, and increased hypoxanthine secretion, which contributed to proliferation, migration and polarization function of macrophages. Consequently, lenvatinib targeted NAD+ metabolism and elevated HCC-derived hypoxanthine to enhance the macrophages polarization from M2 to M1. Glycosaminoglycan binding disorder and positive regulation of cytosolic calcium ion concentration were characteristic features of the reverse polarization. CONCLUSIONS Targeting HCC cells NAD+ metabolism by lenvatinib-TET2 pathway drives metabolite crosstalk, leading to M2 macrophages reverse polarization, thereby suppressing HCC progression. Collectively, these novel insights highlight the role of lenvatinib or its combination therapies as promising therapeutic alternatives for HCC patients with low NAD+ levels or high TET2 levels.
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Affiliation(s)
- Qingcan Sun
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China
| | - Mengying Shen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China
| | - Subin Zhu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China
| | - Yanxia Liao
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China
| | - Dongyan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jingyuan Sun
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zeqin Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Leyuan Wu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China
| | - Lushan Xiao
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China
| | - Li Liu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- State Key Laboratory of Organ Failure Research, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, 510515, China.
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Li J, Xin H, Zhang B, Guo Y, Ding Y, Wu X. Identification of Molecular Markers Predicting the Outcome of Anti-thrombotic Therapy After Percutaneous Coronary Intervention in Patients with Acute Coronary Syndrome and Atrial fibrillation: Evidence from a Meta-analysis and Experimental Study. J Cardiovasc Transl Res 2023; 16:1408-1416. [PMID: 37672183 DOI: 10.1007/s12265-023-10416-3] [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: 03/07/2023] [Accepted: 07/21/2023] [Indexed: 09/07/2023]
Abstract
Acute coronary syndrome (ACS) and atrial fibrillation (AF) often coexist in clinical practice, and patients with these conditions often have a critical illness with high risk of both ischemia and bleeding. This study aims to report potential molecular markers for predicting the efficacy based on a meta-analysis of microarray data from the GEO database. In 40 patients with acute coronary syndrome (ACS) and atrial fibrillation (AF) treated with PCI, P2RX1's effects on platelet aggregation, medication resistance, and predictive value were examined. Twenty up-regulated genes in peripheral blood samples of ACS and AF patients were down-regulated after PCI, while 7 down-regulated genes were up-regulated. ACS affected eight potential genes. P2RX1, one of the four LASSO analysis-retrieved disease characteristic genes, accurately predicted AF patients' thrombosis risk and PCI's anti-thrombotic impact. Therefore, P2RX1 may be a molecular marker to predict the effect of anti-thrombotic therapy in patients with ACS and AF after PCI.
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Affiliation(s)
- Jingrui Li
- The Fourth Department of Cardiovascular, The Second Affiliated Hospital of Qiqihar Medical University, No. 37 Zhonghua West Road, Jianhua District, Qiqihar, 161005, Heilongjiang Province, People's Republic of China
| | - Hongwei Xin
- The Fourth Department of Cardiovascular, The Second Affiliated Hospital of Qiqihar Medical University, No. 37 Zhonghua West Road, Jianhua District, Qiqihar, 161005, Heilongjiang Province, People's Republic of China
| | - Baihui Zhang
- The Fourth Department of Cardiovascular, The Second Affiliated Hospital of Qiqihar Medical University, No. 37 Zhonghua West Road, Jianhua District, Qiqihar, 161005, Heilongjiang Province, People's Republic of China
| | - Yanhong Guo
- Department of Biochemistry, Qiqihar Medical University, Qiqihar, 161005, People's Republic of China
| | - Yuanyuan Ding
- The Fourth Department of Cardiovascular, The Second Affiliated Hospital of Qiqihar Medical University, No. 37 Zhonghua West Road, Jianhua District, Qiqihar, 161005, Heilongjiang Province, People's Republic of China
| | - Xiaojie Wu
- The Fourth Department of Cardiovascular, The Second Affiliated Hospital of Qiqihar Medical University, No. 37 Zhonghua West Road, Jianhua District, Qiqihar, 161005, Heilongjiang Province, People's Republic of China.
