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Hu C, Li Q, Xiang L, Luo Y, Li S, An J, Yu X, Zhang G, Chen Y, Wang Y, Wang D. Comprehensive pan-cancer analysis unveils the significant prognostic value and potential role in immune microenvironment modulation of TRIB3. Comput Struct Biotechnol J 2024; 23:234-250. [PMID: 38161736 PMCID: PMC10757237 DOI: 10.1016/j.csbj.2023.11.043] [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: 07/09/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
TRIB3, a pseudokinase, was previously studied within only some specific cancer types, leaving its comprehensive functions in pan-cancer contexts largely unexplored. Here, we performed an integrated analysis of TRIB3 expression, prognosis, genetic alterations, functional enrichment and tumor immune-related characteristics in 33 cancer types. Our results showed that TRIB3 exhibits high expression levels across 24 different cancer types and correlates closely with unfavorable prognoses. Meanwhile, TRIB3 shows mutations in a wide spectrum of 22 distinct cancer types, with the predominant mutation types being missense mutations and gene amplifications, and significant changes in DNA methylation levels in 14 types of cancer. We further discovered that TRIB3 expression is significantly associated with cancer immune-related genome mutations, such as tumor mutational burden (TMB), microsatellite instability (MSI) and DNA mismatch repair (MMR), and infiltration of immunosuppressive cells, such as CD4+ Th2 cells and myeloid-derived suppressor cells (MDSCs), into the tumor microenvironment. These results indicated that the expression of TRIB3 might reshape the tumor immune microenvironment (TIME) and lead to immunosuppressive "cold" tumors. In addition, our results confirmed that the loss of function of TRIB3 inhibits cell proliferation, promotes apoptosis, and leads to significant enrichment of "hot" tumor-related immune pathways, at least in breast cancer cells, which further supports the important role of TRIB3 in cancer prognosis and TIME regulation. Together, this pan-cancer investigation provided a comprehensive understanding of the critical role of TRIB3 in human cancers, and suggested that TRIB3 might be a promising prognostic biomarker and a potential target for cancer immunotherapy.
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Affiliation(s)
- Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qingzhou Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lei Xiang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yan Luo
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shengrong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jun An
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiankuo Yu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Guochen Zhang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuhui Chen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yumei Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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2
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Lei S, Sun J, Xie Y, Xiao X, He X, Lin S, Zhang H, Huang Z, Wang H, Wu X, Peng H, Liu J. Diverse functions of Tribbles homolog 3 in cancers and its potential as a therapeutic target. Carcinogenesis 2024; 45:527-542. [PMID: 38902892 DOI: 10.1093/carcin/bgae042] [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: 03/07/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024] Open
Abstract
Currently, cancer is the second leading cause of death worldwide, and potential targeted drugs and molecular pathways for cancer development and progression have been a hot research topic worldwide. In recent years, the importance of the kinase superfamily in diseases has been well demonstrated by studies on various molecular mechanisms of kinases and the successful application of their inhibitors in diseases. Pseudokinases are members of the kinase superfamily, which have been increasingly documented to play a crucial role in cancers year after year. As a member of pseudokinases, tribbles homolog 3 (TRIB3) also exerts diverse functions in different cancers through different interacting proteins and molecular pathways, especially in tumor immunity, stemness, drug resistance, metabolism, and autophagy. In addition, peptide drugs targeting TRIB3 have high specificity in preclinical studies, which shows great promise for TRIB3 application in diseases including cancers. In this review, we dissect diverse functions played by TRIB3 in different cancers, describing the underlying mechanisms in detail. Notably, inhibitors and agonists currently available for TRIB3 are discussed, indicating the potential for TRIB3 as a therapeutic target.
