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Chen Z, Zhang L, Ding C, Ren K, Wan D, Lin S. A six-miRNA signature as a novel biomarker for improving prediction of prognosis and patterns of immune infiltration in hepatocellular carcinoma. Am J Transl Res 2022; 14:3610-3637. [PMID: 35836899 PMCID: PMC9274565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the leading causes of tumor-related death. MicroRNAs (miRNAs) belong to a subfamily of functional non-coding RNAs (ncRNAs) and are essential regulators of tumorigenesis. They affect tumor-related therapeutic response, tumor metastasis, and clinical outcomes of several human malignant tumors. However, the prognostic value of miRNAs and their role in the tumor immune microenvironment (TIME) of HCC have not been clarified. MATERIALS AND METHODS Raw RNA-sequencing data (mRNA and miRNA) and clinicopathological characteristics of HCC samples were downloaded from the TCGA-GDC database. The Perl programming language, R software, Cytoscape software, and several online databases were used to clarify the clinical significance and biological functions of miRNAs and their target genes in HCC. RESULTS A total of 424 mRNA-sequencing samples and 425 miRNA-sequencing samples were obtained from the TCGA database. There were 344 HCC cases with complete information in the TCGA dataset and they were randomly categorized into two subgroups. Six miRNAs were identified as independent prognostic biomarkers for HCC patients by univariate and multivariate Cox regression analysis. The constructed prognostic signature, which contains these six miRNAs, was significantly correlated with overall survival (OS). In addition, this prognostic signature is superior to single miRNA in predicting short-term prognosis of HCC patients. We also found that the prognostic signature was significantly associated with tumor-related immune cell infiltration, TIME, and immunotherapeutic response. Furthermore, a total of 4568 potential target genes of six miRNAs were identified. The miRNA-mRNA co-expression network, protein-protein interaction (PPI) network, and functional and pathway enrichment analysis demonstrated that these miRNA-related target genes have important biological effects during the initiation and progression of HCC. CONCLUSIONS This study demonstrates that the miRNA signature can accurately predict the prognosis of HCC patients and provide a basis for novel immunotherapy treatments.
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Affiliation(s)
- Zhitao Chen
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical CollegeHangzhou 310004, Zhejiang, China
| | - Lele Zhang
- First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310003, Zhejiang, China
| | - Chenchen Ding
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical CollegeHangzhou 310004, Zhejiang, China
| | - Kuiwu Ren
- Fuyang People’s HospitalFuyang 236001, Anhui, China
| | - Dalong Wan
- First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310003, Zhejiang, China
| | - Shengzhang Lin
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical CollegeHangzhou 310004, Zhejiang, China
- School of Medicine, Zhejiang University City CollegeHangzhou 310004, Zhejiang, China
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Zhang H, Xu C, Jiang F, Feng J. A Three-Genes Signature Predicting Colorectal Cancer Relapse Reveals LEMD1 Promoting CRC Cells Migration by RhoA/ROCK1 Signaling Pathway. Front Oncol 2022; 12:823696. [PMID: 35619906 PMCID: PMC9127067 DOI: 10.3389/fonc.2022.823696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/28/2022] [Indexed: 01/26/2023] Open
Abstract
Objective Colorectal cancer (CRC) patients that experience early relapse consistently exhibit poor survival. However, no effective approach has been developed for the diagnosis and prognosis prediction of postoperative relapsed CRC. Methods Multiple datasets from the GEO database and TCGA database were utilized for bioinformatics analysis. WGCNA analyses and RRA analysis were performed to identify key genes. The COX/Lasso regression model was used to construct the recurrence model. Subsequent in vitro experiments further validated the potential role of the hub genes in CRC. Results A comprehensive analysis was performed on multiple CRC datasets and a CRC recurrence model was constructed containing LEMD1, SERPINE1, and SIAE. After further validation in two independent databases, we selected LEMD1 for in vitro experiments and found that LEMD1 could regulate CRC cell proliferation, migration, invasion, and promote EMT transition. The Rho-GTPase pulldown experiments further indicated that LEMD1 could affect RhoA activity and regulate cytoskeletal dynamics. Finally, we demonstrated that LEMD1 promoted CRC cell migration through the RhoA/ROCK1 signaling pathway. Conclusions In this study, a CRC relapse model consisting of LEMD1, SERPINE1, and SIAE was constructed by comprehensive analysis of multiple CRC datasets. LEMD1 could promote CRC cell migration through the RhoA/ROCK signaling pathway.