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Wu Y, Luo J, Xu B. Network pharmacology and bioinformatics to identify the molecular mechanisms of Gleditsiae Spina against colorectal cancer. Curr Res Toxicol 2023; 5:100139. [PMID: 38059131 PMCID: PMC10696432 DOI: 10.1016/j.crtox.2023.100139] [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: 08/29/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Objective In this study, network pharmacology, bioinformatics and molecular docking were used to explore the active phytochemicals, hub genes, and potential molecular mechanisms of Gleditsiae Spina in treating of colorectal cancer.. Methods The targets of Gleditsiae Spina, and targets related to CRC were derived from databases. We identified the hub genes for Gleditsiae Spina anti-colorectal cancer following the protein-protein-interaction (PPI) network. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were used to analyze the hub genes from a macro perspective. Finally, we verified the hub genes by molecular docking, GEPIA, HPA, and starBase database. Results We identified nine active phytochemicals and 36 intersection targets. The GO enrichment analysis results showed that Gleditsiae Spina may be involved in gene targets affecting multiple biological processes, including response to radiation, response to ionizing radiation, cyclin-dependent protein kinase holoenzyme complex, serine/threonine protein kinase complex, cyclin-dependent protein serine/threonine kinase regulator activity and protein kinase regulator activity. KEGG enrichment analysis results indicated that the P53 signaling pathway, IL-17 signaling pathway, Toll-like receptor signaling pathway, PI3K-Akt signaling pathway, and JAK-STAT signaling pathway were mainly related to the effect of Gleditsiae Spina on colorectal cancer. Molecular docking analysis suggested that the active phytochemicals of Gleditsiae Spina could combine well with hub genes (PTGS1, PIK3CG, CCND1, CXCL8 and ADRB2). Conclusion This study provides clues for further study of anti-CRC phytochemicals as well as their mechanisms of provides a basis for their development model.
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Affiliation(s)
- Yingzi Wu
- Guangdong Provincial Key Laboratory IRADS and Department of Life Sciences, BNU-HKBU United International College, Zhuhai 519087, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Jinhai Luo
- Guangdong Provincial Key Laboratory IRADS and Department of Life Sciences, BNU-HKBU United International College, Zhuhai 519087, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Baojun Xu
- Guangdong Provincial Key Laboratory IRADS and Department of Life Sciences, BNU-HKBU United International College, Zhuhai 519087, China
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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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Zhang G. Prognostic clinical phenotypes associated with tumor stemness in the immune microenvironment of T-cell exhaustion for hepatocellular carcinoma. Discov Oncol 2023; 14:203. [PMID: 37957420 PMCID: PMC10643807 DOI: 10.1007/s12672-023-00819-8] [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: 04/21/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
T-cell exhaustion (TEX) and high heterogeneity of cancer stem cells (CSCs) are associated with progression, metastasis, and treatment resistance in hepatocellular carcinoma (HCC). Here, we aim to characterize TEX-stemness-related genes (TEXSRGs) and screen for HCC patients who are more sensitive to immunotherapy. The immune cell abundance identifier (ImmuCellAI) was utilized to precisely evaluate the abundance of TEX and screen TEX-related genes. The stemness index (mRNAsi) of samples was analyzed through the one-class logistic regression (OCLR) algorithm. Application of the non-negative matrix decomposition algorithm (NMF) for subtype identification of HCC samples. The different subtypes were assessed for differences in prognosis, tumor microenvironment (TME) landscape, and immunotherapy treatment response. Then, the TEXSRGS-score, which can accurately forecast the survival outcome of HCC patients, was built by LASSO-Cox and multivariate Cox regression, and experimentally validated for the most important TEXSRGs. We also analyzed the expression of TEXSRGs