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Affiliation(s)
- Shiying Lei
- The Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jiajun Sun
- The Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yifang Xie
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
| | - Xiaojuan Xiao
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
| | - Xiaofeng He
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China
| | - Sheng Lin
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China
| | - Huifang Zhang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Zineng Huang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Haiqin Wang
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
| | - Xusheng Wu
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Jing Liu
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
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Cheng Q, Yu DY, Zhou YH, Huang JY. The mechanism and therapeutic potential of lncRNA MIR497HG/miR-16-5p axis in breast cancer. BMC Womens Health 2024; 24:379. [PMID: 38956558 PMCID: PMC11218111 DOI: 10.1186/s12905-024-03208-7] [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: 03/07/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Breast cancer has become a major public health problem in the current society, and its incidence rate ranks the first among Chinese female malignant tumors. This paper once again confirmed the efficacy of lncRNA in tumor regulation by introducing the mechanism of the diagnosis of breast cancer by the MIR497HG/miR-16-5p axis. METHODS The abnormal expression of MIR497HG in breast cancer was determined by RT-qPCR method, and the correlation between MIR497HG expression and clinicopathological characteristics of breast cancer patients was analyzed via Chi-square test. To understand the diagnostic potential of MIR497HG in breast cancer by drawing the receiver operating characteristic curve (ROC). The overexpressed MIR497HG (pcDNA3.1-MIR497HG) was designed and constructed to explore the regulation of elevated MIR497HG on biological function of BT549 and Hs 578T cells through Transwell assays. Additionally, the luciferase gene reporter assay and Pearson analysis evaluated the targeting relationship of MIR497HG to miR-16-5p. RESULTS MIR497HG was decreased in breast cancer and had high diagnostic function, while elevated MIR497HG inhibited the migration and invasion of BT549 and Hs 578T cells. In terms of functional mechanism, miR-16-5p was the target of MIR497HG, and MIR497HG reversely regulated the miR-16-5p. miR-16-5p mimic reversed the effects of upregulated MIR497HG on cell biological function. CONCLUSIONS In general, MIR497HG was decreased in breast cancer, and the MIR497HG/miR-16-5p axis regulated breast cancer tumorigenesis, providing effective insights for the diagnosis of patients.
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Affiliation(s)
- Quan Cheng
- Department of Chinese Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Dong-Yang Yu
- Department of Urology, People's Hospital of Yilong County, Nanchong, 637600, China
| | - Yong-Hong Zhou
- Department of General Surgery (Thyroid Gland/Blood Vessel), The First People's Hospital of Neijiang, No. 1866, West Section of Han'an Avenue, Neijiang, 641099, China
| | - Jian-Yuan Huang
- Department of General Surgery (Thyroid Gland/Blood Vessel), The First People's Hospital of Neijiang, No. 1866, West Section of Han'an Avenue, Neijiang, 641099, China.
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Zhang C, Lin Q, Li C, Chen Z, Deng M, Weng H, Zhu X. Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma. Sci Rep 2023; 13:13894. [PMID: 37626099 PMCID: PMC10457392 DOI: 10.1038/s41598-023-38568-x] [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: 04/03/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. This study aimed to determine the prognostic significance of endoplasmic reticulum (ER) stress-related genes in DLBCL. ER stress-related genes were obtained from the molecular signatures database. Gene expression data and clinical outcomes from the gene expression omnibus and TCGA datasets were collected, and differentially expressed genes (DEGs) were screened out. Gene ontology enrichment analysis, the kyoto encyclopaedia of genes and genomes pathway analysis, and geneset enrichment analysis were used to analyse the possible biological function of ER stress-related DEGs in DLBCL. Protein-protein interaction network construction using the STRING online and hub genes were identified by cytoHubba on Cytoscape software. The significant prognosis-related genes were screened, and the differential expression was validated. The immune microenvironment assessment of significant genes were evaluated. Next, the nomogram was built using univariate and multivariate Cox regression analysis. 26 ER stress-related DEGs were screened. Functional enrichment analysis showed them to be involved in the regulation of the endoplasmic reticulum mainly. NUPR1 and TRIB3 were identified as the most significant prognostic-related genes by comparison with the GSE10846, GSE11318, and TCGA datasets. NUPR1 was correlated with a good prognosis and immune infiltration in DLBCL; on the other hand, high expression of TRIB3 significantly correlated with a poor prognosis, which was an independent prognostic factor for DLBCL. In summary, we identified NUPR1 and TRIB3 as critical ER stress-related genes in DLBCL. NUPR1 might be involved in immune infiltration in DLBCL, and TRIB3 might serve as a potential therapeutic target and prognostic factor in DLBCL.
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Affiliation(s)
- Chaofeng Zhang
- Department of Hematology and Rheumatology, The Affiliated Hospital of Putian University, Putian, Fujian Province, China
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qi Lin
- Department of Pharmacy, The Affiliated Hospital of Putian University, Putian, Fujian Province, China
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Chaoqi Li
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Zhimin Chen
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Mengmeng Deng
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Huixin Weng
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Xiongpeng Zhu
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China.
- Department of Haematology, Quanzhou First Hospital of Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China.
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Velasco G, Link W. Pseudokinases, Tribbles Proteins and Cancer. Cancers (Basel) 2023; 15:3547. [PMID: 37509210 PMCID: PMC10376989 DOI: 10.3390/cancers15143547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The human kinome comprises 518 protein kinases, of which approximately 10% lack one or more of the conserved amino acids necessary for catalytic activity [...].