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Affiliation(s)
- Hui Zhang
- Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Chenxin Xu
- Research Center for Clinical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Feng Jiang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Research Center for Clinical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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Saad M, He S, Thorstad W, Gay H, Barnett D, Zhao Y, Ruan S, Wang X, Li H. Learning-based Cancer Treatment Outcome Prognosis using Multimodal Biomarkers. IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES 2022; 6:231-244. [PMID: 35520102 PMCID: PMC9066560 DOI: 10.1109/trpms.2021.3104297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Predicting early in treatment whether a tumor is likely to be responsive is a difficult yet important task to support clinical decision-making. Studies have shown that multimodal biomarkers could provide complementary information and lead to more accurate treatment outcome prognosis than unimodal biomarkers. However, the prognosis accuracy could be affected by multimodal data heterogeneity and incompleteness. The small-sized and imbalance datasets also bring additional challenges for training a designed prognosis model. In this study, a modular framework employing multimodal biomarkers for cancer treatment outcome prediction was proposed. It includes four modules of synthetic data generation, deep feature extraction, multimodal feature fusion, and classification to address the challenges described above. The feasibility and advantages of the designed framework were demonstrated through an example study, in which the goal was to stratify oropharyngeal squamous cell carcinoma (OPSCC) patients with low- and high-risks of treatment failures by use of positron emission tomography (PET) image data and microRNA (miRNA) biomarkers. The superior prognosis performance and the comparison with other methods demonstrated the efficiency of the proposed framework and its ability of enabling seamless integration, validation and comparison of various algorithms in each module of the framework. The limitation and future work was discussed as well.
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Affiliation(s)
- Maliazurina Saad
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. She is now with the MD Anderson Cancer Center, Houston, TX, USA
| | - Shenghua He
- Department of Computer Science and Engineering, Washington University, Saint louis, MO, USA
| | - Wade Thorstad
- Department of Radiation Oncology, Washington University School of Medicine, Saint louis, MO, USA
| | - Hiram Gay
- Department of Radiation Oncology, Washington University School of Medicine, Saint louis, MO, USA
| | - Daniel Barnett
- Carle Cancer Center, Carle Foundation Hospital, Urbana, IL, USA
| | - Yujie Zhao
- Mao Clinic at Florida, Jacksonville, FL, USA
| | - Su Ruan
- Laboratoire LITIS (EA 4108), Equipe Quantif, University of Rouen, France
| | - Xiaowei Wang
- Department of Pharmacology and Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Hua Li
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Cancer Center at Illinois, and Carle Foundation Hospital, Urbana, IL, USA
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Li L, Xie R, Wei Q. Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer. PeerJ 2021; 9:e11893. [PMID: 34395102 PMCID: PMC8325912 DOI: 10.7717/peerj.11893] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/29/2021] [Indexed: 01/07/2023] Open
Abstract
Background We investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis. Methods We obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan-Meier (K-M) curve and receiver operating characteristic (ROC) curves to explore the signature's efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network. Results We found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1. Conclusion Our study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis.