and the infiltration of CD8+ T cells in clinical samples using qRT-PCR and immunohistochemistry (IHC). Based on 146 TEXSRGs, we found two distinct clinical phenotypes with different TEX infiltration abundance, tumor stemness index, enrichment pathways, mutational landscape, and immune cell infiltration through the non-negative matrix decomposition algorithm (NMF), which were confirmed in the ICGC dataset. Utilizing eight TEXSRGs linked to clinical outcome, we created a TEXSRGs-score model to further improve the clinical applicability. Patients can be divided into two groups with substantial differences in the characteristics of immune cell infiltration, TEX infiltration abundance, and survival outcomes. The results of qRT-PCR and IHC analysis showed that PAFAH1B3, ZIC2, and ESR1 were differentially expressed in HCC and normal tissues and that patients with high TEXSRGs-scores had higher TEX infiltration abundance and tumor stemness gene expression. Regarding immunotherapy reaction and immune cell infiltration, patients with various TEXSRGs-score levels had various clinical traits. The outcome and immunotherapy efficacy of patients with low TEXSRGs-score was favorable. In conclusion, we identified two clinical subtypes with different prognoses, TEX infiltration abundance, tumor cell stemness index, and immunotherapy response based on TEXSRGs, and developed and validated a TEXSRGs-score capable of accurately predicting survival outcomes in HCC patients by comprehensive bioinformatics analysis. We believe that the TEXSRGs-score has prospective clinical relevance for prognostic assessment and may help physicians select prospective responders in preference to current immune checkpoint inhibitors (ICIs).
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Affiliation(s)
- Genhao Zhang
- Department of Blood Transfusion, Zhengzhou University First Affiliated Hospital, Zhengzhou, China.
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Wang Y, Wei B, Zhao T, Shen H, Liu X, Wang J, Wang Q, Shen R, Feng D. Machine learning-based prediction models for parathyroid carcinoma using pre-surgery cognitive function and clinical features. Sci Rep 2023; 13:19007. [PMID: 37923800 PMCID: PMC10624903 DOI: 10.1038/s41598-023-46294-7] [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] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
Patients with parathyroid carcinoma (PC) are often diagnosed postoperatively, due to incomplete resection during the initial surgery, resulting in poor outcomes. The aim of our study was to investigate the pre-surgery indicators of PC and try to develop a predictive model for PC utilizing machine learning. Evaluation of pre-surgery neuropsychological function and confirmation of pathology were carried out in 133 patients with primary hyperparathyroidism in Beijing Chaoyang Hospital from December 2019 to January 2023. Patients were randomly divided into a training cohort (n = 93) and a validating cohort (n = 40). Analysis of the clinical dataset, two machine learning including the extreme gradient boosting (XGBoost) and the least absolute shrinkage and selection operator (LASSO) regression were utilized to develop the prediction model for PC. Logistic regression analysis was also conducted for comparison. Significant differences in elevated parathyroid hormone and decreased serum phosphorus in PC compared to (BP). The lower score of MMSE and MOCA was observed in PC and a cutoff of MMSE < 24 was the optimal threshold to stratify PC from BP (area under the curve AUC 0.699 vs 0.625). The predicted probability of PC by machine learning was similar to the observed probability in the test set, whereas the logistic model tended to overpredict the possibility of PC. The XGBoost model attained a higher AUC than the logistic algorithms and LASSO models. (0.835 vs 0.683 vs 0.607). Preoperative cognitive function may be a probable predictor for PC. The cognitive function-based prediction model based on the XGBoost algorithm outperformed LASSO and logistic regression, providing valuable preoperative assistance to surgeons in clinical decision-making for patients suspected PC.
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Affiliation(s)
- Yuting Wang
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Bojun Wei
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.
