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Wang L, Peng F, Li ZH, Deng YF, Ruan MN, Mao ZG, Li L. Identification of AKI signatures and classification patterns in ccRCC based on machine learning. Front Med (Lausanne) 2023; 10:1195678. [PMID: 37293297 PMCID: PMC10244623 DOI: 10.3389/fmed.2023.1195678] [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: 03/28/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Background Acute kidney injury can be mitigated if detected early. There are limited biomarkers for predicting acute kidney injury (AKI). In this study, we used public databases with machine learning algorithms to identify novel biomarkers to predict AKI. In addition, the interaction between AKI and clear cell renal cell carcinoma (ccRCC) remain elusive. Methods Four public AKI datasets (GSE126805, GSE139061, GSE30718, and GSE90861) treated as discovery datasets and one (GSE43974) treated as a validation dataset were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between AKI and normal kidney tissues were identified using the R package limma. Four machine learning algorithms were used to identify the novel AKI biomarkers. The correlations between the seven biomarkers and immune cells or their components were calculated using the R package ggcor. Furthermore, two distinct ccRCC subtypes with different prognoses and immune characteristics were identified and verified using seven novel biomarkers. Results Seven robust AKI signatures were identified using the four machine learning methods. The immune infiltration analysis revealed that the numbers of activated CD4 T cells, CD56dim natural killer cells, eosinophils, mast cells, memory B cells, natural killer T cells, neutrophils, T follicular helper cells, and type 1 T helper cells were significantly higher in the AKI cluster. The nomogram for prediction of AKI risk demonstrated satisfactory discrimination with an Area Under the Curve (AUC) of 0.919 in the training set and 0.945 in the testing set. In addition, the calibration plot demonstrated few errors between the predicted and actual values. In a separate analysis, the immune components and cellular differences between the two ccRCC subtypes based on their AKI signatures were compared. Patients in the CS1 had better overall survival, progression-free survival, drug sensitivity, and survival probability. Conclusion Our study identified seven distinct AKI-related biomarkers based on four machine learning methods and proposed a nomogram for stratified AKI risk prediction. We also confirmed that AKI signatures were valuable for predicting ccRCC prognosis. The current work not only sheds light on the early prediction of AKI, but also provides new insights into the correlation between AKI and ccRCC.
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Affiliation(s)
- Li Wang
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Fei Peng
- Department of Cardiology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Zhen Hua Li
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yu Fei Deng
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Meng Na Ruan
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhi Guo Mao
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Lin Li
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
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Epigenetic Regulation of MAP3K8 in EBV-Associated Gastric Carcinoma. Int J Mol Sci 2023; 24:ijms24031964. [PMID: 36768307 PMCID: PMC9916342 DOI: 10.3390/ijms24031964] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
Super-enhancers (SEs) regulate gene expressions, which are critical for cell type-identity and tumorigenesis. Although genome wide H3K27ac profiling have revealed the presence of SE-associated genes in gastric cancer (GC), their roles remain unclear. In this study, ChIP-seq and HiChIP-seq experiments revealed mitogen-activated protein kinase 8 (MAP3K8) to be an SE-associated gene with chromosome interactions in Epstein-Barr virus-associated gastric carcinoma (EBVaGC) cells. CRISPRi mediated repression of the MAP3K8 SEs attenuated MAP3K8 expression and EBVaGC cell proliferation. The results were validated by treating EBVaGC cells with bromodomain and the extra-terminal motif (BET) inhibitor, OTX015. Further, functional analysis of MAP3K8 in EBVaGC revealed that silencing MAP3K8 could inhibit the cell proliferation, colony formation, and migration of EBVaGC cells. RNA-seq and pathway analysis indicated that knocking down MAP3K8 obstructed the notch signaling pathway and epithelial-mesenchymal transition (EMT) in EBVaGC cells. Further, analysis of the cancer genome atlas (TCGA) and GSE51575 databases exhibited augmented MAP3K8 expression in gastric cancer and it was found to be inversely correlated with the disease-free progression of GC. Moreover, Spearman's correlation revealed that MAP3K8 expression was positively correlated with the expressions of notch pathway and EMT related genes, such as, Notch1, Notch2, C-terminal binding protein 2 (CTBP2), alpha smooth muscle actin isotype 2 (ACTA2), transforming growth factor beta receptor 1 (TGFβR1), and snail family transcriptional repressors 1/2 (SNAI1/SNAI2) in GC. Taken together, we are the first to functionally interrogate the mechanism of SE-mediated regulation of MAP3K8 in EBVaGC cell lines.