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Affiliation(s)
- Lili Li
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongrong Xie
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Mohamad SFS, Elias MH. Potential treatment for chronic myeloid leukemia using microRNA: in silico comparison between plants and human microRNAs in targeting BCR-ABL1 gene. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00156-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by the expression of the BCR-ABL1 fusion gene. Tyrosine kinase inhibitors (TKI) are used to treat CML, but mutations in the tyrosine kinase domain contribute to CML chemo-resistance. Therefore, finding alternative molecular-targeted therapy is important for the comprehensive treatment of CML. MicroRNAs (miRNA) are small non-coding regulatory RNAs which suppress the expression of their target genes by binding to the 3′ untranslated region (3′UTR) of the target mRNA. Hypothetically, the miRNA-mRNA interaction would suppress BCR-ABL1 expression and consequently reduce and inhibit CML cell proliferation. Thus, our objective was to determine the target interaction of human and plant miRNAs targeting the 3′UTR region of BCR-ABL1 in terms of miRNA binding conformity, protein interaction network, and pathways using in silico analysis. The 3′UTR sequence of BCR-ABL1 is obtained from Ensembl Genome Browser while the binding conformity was determined using the PsRNATarget Analysis Server, RNA22, Target Rank Server, and DIANA TOOLS. Protein-protein interaction network and pathway analysis are determined using STRING, Cytoscape, and KEGG pathway analysis.
Results
Five plants and five human miRNAs show strong binding conformity with 3′UTR of BCR-ABL1. The strongest binding conformity was shown by Oryza sativa’s Osa-miR1858a and osa-miR1858b with −24.4 kcal/mol folding energy and a p value of 0.0077. Meanwhile, in human miRNA, the hsa-miR-891a-3p shows the highest miTG score of 0.99 with −12 kcal/mol folding energy and a p value of 0.037. Apart from ABL1, osa-miR1858a/osa-miR1858b and hsa-miR891a-3p also target other 720 and 645 genes, respectively. The interaction network of Osa-miR1858a/osa-miR1858b and hsa-miR891a-3p identifies nineteen and twelve ABL1’s immediate neighboring proteins, respectively. The pathways analysis focuses on the RAS, MAPK, CML, and hematopoietic cell lineage pathway.
Conclusion
Both plant and human miRNAs tested in this study could be a potential therapeutic prospect in CML treatment, but thermodynamically, osa-miR1858a/osa-miR1858b binding to ABL1 is more favorable. However, it is important to carry out more research in vitro and in vivo and clinical studies to assess its efficacy as a targeted therapy for CML.
Graphical abstract
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Stempor PA, Avni D, Leibowitz R, Sidi Y, Stępień M, Dzieciątkowski T, Dobosz P. Comprehensive Analysis of Correlations in the Expression of miRNA Genes and Immune Checkpoint Genes in Bladder Cancer Cells. Int J Mol Sci 2021; 22:2553. [PMID: 33806327 PMCID: PMC7961343 DOI: 10.3390/ijms22052553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Personalised medicine is the future and hope for many patients, including those with cancers. Early detection, as well as rapid, well-selected treatment, are key factors leading to a good prognosis. MicroRNA mediated gene regulation is a promising area of development for new diagnostic and therapeutic methods, crucial for better prospects for patients. Bladder cancer is a frequent neoplasm, with high lethality and lacking modern, advanced therapeutic modalities, such as immunotherapy. MicroRNAs are involved in bladder cancer pathogenesis, proliferation, control and response to treatment, which we summarise in this perspective in response to lack of recent review publications in this field. We further performed a correlation-based analysis of microRNA and gene expression data in bladder cancer (BLCA) TCGA dataset. We identified 27 microRNAs hits with opposite expression profiles to genes involved in immune response in bladder cancer, and 24 microRNAs hits with similar expression profiles. We discuss previous studies linking the functions of these microRNAs to bladder cancer and assess if they are good candidates for personalised medicine therapeutics and diagnostics. The discussed functions include regulation of gene expression, interplay with transcription factors, response to treatment, apoptosis, cell proliferation and angiogenesis, initiation and development of cancer, genome instability and tumour-associated inflammatory reaction.
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Affiliation(s)
- Przemysław A. Stempor
- SmartImmune Ltd, Accelerate Cambridge, University of Cambridge Judge Business School, Cambridge CB4 1EE, UK;
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashome 52621, Israel;
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center, Be’er Yaakov, Tel Hashome 52621, Israel;
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Yechezkel Sidi
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Maria Stępień
- Faculty of Medicine, Medical University of Lublin, 20-059 Lublin, Poland;
| | | | - Paula Dobosz
- Department of Hematology, Transplantationand Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
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Muthusami S, Ramachandran I, Krishnamoorthy S, Sambandam Y, Ramalingam S, Queimado L, Chaudhuri G, Ramachandran IK. Regulation of MicroRNAs in Inflammation-Associated Colorectal Cancer: A Mechanistic Approach. Endocr Metab Immune Disord Drug Targets 2021; 21:67-76. [DOI: 10.2174/1871530320666200917112802] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 11/22/2022]
Abstract
The development of colorectal cancer (CRC) is a multistage process. The inflammation of
the colon as in inflammatory bowel disease (IBD) such as ulcerative colitis (UC) or Crohn’s disease
(CD) is often regarded as the initial trigger for the development of inflammation-associated CRC.