| | - Teng Zhao
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hong Shen
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xing Liu
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jiacheng Wang
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Qian Wang
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Rongfang Shen
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Dalin Feng
- Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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Zheng Y, Chen Z, Huang S, Zhang N, Wang Y, Hong S, Chan JSK, Chen KY, Xia Y, Zhang Y, Lip GY, Qin J, Tse G, Liu T. Machine Learning in Cardio-Oncology: New Insights from an Emerging Discipline. Rev Cardiovasc Med 2023; 24:296. [PMID: 39077576 PMCID: PMC11273149 DOI: 10.31083/j.rcm2410296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 07/31/2024] Open
Abstract
A growing body of evidence on a wide spectrum of adverse cardiac events following oncologic therapies has led to the emergence of cardio-oncology as an increasingly relevant interdisciplinary specialty. This also calls for better risk-stratification for patients undergoing cancer treatment. Machine learning (ML), a popular branch discipline of artificial intelligence that tackles complex big data problems by identifying interaction patterns among variables, has seen increasing usage in cardio-oncology studies for risk stratification. The objective of this comprehensive review is to outline the application of ML approaches in cardio-oncology, including deep learning, artificial neural networks, random forest and summarize the cardiotoxicity identified by ML. The current literature shows that ML has been applied for the prediction, diagnosis and treatment of cardiotoxicity in cancer patients. In addition, role of ML in gender and racial disparities for cardiac outcomes and potential future directions of cardio-oncology are discussed. It is essential to establish dedicated multidisciplinary teams in the hospital and educate medical professionals to become familiar and proficient in ML in the future.
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Affiliation(s)
- Yi Zheng
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
| | - Ziliang Chen
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
| | - Shan Huang
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
| | - Nan Zhang
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
| | - Yueying Wang
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
| | - Shenda Hong
- National Institute of Health Data Science at Peking University, Peking
University, 100871 Beijing, China
- Institute of Medical Technology, Peking University Health Science Center,
100871 Beijing, China
| | - Jeffrey Shi Kai Chan
- Cardio-Oncology Research Unit, Cardiovascular Analytics Group, PowerHealth Limited, 999077 Hong
Kong, China
| | - Kang-Yin Chen
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
| | - Yunlong Xia
- Department of Cardiology, First Affiliated Hospital of Dalian Medical
University, 116011 Dalian, Liaoning, China
| | - Yuhui Zhang
- Heart Failure Center, State Key Laboratory of Cardiovascular Disease,
Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of
Medical Sciences and Peking Union Medical College, 100037 Beijing, China
| | - Gregory Y.H. Lip
- Liverpool Centre for Cardiovascular Science, University of Liverpool,
Liverpool John Moores University and Liverpool Heart & Chest Hospital, L69 3BX
Liverpool, UK
- Danish Center for Health Services Research, Department of Clinical Medicine,
Aalborg University, 999017 Aalborg, Denmark
| | - Juan Qin
- Section of Cardio-Oncology & Immunology, Division of Cardiology and the
Cardiovascular Research Institute, University of California San Francisco, San
Francisco, CA 94143, USA
| | - Gary Tse
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
- Cardio-Oncology Research Unit, Cardiovascular Analytics Group, PowerHealth Limited, 999077 Hong
Kong, China
- School of Nursing and Health Studies, Hong Kong Metropolitan University,
999077 Hong Kong, China
| | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular
Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second
Hospital of Tianjin Medical University, 300211 Tianjin, China
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Zeng Y, Wang C, Ye Q, Liu G, Zhang L, Wan J, Zhu Y. Machine learning model of imipenem-resistant Klebsiella pneumoniae based on MALDI-TOF-MS platform: An observational study. Health Sci Rep 2023; 6:e1108. [PMID: 37711674 PMCID: PMC10497903 DOI: 10.1002/hsr2.1108] [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: 10/20/2022] [Revised: 01/11/2023] [Accepted: 01/30/2023] [Indexed: 09/16/2023] Open
Abstract
Background and Aim Machine learning is an important branch and supporting technology of artificial intelligence, we established four machine learning model for the drug sensitivity of Klebsiella pneumoniae to imipenem based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and compared their diagnostic effect. Methods The data of MALDI-TOF-MS and imipenem sensitivity of 174 cases of K. pneumoniae isolated from clinical specimens in the laboratory of microbiology department of Tianjin Haihe Hospital from 2019 January to 2020 December were collected. The mass spectrometry and imipenem sensitivity of 70 cases of imipenem-sensitive and 70 resistant cases were randomly selected to establish the training set model, 17 cases of sensitive and 17 cases of resistant cases were randomly selected to establish the test set model. Mass spectral peak data were subjected to orthogonal partial least squares discriminant analysis (OPLS-DA), the training set data model was established by machine learning least absolute shrinkage and selection operator (LASSO) algorithm, logistic regression (LR) algorithm, support vector machines (SVM) algorithm, neural network (NN) algorithm, the area under the curve (AUC) and confusion matrix of training set and test set model were calculated and selected by Grid search and 3-fold Cross-validation respectively, the accuracy of the prediction model was verified by test set confusion matrix. Results The R²Y and Q² of OPLS-DA were 0.546 and 0.0178. The AUC of the best training set and test set models were 0.9726 and 0.9100, 1.0000 and 0.8581, 0.8462 and 0.6263, 1.0000 and 0.7180 evaluated by LASSO, LR, SVM and NN model respectively. The accuracy of the LASSO, LR, SVM and NN model were 87%, 79%, 62%, and 68% in test set, respectively. Conclusion The LASSO prediction model of K. pneumoniae sensitivity to imipenem established in this study has a high accuracy rate and has potential clinical decision support ability.