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Dai YY, Gao YP, Chen LX, Liu JS, Zeng C, Zhou JD, Wu HL. Predicting prognosis and immune responses in hepatocellular carcinoma based on N7-methylguanosine-related long noncoding RNAs. Front Genet 2022; 13:930446. [PMID: 36110218 PMCID: PMC9468367 DOI: 10.3389/fgene.2022.930446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC), which has high rates of recurrence and metastasis and is the main reason and the most common tumor for cancer mortality worldwide, has an unfavorable prognosis. N7-methylguanosine (m7G) modification can affect the formation and development of tumors by affecting gene expression and other biological processes. In addition, many previous studies have confirmed the unique function of long noncoding RNAs (lncRNAs) in tumor progression; however, studies exploring the functions of m7G-related lncRNAs in HCC patients has been limited. Methods: Relevant RNA expression information was acquired from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov), and m7G-related lncRNAs were identified via gene coexpression analysis. Afterward, univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression, and multivariate regression analyses were implemented to construct an ideal risk model whose validity was verified using Kaplan–Meier survival, principal component, receiver operating characteristic (ROC) curve, and nomogram analyses. In addition, the potential functions of lncRNAs in the novel signature were explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analyses and gene set enrichment analysis (GSEA). At last, in both risk groups and subtypes classified based on the expression of the risk-related lncRNAs, we analyzed the immune characteristics and drug sensitivity of patients. Results: After rigorous screening processes, we built a model based on 11 m7G-related lncRNAs for predicting patient overall survival (OS). The results suggested that the survival status of patients with high-risk scores was lower than that of patients with low-risk scores, and a high-risk score was related to malignant clinical features. Cox regression analysis showed that the m7G risk score was an independent prognostic parameter. Moreover, immune cell infiltration and immunotherapy sensitivity differed between the risk groups. Conclusion: The m7G risk score model constructed based on 11 m7G-related lncRNAs can effectively assess the OS of HCC patients and may offer support for making individualized treatment and immunotherapy decisions for HCC patients.
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Affiliation(s)
- Yu-yang Dai
- Department of Radiology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu Province, China
- Department of Radiology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Yi-ping Gao
- Department of Interventional Radiology, Nanfang Hospital Affiliated to Southern Medical University, Guangzhou, Guangdong, China
| | - Lin-xin Chen
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, School of Ophthalmology and Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jin-song Liu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Cheng Zeng
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Jian-dong Zhou
- Department of Nephrology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
- Department of Nephrology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Hong-lin Wu
- Department of Radiology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu Province, China
- Department of Radiology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
- *Correspondence: Hong-lin Wu,
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Gong Y, Lv Y, Xu F, Xiu Y, Lu Y, Liu Z, Deng L. LAMTOR3 is a prognostic biomarker in kidney renal clear cell carcinoma. J Clin Lab Anal 2022; 36:e24648. [PMID: 36082464 PMCID: PMC9459259 DOI: 10.1002/jcla.24648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022] Open
Abstract
Objective The objective of the study was to investigate the expression of LAMTOR3 in kidney renal clear cell carcinoma (KIRC) and its clinical significance. Methods The expression of LAMTOR3 in KIRC and its relationship with clinical features were analyzed using the UALCAN online database. The results were verified using KIRC gene chip data and clinical specimens. The prognosis of KIRC patients was analyzed with the GEPIA2 database. GO, KEGG, and GSEA analyses were conducted to analyze the possible molecular mechanism of LAMTOR3 in KIRC. Immunohistochemical (IHC) and hematoxylin and eosin (H&E) staining were used for histopathological detection. Results UALCAN database analysis showed that LAMTOR3 expression in KIRC was significantly lower than in normal kidney tissues and correlated with the clinical stage, pathological grade, and tumor genotype (p < .05). GSE53757 dataset analysis consistently showed that the expression of LAMTOR3 in KIRC was significantly lower than in normal kidney tissues (p < .01). GEPIA2 database analysis indicated that patients with low LAMTOR3 expression had poor overall and disease‐free survival rates. GSEA analysis suggested that LAMTOR3 positively regulated the citrate cycle and drug metabolism cytochrome P450 and negatively regulated folate biosynthesis and olfactory transduction. The expression of LAMTOR3 in KIRC was also significantly correlated with immune cell infiltration. Finally, IHC showed that LAMTOR3 expression in the KIRC tissues was lower than in the adjacent normal tissues. Conclusion LAMTOR3 expression is significantly lower in KIRC. LAMTOR3 may be a potential marker for KIRC diagnosis and therapy.
