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Jin R, Du F, Han X, Guo J, Song W, Xia Y, Yue X, Yang D, Tong J, Zhang Q, Liu Y. Prognostic Value of Insulin Growth Factor-Like Receptor 1 (IGFLR1) in Stage II and III Colorectal Cancer and Its Association with Immune Cell Infiltration. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05006-1. [PMID: 39141178 DOI: 10.1007/s12010-024-05006-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/15/2024]
Abstract
IGFLR1 is a novel biomarker, and some evidences suggested that is involved in the immune microenvironment of CRC. Here, we explored the expression of IGFLR1 and its association with the prognosis as well as immune cell infiltration in CRC, with the aim to provide a basis for further studies on IGFLR1. Immunohistochemical staining for IGFLR1, TIM-3, FOXP3, CD4, CD8, and PD-1 was performed in eligible tissues to analyze the expression of IGFLR1 and its association with prognosis and immune cell infiltration. Then, we screened colon cancer samples from TCGA and grouped patients according to IGFLR1-related genes. We also evaluated the co-expression and immune-related pathways of IGFLR1 to identify the potential mechanism of it in CRC. When P < 0.05, the results were considered statistically significant. IGFLR1 and IGFLR1-related genes were associated with the prognosis and immune cell infiltration (P < 0.05). In stage II and III CRC tissue and normal tissue, we found (1) IGFLR1 was expressed in both the cell membrane and cytoplasm and which was differentially expressed between cancer tissue and normal tissue. IGFLR1 expression was associated with the expression of FOXP3, CD8, and gender but was not associated with microsatellite instability. (2) IGFLR1 was an independent prognostic factor and patients with high IGFLR1 had a better prognosis. (3) A model including IGFLR1, FOXP3, PD-1, and CD4 showed good prognostic stratification ability. (4) There was a significant interaction between IGFLR1 and GATA3, and IGFLR1 had a significant co-expression with related factors in the INFR pathway. IGFLR1 has emerged as a new molecule related to disease prognosis and immune cell infiltration in CRC patients and showed a good ability to predict the prognosis of patients.
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Affiliation(s)
- Ran Jin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fenqi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinhao Han
- Department of Biostatistics, Public Health School of Harbin Medical University, Harbin, China
| | - Junnan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wenjie Song
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yixiu Xia
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinyu Yue
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Da Yang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinxue Tong
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Qiuju Zhang
- Health Management Centre, Harbin Medical University Cancer Hospital, Harbin, China.
- Department of Biostatistics, Public Health School of Harbin Medical University, Harbin, China.
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
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Wang HX, Zhao ZP, Du XY, Peng SL, Xu HY, Tang W, Yang L. SLFN11 promotes clear cell renal cell carcinoma progression via the PI3K/AKT signaling pathway. Med Oncol 2024; 41:54. [PMID: 38206539 DOI: 10.1007/s12032-023-02262-9] [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: 08/25/2023] [Accepted: 11/18/2023] [Indexed: 01/12/2024]
Abstract
SLFN11 is abnormally expressed and associated with survival outcomes in various human cancers. However, the role of SLFN11 in clear cell renal cell carcinoma (ccRCC) remains unclear. This study aimed to investigate the clinical value and potential functions of SLFN11 in ccRCC. Comprehensive bioinformatics analyses were performed using online databases. Quantitative real-time PCR (qPCR) and western blotting were used to validate the expression data. CCK8, flow cytometry analysis, and EdU staining were performed to determine the level of cell proliferation. Flow cytometry analysis was also used to detect cell apoptosis. Wound-healing assay and Transwell assays were performed to assess cell migration and invasion capability, respectively. SLFN11 was overexpressed and was an independent prognostic factor in ccRCC. SLFN11 knockdown inhibited cell proliferation, migration, and invasion and promoted apoptosis. Functional and pathway enrichment analyses suggested that SLFN11 may have an impact on tumorigenesis in ccRCC through regulation of the inflammatory response, the PI3K/AKT signaling pathway and other effectors. Furthermore, SLFN11 knockdown inhibited the phosphorylation of the PI3K/AKT signaling pathway and could be activated by 740 Y-P. Finally, we demonstrated that miR-183 may specifically target SLFN11, and miR-183 expression was correlated with predicted survival. SLFN11 may play a critical role in ccRCC progression and may serve as a novel prognostic biomarker in ccRCC.