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Affiliation(s)
- Yu Zeng
- School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghaiChina
| | - Chao Wang
- Department of Clinical LaboratoryFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
| | - Qing Ye
- Department of HepatologyThe Third Central Hospital of TianjinTianjinChina
| | - Gang Liu
- Department of Clinical LaboratoryTianjin Haihe HospitalTianjinChina
| | - Lixia Zhang
- Department of Clinical LaboratoryTianjin Haihe HospitalTianjinChina
| | - Jingjing Wan
- School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghaiChina
| | - Yu Zhu
- Department of Clinical LaboratoryThe Third Central Hospital of TianjinTianjinChina
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Yu J, Li M, Ren B, Cheng L, Wang X, Ma Z, Yong WP, Chen X, Wang L, Goh BC. Unleashing the efficacy of immune checkpoint inhibitors for advanced hepatocellular carcinoma: factors, strategies, and ongoing trials. Front Pharmacol 2023; 14:1261575. [PMID: 37719852 PMCID: PMC10501787 DOI: 10.3389/fphar.2023.1261575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent primary liver cancer, representing approximately 85% of cases. The diagnosis is often made in the middle and late stages, necessitating systemic treatment as the primary therapeutic option. Despite sorafenib being the established standard of care for advanced HCC in the past decade, the efficacy of systemic therapy remains unsatisfactory, highlighting the need for novel treatment modalities. Recent breakthroughs in immunotherapy have shown promise in HCC treatment, particularly with immune checkpoint inhibitors (ICIs). However, the response rate to ICIs is currently limited to approximately 15%-20% of HCC patients. Recently, ICIs demonstrated greater efficacy in "hot" tumors, highlighting the urgency to devise more effective approaches to transform "cold" tumors into "hot" tumors, thereby enhancing the therapeutic potential of ICIs. This review presented an updated summary of the factors influencing the effectiveness of immunotherapy in HCC treatment, identified potential combination therapies that may improve patient response rates to ICIs, and offered an overview of ongoing clinical trials focusing on ICI-based combination therapy.
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Affiliation(s)
- Jiahui Yu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Mengnan Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Boxu Ren
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Le Cheng
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Xiaoxiao Wang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Zhaowu Ma
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Wei Peng Yong
- Department of Haematology–Oncology, National University Cancer Institute, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiaoguang Chen
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Lingzhi Wang
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Department of Haematology–Oncology, National University Cancer Institute, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
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Spârchez Z, Crăciun R, Nenu I, Mocan LP, Spârchez M, Mocan T. Refining Liver Biopsy in Hepatocellular Carcinoma: An In-Depth Exploration of Shifting Diagnostic and Therapeutic Applications. Biomedicines 2023; 11:2324. [PMID: 37626820 PMCID: PMC10452389 DOI: 10.3390/biomedicines11082324] [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: 07/26/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 08/27/2023] Open
Abstract
The field of hepatocellular carcinoma (HCC) has faced significant change on multiple levels in the past few years. The increasing emphasis on the various HCC phenotypes and the emergence of novel, specific therapies have slowly paved the way for a personalized approach to primary liver cancer. In this light, the role of percutaneous liver biopsy of focal lesions has shifted from a purely confirmatory method to a technique capable of providing an in-depth characterization of any nodule. Cancer subtype, gene expression, the mutational profile, and tissue biomarkers might soon become widely available through biopsy. However, indications, expectations, and techniques might suffer changes as the aim of the biopsy evolves from providing minimal proof of the disease to high-quality specimens for extensive analysis. Consequently, a revamped position of tissue biopsy is expected in HCC, following the reign of non-invasive imaging-only diagnosis. Moreover, given the advances in techniques that have recently reached the spotlight, such as liquid biopsy, concomitant use of all the available methods might gather just enough data to improve therapy selection and, ultimately, outcomes. The current review aims to discuss the changing role of liver biopsy and provide an evidence-based rationale for its use in the era of precision medicine in HCC.