Many cytokines such as tumor necrosis factor alpha (TNF-α) and interleukins (ILs) are known to exert
proinflammatory actions, and inflammation initiates or promotes tumorigenesis of various cancers,
including CRC, through differential regulation of microRNAs (miRNAs/miRs). miRNAs can be
oncogenic miRNAs (oncomiRs) or anti-oncomiRs/tumor suppressor miRNAs, and they play key roles
during colorectal carcinogenesis. However, the functions and molecular mechanisms of regulation of
miRNAs involved in inflammation-associated CRC are still anecdotal and largely unknown.
Consolidating the published results and offering perspective solutions to circumvent CRC, the current
review is focused on the role of miRNAs and their regulation in the development of CRC. We have
also discussed the model systems adapted by researchers to delineate the role of miRNAs in
inflammation-associated CRC.
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Affiliation(s)
- Sridhar Muthusami
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641 021, Tamil Nadu, India
| | - Ilangovan Ramachandran
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600 113, Tamil Nadu, India
| | - Sneha Krishnamoorthy
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641 021, Tamil Nadu, India
| | - Yuvaraj Sambandam
- Department of Surgery, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram 603 203, Tamil Nadu, India
| | - Lurdes Queimado
- Departments of Otorhinolaryngology - Head and Neck Surgery, Cell Biology, Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States
| | - Gautam Chaudhuri
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States
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Wang N, Zhou P, Chen Y, Qu H, Lu K, Xia J. MicroRNA-149: A review of its role in digestive system cancers. Pathol Res Pract 2020; 216:153266. [PMID: 33197838 DOI: 10.1016/j.prp.2020.153266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/18/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a group of highly conserved, short (18-25 nucleotide long) non-coding RNAs which play important functional roles in cellular differentiation, biological development, pathogenesis and disease susceptibility and have been linked to both tumorigenesis and the malignant progression of various cancers. miRNAs primarily exert their function through the negative regulation of their target gene's transcription via the specific recognition of their 3' untranslated region. A single miRNA can regulate multiple target genes and most miRNAs are controlled by several factors. Recent studies have shown that microRNA-149 (miR-149) plays a pivotal role in the pathogenesis of digestive system cancers and may act as a potential diagnostic marker and therapeutic target. In this review, we summarize and discuss the most recent reports describing miR-149 in digestive system cancers, including its single nucleotide polymorphisms, expression levels, target genes, drug sensitivity and clinical significance.
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Affiliation(s)
- Ning Wang
- Department of General Surgery, The Affiliated Wuxi NO.2 People's Hospital of Nanjing Medical University, Wu Xi, Jiangsu, China
| | - Peng Zhou
- Department of General Surgery, The Affiliated Wuxi NO.2 People's Hospital of Nanjing Medical University, Wu Xi, Jiangsu, China
| | - Yigang Chen
- Department of General Surgery, The Affiliated Wuxi NO.2 People's Hospital of Nanjing Medical University, Wu Xi, Jiangsu, China
| | - Huiheng Qu
- Department of General Surgery, The Affiliated Wuxi NO.2 People's Hospital of Nanjing Medical University, Wu Xi, Jiangsu, China
| | - Keyu Lu
- Department of General Surgery, The Affiliated Wuxi NO.2 People's Hospital of Nanjing Medical University, Wu Xi, Jiangsu, China
| | - Jiazeng Xia
- Department of General Surgery, The Affiliated Wuxi NO.2 People's Hospital of Nanjing Medical University, Wu Xi, Jiangsu, China.
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