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Affiliation(s)
- He-Xi Wang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Zhi-Peng Zhao
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xiao-Yi Du
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Sen-Lin Peng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Hao-Yu Xu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Wei Tang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Lei Yang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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Zhou J, Liang G, Liu L, Feng S, Zheng Z, Wu Y, Chen X, Li X, Wang L, Wang L, Song Z. Single-cell RNA-seq reveals abnormal differentiation of keratinocytes and increased inflammatory differentiated keratinocytes in atopic dermatitis. J Eur Acad Dermatol Venereol 2023; 37:2336-2348. [PMID: 37326015 DOI: 10.1111/jdv.19256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) is a chronic and recurrent inflammatory skin disease characterized by severe pruritus and eczematous lesions. Heterogeneity of AD has been reported among different racial groups according to clinical, molecular and genetic differences. OBJECTIVE This study aimed to conduct an in-depth transcriptome analysis of AD in Chinese population. METHODS We performed single-cell RNA sequencing (scRNA-seq) analysis of skin biopsies from five Chinese adult patients with chronic AD and from four healthy controls, combined with multiplexed immunohistochemical analysis in whole-tissue skin biopsies. We explored the functions of IL19 in vitro. RESULTS ScRNA-seq analysis was able to profile a total of 87,853 cells, with keratinocytes (KCs) in AD manifesting highly expressed keratinocyte activation and pro-inflammatory genes. KCs demonstrated a novel IL19+ IGFL1+ subpopulation that increased in AD lesions. Inflammatory cytokines IFNG, IL13, IL26 and IL22 were highly expressed in AD lesions. In vitro, IL19 directly downregulated KRT10 and LOR in HaCaT cells and activated HaCaT cells to produce TSLP. CONCLUSION Abnormal proliferation and differentiation of keratinocytes contribute immensely to the pathogenesis of AD, whereas AD chronic lesions have witnessed significant presence of IL19+ IGFL1+ KCs, which may be involved in the disruption of the skin barrier, the connection and magnification of Th2 and Th17 inflammatory responses, and mediation of skin pruritus. Furthermore, progressive activation of multiple immune axes dominated by Type 2 inflammatory reaction occur in AD chronic lesions.
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Affiliation(s)
- Jie Zhou
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Gaopeng Liang
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Lu Liu
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Shujing Feng
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zhengni Zheng
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yaguang Wu
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xiaoling Chen
- Institute of Immunology PLA & Department of Immunology, Army Medical University, Chongqing, China
| | - Xiangqian Li
- Institute of Immunology PLA & Department of Immunology, Army Medical University, Chongqing, China
| | - Lina Wang
- Institute of Immunology PLA & Department of Immunology, Army Medical University, Chongqing, China
- Department of Immunology, College of Basic Medicine, Qingdao University, Qingdao, China
- Department of Immunology, College of Basic Medicine, Weifang Medical University, Weifang, China
| | - Li Wang
- Institute of Immunology PLA & Department of Immunology, Army Medical University, Chongqing, China
| | - Zhiqiang Song
- Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, China
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Deo R, Dubin RF, Ren Y, Murthy AC, Wang J, Zheng H, Zheng Z, Feldman H, Shou H, Coresh J, Grams M, Surapaneni AL, Bhat Z, Cohen JB, Rahman M, He J, Saraf SL, Go AS, Kimmel PL, Vasan RS, Segal MR, Li H, Ganz P. Proteomic cardiovascular risk assessment in chronic kidney disease. Eur Heart J 2023; 44:2095-2110. [PMID: 37014015 PMCID: PMC10281556 DOI: 10.1093/eurheartj/ehad115] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/21/2023] [Accepted: 02/16/2023] [Indexed: 04/05/2023] Open
Abstract
AIMS Chronic kidney disease (CKD) is widely prevalent and independently increases cardiovascular risk. Cardiovascular risk prediction tools derived in the general population perform poorly in CKD. Through large-scale proteomics discovery, this study aimed to create more accurate cardiovascular risk models. METHODS AND RESULTS Elastic net regression was used to derive a proteomic risk model for incident cardiovascular risk in 2182 participants from the Chronic Renal Insufficiency Cohort. The model was then validated in 485 participants from the Atherosclerosis Risk in Communities cohort. All participants had CKD and no history of cardiovascular disease at study baseline when ∼5000 proteins were measured. The proteomic risk model, which consisted of 32 proteins, was superior to both the 2013 ACC/AHA Pooled Cohort Equation and a modified Pooled Cohort Equation that included estimated glomerular filtrate rate. The Chronic Renal Insufficiency Cohort internal validation set demonstrated annualized receiver operating characteristic area under the curve values from 1 to 10 years ranging between 0.84 and 0.89 for the protein and 0.70 and 0.73 for the clinical models. Similar findings were observed in the Atherosclerosis Risk in Communities validation cohort. For nearly half of the individual proteins independently associated with cardiovascular risk, Mendelian randomization suggested a causal link to cardiovascular events or risk factors. Pathway analyses revealed enrichment of proteins involved in immunologic function, vascular and neuronal development, and hepatic fibrosis. CONCLUSION In two sizeable populations with CKD, a proteomic risk model for incident cardiovascular disease surpassed clinical risk models recommended in clinical practice, even after including estimated glomerular filtration rate. New biological insights may prioritize the development of therapeutic strategies for cardiovascular risk reduction in the CKD population.