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Affiliation(s)
- Zeno Spârchez
- Department of Gastroenterology, “Prof. Dr. O. Fodor” Regional Institute of Gastroenterology and Hepatology, 400162 Cluj-Napoca, Romania; (Z.S.); (I.N.); (T.M.)
- Department of Internal Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania
| | - Rareș Crăciun
- Department of Gastroenterology, “Prof. Dr. O. Fodor” Regional Institute of Gastroenterology and Hepatology, 400162 Cluj-Napoca, Romania; (Z.S.); (I.N.); (T.M.)
- Department of Internal Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania
| | - Iuliana Nenu
- Department of Gastroenterology, “Prof. Dr. O. Fodor” Regional Institute of Gastroenterology and Hepatology, 400162 Cluj-Napoca, Romania; (Z.S.); (I.N.); (T.M.)
- Department of Physiology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Lavinia Patricia Mocan
- Department of Histology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Mihaela Spârchez
- 2nd Pediatric Department, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400124 Cluj-Napoca, Romania;
| | - Tudor Mocan
- Department of Gastroenterology, “Prof. Dr. O. Fodor” Regional Institute of Gastroenterology and Hepatology, 400162 Cluj-Napoca, Romania; (Z.S.); (I.N.); (T.M.)
- UBBMed Department, Babeș-Bolyai University, 400349 Cluj-Napoca, Romania
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Zhang C, Zhou W. Machine learning-based identification of glycosyltransferase-related mRNAs for improving outcomes and the anti-tumor therapeutic response of gliomas. Front Pharmacol 2023; 14:1200795. [PMID: 37663248 PMCID: PMC10468601 DOI: 10.3389/fphar.2023.1200795] [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: 04/05/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Background: Glycosyltransferase participates in glycosylation modification, and glycosyltransferase alterations are involved in carcinogenesis, progression, and immune evasion, leading to poor outcomes. However, in-depth studies on the influence of glycosyltransferase on clinical outcomes and treatments are lacking. Methods: The analysis of differentially expressed genes was performed using the Gene Expression Profiling Interactive Analysis 2 database. A total of 10 machine learning algorithms were introduced, namely, random survival forest, elastic network, least absolute shrinkage and selection operator, Ridge, stepwise Cox, CoxBoost, partial least squares regression for Cox, supervised principal components, generalized boosted regression modeling, and survival support vector machine. Gene Set Enrichment Analysis was performed to explore signaling pathways regulated by the signature. Cell-type identification by estimating relative subsets of RNA transcripts was used for estimating the fractions of immune cell types. Results: Here, we analyzed the genomic and expressive alterations in glycosyltransferase-related genes in gliomas. A combination of 80 machine learning algorithms was introduced to establish the glycosyltransferase-related mRNA signature (GRMS) based on 2,030 glioma samples from The Cancer Genome Atlas Program, Chinese Glioma Genome Atlas, Rembrandt, Gravendeel, and Kamoun cohorts. The GRMS was identified as an independent hazardous factor for overall survival and exhibited stable and robust performance. Notably, gliomas in the high-GRMS subgroup exhibited abundant tumor-infiltrating lymphocytes and tumor mutation burden values, increased expressive levels of hepatitis A virus cellular receptor 2 and CD274, and improved progression-free survival when subjected to anti-tumor immunotherapy. Conclusion: The GRMS may act as a powerful and promising biomarker for improving the clinical prognosis of glioma patients.