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Affiliation(s)
- Yun Gong
- Health Management Center Jiangxi Provincial People's Hospital (The First Affiliated Hospital of Nanchang Medical College) Nanchang China
| | - Yue Lv
- Department of Urology The First Affiliated Hospital, Harbin Medical University Harbin China
| | - Fanghua Xu
- Department of Pathology Pingxiang People's Hospital (Pingxiang Hospital Affiliated to Southern Medical University) Pingxiang China
| | - Youcheng Xiu
- Department of Urology The First Affiliated Hospital, Harbin Medical University Harbin China
| | - Yinhui Lu
- Health Management Center Jiangxi Provincial People's Hospital (The First Affiliated Hospital of Nanchang Medical College) Nanchang China
| | - Zan Liu
- Department of Urology The First Affiliated Hospital, Harbin Medical University Harbin China
| | - Leihong Deng
- Department of Ultrasound Medicine The First Affiliated Hospital of Nanchang University Nanchang China
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Ding JT, Yu XT, He JH, Chen DZ, Guo F. A Pan-Cancer Analysis Revealing the Dual Roles of Lysine (K)-Specific Demethylase 6B in Tumorigenesis and Immunity. Front Genet 2022; 13:912003. [PMID: 35783266 PMCID: PMC9246050 DOI: 10.3389/fgene.2022.912003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Epigenetic-targeted therapy has been increasingly applied in the treatment of cancers. Lysine (K)-specific demethylase 6B (KDM6B) is an epigenetic enzyme involved in the coordinated control between cellular intrinsic regulators and the tissue microenvironment whereas the pan-cancer analysis of KDM6B remains unavailable. Methods: The dual role of KDM6B in 33 cancers was investigated based on the GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) databases. TIMER2 and GEPIA2 were applied to investigate the KDM6B levels in different subtypes or stages of tumors. Besides, the Human Protein Atlas database allowed us to conduct a pan-cancer study of the KDM6B protein levels. GEPIA2 and Kaplan–Meier plotter were used for the prognosis analysis in different cancers. Characterization of genetic modifications of the KDM6B gene was analyzed by the cBioPortal. DNA methylation levels of different KDM6B probes in different TCGA tumors were analyzed by MEXPRESS. TIMER2 was applied to determine the association of the KDM6B expression and immune infiltration and DNA methyltransferases. Spearman correlation analysis was used to assess the association of the KDM6B expression with TMB (tumor mutation burden) and MSI (microsatellite instability). The KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis and GO (Gene ontology) enrichment analysis were used to further investigate the potential mechanism of KDM6B in tumor pathophysiology. Results: KDM6B was downregulated in 11 cancer types and upregulated across five types. In KIRC (kidney renal clear cell carcinoma) and OV (ovarian serous cystadenocarcinoma), the KDM6B level was significantly associated with the pathological stage. A high level of KDM6B was related to poor OS (overall survival) outcomes for THCA (thyroid carcinoma), while a low level was correlated with poor OS and DFS (disease-free survival) prognosis of KIRC. The KDM6B expression level was associated with TMB, MSI, and immune cell infiltration, particularly cancer-associated fibroblasts, across various cancer types with different correlations. Furthermore, the enrichment analysis revealed the relationship between H3K4 and H3K27 methylation and KDM6B function. Conclusion: Dysregulation of the DNA methyltransferase activity and methylation levels of H3K4 and H3K27 may involve in the dual role of KDM6B in tumorigenesis and development. Our study offered a relatively comprehensive understanding of KDM6B’s dual role in cancer development and response to immunotherapy.
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Affiliation(s)
- Jia-Tong Ding
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, China
- The Second Clinical Medical College of Nanchang University, Nanchang, China
| | - Xiao-Ting Yu
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jin-Hao He
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - De-Zhi Chen
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fei Guo
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, China
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Fei Guo,
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