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Affiliation(s)
- Rajat Deo
- Division of Cardiovascular Medicine, Electrophysiology Section, Perelman School of Medicine at the University of Pennsylvania, One Convention Avenue, Level 2 / City Side, Philadelphia, PA 19104, USA
| | - Ruth F Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Yue Ren
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Ashwin C Murthy
- Division of Cardiovascular Medicine, Electrophysiology Section, Perelman School of Medicine at the University of Pennsylvania, One Convention Avenue, Level 2 / City Side, Philadelphia, PA 19104, USA
| | - Jianqiao Wang
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Haotian Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Harold Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Josef Coresh
- Department of Epidemiology; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University, 2024 E. Monument Street, Room 2-635, Suite 2-600, Baltimore, MD 21287, USA
| | - Morgan Grams
- Department of Epidemiology; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University, 2024 E. Monument Street, Room 2-635, Suite 2-600, Baltimore, MD 21287, USA
| | - Aditya L Surapaneni
- Department of Epidemiology; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Zeenat Bhat
- Division of Nephrology, University of Michigan, 5100 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105, USA
| | - Jordana B Cohen
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
- Renal, Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, 831 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Mahboob Rahman
- Department of Medicine, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Wearn Bldg. 3 Floor. Rm 352, Cleveland, OH 44106, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, SL 18, New Orleans, LA 70112, USA
| | - Santosh L Saraf
- Division of Hematology and Oncology, University of Illinois at Chicago, 1740 West Taylor Street, Chicago, IL 60612, USA
| | - Alan S Go
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA 94612, USA
- Departments of Epidemiology, Biostatistics and Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Ramachandran S Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Section of Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, 550 16th Street, 2nd Floor, Box #0560, San Francisco, CA 94143, USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Peter Ganz
- Division of Cardiology, Zuckerberg San Francisco General Hospital and Department of Medicine, University of California, San Francisco, 1001 Potrero Avenue, 5G1, San Francisco, CA 94110, USA
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Sologova SS, Zavadskiy SP, Mokhosoev IM, Moldogazieva NT. Short Linear Motifs Orchestrate Functioning of Human Proteins during Embryonic Development, Redox Regulation, and Cancer. Metabolites 2022; 12:metabo12050464. [PMID: 35629968 PMCID: PMC9144484 DOI: 10.3390/metabo12050464] [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: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
Short linear motifs (SLiMs) are evolutionarily conserved functional modules of proteins that represent amino acid stretches composed of 3 to 10 residues. The biological activities of two short peptide segments of human alpha-fetoprotein (AFP), a major embryo-specific and cancer-related protein, have been confirmed experimentally. This is a heptapeptide segment LDSYQCT in domain I designated as AFP14–20 and a nonapeptide segment EMTPVNPGV in domain III designated as GIP-9. In our work, we searched the UniprotKB database for human proteins that contain SLiMs with sequence similarity to the both segments of human AFP and undertook gene ontology (GO)-based functional categorization of retrieved proteins. Gene set enrichment analysis included GO terms for biological process, molecular function, metabolic pathway, KEGG pathway, and protein–protein interaction (PPI) categories. We identified the SLiMs of interest in a variety of non-homologous proteins involved in multiple cellular processes underlying embryonic development, cancer progression, and, unexpectedly, the regulation of redox homeostasis. These included transcription factors, cell adhesion proteins, ubiquitin-activating and conjugating enzymes, cell signaling proteins, and oxidoreductase enzymes. They function by regulating cell proliferation and differentiation, cell cycle, DNA replication/repair/recombination, metabolism, immune/inflammatory response, and apoptosis. In addition to the retrieved genes, new interacting genes were identified. Our data support the hypothesis that conserved SLiMs are incorporated into non-homologous proteins to serve as functional blocks for their orchestrated functioning.