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Affiliation(s)
- Chunyu Zhang
- School of Medicine, Tongji University, Shanghai, China
| | - Wei Zhou
- Department of Anesthesiology, Huzhou Central Hospital, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Huzhou, Zhejiang, China
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Wang Y, Wan X, Du S. Integrated analysis revealing a novel stemness-metabolism-related gene signature for predicting prognosis and immunotherapy response in hepatocellular carcinoma. Front Immunol 2023; 14:1100100. [PMID: 37622118 PMCID: PMC10445950 DOI: 10.3389/fimmu.2023.1100100] [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: 11/16/2022] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant lethal tumor and both cancer stem cells (CSCs) and metabolism reprogramming have been proven to play indispensable roles in HCC. This study aimed to reveal the connection between metabolism reprogramming and the stemness characteristics of HCC, established a new gene signature related to stemness and metabolism and utilized it to assess HCC prognosis and immunotherapy response. The clinical information and gene expression profiles (GEPs) of 478 HCC patients came from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). The one-class logistic regression (OCLR) algorithm was employed to calculate the messenger ribonucleic acid expression-based stemness index (mRNAsi), a new stemness index quantifying stemness features. Differentially expressed analyses were done between high- and low-mRNAsi groups and 74 differentially expressed metabolism-related genes (DEMRGs) were identified with the help of metabolism-related gene sets from Molecular Signatures Database (MSigDB). After integrated analysis, a risk score model based on the three most efficient prognostic DEMRGs, including Recombinant Phosphofructokinase Platelet (PFKP), phosphodiesterase 2A (PDE2A) and UDP-glucuronosyltransferase 1A5 (UGT1A5) was constructed and HCC patients were divided into high-risk and low-risk groups. Significant differences were found in pathway enrichment, immune cell infiltration patterns, and gene alterations between the two groups. High-risk group patients tended to have worse clinical outcomes and were more likely to respond to immunotherapy. A stemness-metabolism-related model composed of gender, age, the risk score model and tumor-node-metastasis (TNM) staging was generated and showed great discrimination and strong ability in predicting HCC prognosis and immunotherapy response.
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Affiliation(s)
| | | | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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Koelsch N, Manjili MH. From Reductionistic Approach to Systems Immunology Approach for the Understanding of Tumor Microenvironment. Int J Mol Sci 2023; 24:12086. [PMID: 37569461 PMCID: PMC10419122 DOI: 10.3390/ijms241512086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
The tumor microenvironment (TME) is a complex and dynamic ecosystem that includes a variety of immune cells mutually interacting with tumor cells, structural/stromal cells, and each other. The immune cells in the TME can have dual functions as pro-tumorigenic and anti-tumorigenic. To understand such paradoxical functions, the reductionistic approach classifies the immune cells into pro- and anti-tumor cells and suggests the therapeutic blockade of the pro-tumor and induction of the anti-tumor immune cells. This strategy has proven to be partially effective in prolonging patients' survival only in a fraction of patients without offering a cancer cure. Recent advances in multi-omics allow taking systems immunology approach. This essay discusses how a systems immunology approach could revolutionize our understanding of the TME by suggesting that internetwork interactions of the immune cell types create distinct collective functions independent of the function of each cellular constituent. Such collective function can be understood by the discovery of the immunological patterns in the TME and may be modulated as a therapeutic means for immunotherapy of cancer.