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Affiliation(s)
- Susanna S. Sologova
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
| | - Sergey P. Zavadskiy
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
| | - Innokenty M. Mokhosoev
- Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Nurbubu T. Moldogazieva
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
- Correspondence:
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Wang PY, Yang S, Bao YJ. An Integrative Analysis Framework for Identifying the Prognostic Markers from Multidimensional RNA Data of Clear Cell Renal Cell Carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:671-686. [PMID: 35063405 DOI: 10.1016/j.ajpath.2021.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/13/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The altered regulatory status of long noncoding RNA (lncRNA), miRNA, and mRNA and their interactions play critical roles in tumor proliferation, metastasis, and progression, which ultimately influence cancer prognosis. However, there are limited studies of comprehensive identification of prognostic biomarkers from combined data sets of the three RNA types in the highly metastatic clear cell renal cell carcinoma (ccRCC). The current study employed an integrative analysis framework of functional genomics approaches and machine learning methods to the lncRNA, miRNA, and mRNA data and identified 16 RNAs (3 lncRNAs, 6 miRNAs, and 7 mRNAs) of prognostic value, with 9 of them novel. A 16 RNA-based score was established for prognosis prediction of ccRCC with significance (P < 0.0001). The area under the curve for the score model was 0.868 to 0.870 in the training cohort and 0.714 to 0.778 in the validation cohort. Construction of the lncRNA-miRNA-mRNA interaction network showed that the downstream mRNAs and upstream lncRNAs in the network initiated from the miRNA or lncRNA markers exhibit significant enrichment in functional classifications associated with cancer metastasis, proliferation, progression, or prognosis. The functional analysis provided clear support for the role of the RNA biomarkers in predicting cancer prognosis. This study provides promising biomarkers for predicting prognosis of ccRCC using multidimensional RNA data, and these findings are expected to facilitate potential clinical applications of the biomarkers.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Kaplan-Meier Estimate
- Male
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Prognosis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Peng-Ying Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Yun-Juan Bao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China.
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Da Q, Ren M, Huang L, Qu J, Yang Q, Xu J, Ma Q, Mao X, Cai Y, Zhao D, Luo J, Yan Z, Sun L, Ouyang K, Zhang X, Han Z, Liu J, Wang T. Identification and Validation of a Ferroptosis-Related Signature for Predicting Prognosis and Immune Microenvironment in Papillary Renal Cell Carcinoma. Int J Gen Med 2022; 15:2963-2977. [PMID: 35313551 PMCID: PMC8934172 DOI: 10.2147/ijgm.s354882] [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: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 11/30/2022] Open
Abstract
Objective We aimed to explore the prognostic patterns of ferroptosis-related genes in papillary renal cell carcinoma (PRCC) and investigate the relationship between ferroptosis-related genes and PRCC tumor immune microenvironment. Methods We obtained the mRNA expression and corresponding clinical data of PRCC from the public tumor cancer genome atlas database (TCGA). The PRCC patients were randomly divided into two cohort, training cohort and verification cohort, respectively. Univariate Cox regression, LASSO Cox regression, multivariate Cox regression analysis were utilized to construct ferroptosis signature for PRCC patients. And then, risk prognostic model was established and verified. The correlation of ferroptosis-related signature with survival and immune microenvironment was systematically analyzed. Results A 4-genes ferroptosis signature (CDKN1A, MIOX, PSAT1, and RRM2) was constructed. Multivariate Cox regression assay indicates that the risk score of ferroptosis signature was an independent prognostic indicator (HR=1.391, p<0.001). The survival curve shows that the high-risk group has a poorer prognosis than the low-risk group (p<0.001). The risk prognostic model was established based on prognostic factors of clinical-stage, hemoglobin, and risk score. The time-dependent receiver operating characteristic curve (ROC) analysis proves the predictive capacity of the ferroptosis signature, the 3 years area under the curve (AUC) is 0.890, and the 5 years AUC is 0.733. Further analysis suggested that cell cycle, pentose phosphate pathway, P53 signaling pathway were significantly enriched in the high-risk group. The significantly different fractions of dendritic cells resting, macrophage cells, and T cells follicular helper were observed in risk groups. Conclusion This study implicates a ferroptosis signature which has a good predict capacity of the prognosis in PRCC patients. Ferroptosis-related genes may have a key role in the process of anti-tumor and serve as therapeutic targets for PRCC.