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Affiliation(s)
- Nicholas Koelsch
- Department of Microbiology & Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA;
| | - Masoud H. Manjili
- Department of Microbiology & Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA;
- VCU Massey Cancer Center, 401 College Street, Boc 980035, Richmond, VA 23298, USA
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Zhou H, Li XX, Huang YP, Wang YX, Zou H, Xiong L, Liu ZT, Wen Y, Zhang ZJ. Prognosis prediction and comparison between pancreatic signet ring cell carcinoma and pancreatic duct adenocarcinoma: a retrospective observational study. Front Endocrinol (Lausanne) 2023; 14:1205594. [PMID: 37534212 PMCID: PMC10390323 DOI: 10.3389/fendo.2023.1205594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/29/2023] [Indexed: 08/04/2023] Open
Abstract
Background Pancreatic signet ring cell carcinoma (PSRCC) is a rare and aggressive cancer that has been reported primarily as case reports. Due to limited large-scale epidemiological and prognostic analyses, the outcomes of PSRCC patients varies greatly in the absence of recognized first-line treatment strategies. This study aimed to compare the clinical features, treatment, and prognosis of PSRCC and pancreatic ductal cell carcinoma (PDAC), the most common subtype of pancreatic cancer, and to establish predictive models for these subtypes. Methods The data on PSRCC and PDAC patients from 1998 to 2018 was obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Thereafter, the clinical, demographic, and treatment characteristics of the two groups and the differences and influencing factors of the two groups were evaluated by propensity score matching (PSM), Kaplan-Meier survival curves, Cox risk regression analyses, and least absolute shrinkage and selection operator (LASSO) analysis. Next, prognosis models were constructed and validated by KM and ROC analysis. Finally, a nomogram was constructed, based on the results of these analyses, to predict survival outcomes of PSRCC and PDAC patients. Results A total of 84,789 patients (432 PSRCC and 84357 PDAC patients) were included in this study. The results of the study revealed that, compared to the PDAC patients, PSRCC patients were more likely to be male, aged between 58-72 years, have larger tumor masses, and less likely to undergo chemotherapy. Before PSM, the overall survival and cancer-specific survival of the PSRCC group were significantly lower than those PDAC group, but there was no difference in the prognosis of the two groups after PSM. Additionally, lymph node ratio (LNR), log odds of positive lymph node (LODDS), tumor size, age, T-stage, marital status, and summary stage were found to be independent prognostic factors for PSRCC. Lastly, the prediction model and nomogram based on these prognostic factors could accurately predict the survival rate of the patients in SEER datasets and external validation datasets. Conclusion The prognosis of PSRCC and PDAC patients is similar under the same conditions; however, PSRCC patients may have more difficulty in receiving better treatment, thus resulting in their poor prognosis.
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Affiliation(s)
- Hui Zhou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiao-xue Li
- Department of Obstetrics and Gynecology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun-peng Huang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yong-xiang Wang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Heng Zou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Li Xiong
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhong-tao Liu
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu Wen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zi-jian Zhang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Han Y, Akhtar J, Liu G, Li C, Wang G. Early warning and diagnosis of liver cancer based on dynamic network biomarker and deep learning. Comput Struct Biotechnol J 2023; 21:3478-3489. [PMID: 38213892 PMCID: PMC10782000 DOI: 10.1016/j.csbj.2023.07.002] [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: 04/12/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 01/13/2024] Open
Abstract
Background Early detection of complex diseases like hepatocellular carcinoma remains challenging due to their network-driven pathology. Dynamic network biomarkers (DNB) based on monitoring changes in molecular correlations may enable earlier predictions. However, DNB analysis often overlooks disease heterogeneity. Methods We integrated DNB analysis with graph convolutional neural networks (GCN) to identify critical transitions during hepatocellular carcinoma development in a mouse model. A DNB-GCN model was constructed using transcriptomic data and gene expression levels as node features. Results DNB analysis identified a critical transition point at 7 weeks of age despite histological examinations being unable to detect cancerous changes at that time point. The DNB-GCN model achieved 100% accuracy in classifying healthy and cancerous mice, and was able to accurately predict the health status of newly introduced mice. Conclusion The integration of DNB analysis and GCN demonstrates potential for the early detection of complex diseases by capturing network structures and molecular features that conventional biomarker discovery methods overlook. The approach warrants further development and validation.
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Affiliation(s)
- Yukun Han
- Institute of Modern Biology, Nanjing University, Nanjing 210023, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Javed Akhtar
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guozhen Liu
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chenzhong Li
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guanyu Wang
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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