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Affiliation(s)
- Qingen Da
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Mingming Ren
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Lei Huang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Jianhua Qu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Qiuhua Yang
- Vascular Biology Center, Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Jiean Xu
- Shenzhen Graduate School, Peking University, Shenzhen, People’s Republic of China
| | - Qian Ma
- Shenzhen Graduate School, Peking University, Shenzhen, People’s Republic of China
| | - Xiaoxiao Mao
- Shenzhen Graduate School, Peking University, Shenzhen, People’s Republic of China
| | - Yongfeng Cai
- Shenzhen Graduate School, Peking University, Shenzhen, People’s Republic of China
| | - Dingwei Zhao
- Shenzhen Graduate School, Peking University, Shenzhen, People’s Republic of China
| | - Junhua Luo
- Department of Urological Surgery, Peking University Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Zilong Yan
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Lu Sun
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Xiaowei Zhang
- School of Basic Medical Sciences, Peking University, Beijing, People’s Republic of China
| | - Zhen Han
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
| | - Jikui Liu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
- Correspondence: Jikui Liu, Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China, Email
| | - Tao Wang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China
- Tao Wang, Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People’s Republic of China, Email
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8
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Ren X, Ma L, Wang N, Zhou R, Wu J, Xie X, Zhang H, Liu D, Ma X, Dang C, Kang H, Zhou Z. Antioxidant Gene Signature Impacts the Immune Infiltration and Predicts the Prognosis of Kidney Renal Clear Cell Carcinoma. Front Genet 2021; 12:721252. [PMID: 34490047 PMCID: PMC8416991 DOI: 10.3389/fgene.2021.721252] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/30/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Oxidative stress is related to oncogenic transformation in kidney renal clear cell carcinoma (KIRC). We intended to identify a prognostic antioxidant gene signature and investigate its relationship with immune infiltration in KIRC. Methods: With the support of The Cancer Genome Atlas (TCGA) database, we researched the gene expression and clinical data of KIRC patients. Antioxidant related genes with significant differences in expression between KIRC and normal samples were then identified. Through univariate and multivariate Cox analysis, a prognostic gene model was established and all patients were divided into high- and low-risk subgroups. Single sample gene set enrichment analysis was adopted to analyze the immune infiltration, HLA expression, and immune checkpoint genes in different risk groups. Finally, the prognostic nomogram model was established and evaluated. Results: We identified six antioxidant genes significantly correlated with the outcome of KIRC patients as independent predictors, namely DPEP1 (HR = 0.97, P < 0.05), GSTM3 (HR = 0.97, P < 0.05), IYD (HR = 0.33, P < 0.05), KDM3B (HR = 0.96, P < 0.05), PRDX2 (HR = 0.99, P < 0.05), and PRXL2A (HR = 0.96, P < 0.05). The high- and low-risk subgroups of KIRC patients were grouped according to the six-gene signature. Patients with higher risk scores had poorer prognosis, more advanced grade and stage, and more abundance of M0 macrophages, regulatory T cells, and follicular helper T cells. There were statistically significant differences in HLA and checkpoint gene expression between the two risk subgroups. The performance of the nomogram was favorable (concordance index = 0.766) and reliably predicted the 3-year (AUC = 0.792) and 5-year (AUC = 0.766) survival of patients with KIRC. Conclusion: The novel six antioxidant related gene signature could effectively forecast the prognosis of patients with KIRC, supply insights into the interaction between cellular antioxidant mechanisms and cancer, and is an innovative tool for selecting potential patients and targets for immunotherapy.
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Affiliation(s)
- Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ruina Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jianhua Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Xie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Di Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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