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Affiliation(s)
- Guillermo Velasco
- Department of Biochemistry and Molecular Biology, School of Biology, Complutense University, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 28040 Madrid, Spain
| | - Wolfgang Link
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
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The functions and molecular mechanisms of Tribbles homolog 3 (TRIB3) implicated in the pathophysiology of cancer. Int Immunopharmacol 2023; 114:109581. [PMID: 36527874 DOI: 10.1016/j.intimp.2022.109581] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Currently, cancer ranks as the second leading cause of death worldwide, and at the same time, the burden of cancer continues to increase. The underlying molecular pathways involved in the initiation and development of cancer are the subject of considerable research worldwide. Further understanding of these pathways may lead to new cancer treatments. Growing data suggest that Tribble's homolog 3 (TRIB3) is essential in oncogenesis in many types of cancer. The mammalian tribbles family's proteins regulate various cellular and physiological functions, such as the cell cycle, stress response, signal transduction, propagation, development, differentiation, immunity, inflammatory processes, and metabolism. To exert their activities, Tribbles proteins must alter key signaling pathways, including the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3 kinase (PI3K)/AKT pathways. Recent evidence supports that TRIB3 dysregulation has been linked to various diseases, including tumor development and chemoresistance. It has been speculated that TRIB3 may either promote or inhibit the onset and development of cancer. However, it is still unclear how TRIB3 performs this dual function in cancer. In this review, we present and discuss the most recent data on the role of TRIB3 in cancer pathophysiology and chemoresistance. Furthermore, we describe in detail the molecular mechanism TRIB3 regulates in cancer.
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TRIB3 Modulates PPARγ-Mediated Growth Inhibition by Interfering with the MLL Complex in Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms231810535. [PMID: 36142452 PMCID: PMC9503934 DOI: 10.3390/ijms231810535] [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: 08/12/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
Aberrant expression or activity of proteins are amongst the best understood mechanisms that can drive cancer initiation and progression, as well as therapy resistance. TRIB3, a member of the Tribbles family of pseudokinases, is often dysregulated in cancer and has been associated with breast cancer initiation and metastasis formation. However, the underlying mechanisms by which TRIB3 contributes to these events are unclear. In this study, we demonstrate that TRIB3 regulates the expression of PPARγ, a transcription factor that has gained attention as a potential drug target in breast cancer for its antiproliferative actions. Proteomics and phosphoproteomics analyses together with classical biochemical assays indicate that TRIB3 interferes with the MLL complex and reduces MLL-mediated H3K4 trimethylation of the PPARG locus, thereby reducing PPARγ mRNA expression. Consequently, the overexpression of TRIB3 blunts the antiproliferative effect of PPARγ ligands in breast cancer cells, while reduced TRIB3 expression gives the opposite effect. In conclusion, our data implicate TRIB3 in epigenetic gene regulation and suggest that expression levels of this pseudokinase may serve as a predictor of successful experimental treatments with PPARγ ligands in breast cancer.
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Danger R, Feseha Y, Brouard S. The Pseudokinase TRIB1 in Immune Cells and Associated Disorders. Cancers (Basel) 2022; 14:cancers14041011. [PMID: 35205759 PMCID: PMC8869936 DOI: 10.3390/cancers14041011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary TRIB1 is at the center of major cell signaling pathways. In this review, we describe its role in immune cells and highlight TRIB1 interacting partners which suggests cell-specific functions and that TRIB1 is involved in cellular homeostasis and also in different cancers and immune-related disorders. Abstract Research advances in Tribbles homolog (TRIB) genes have established the consensus that this protein family plays roles in diverse biological conditions and regulates intracellular signaling networks and several human diseases. In this review, we focus on one member of the family, TRIB1, and its role at the crossroads of immune signaling. TRIB1 directly interacts with transcription factors such as FOXP3 and C/EBPα, with several signaling molecules such as MEK1 and MALT1 and directly acts on key cell signaling pathways such as the MAPK and NF-κB pathways. Altogether, these interactions emphasize that TRIB1 is at the center of major cell signaling pathways while TRIB1 has cell-specific roles, potentially depending on the expressing cells and binding partners. In this review, we describe its roles in immune cells and highlight the interacting partners explaining these functions which suggests TRIB1 as a precise mediator of cellular homeostasis as well as in different cancers and immune-related disorders.
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Affiliation(s)
- Richard Danger
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, F-44000 Nantes, France; (R.D.); (Y.F.)
| | - Yodit Feseha
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, F-44000 Nantes, France; (R.D.); (Y.F.)
| | - Sophie Brouard
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, F-44000 Nantes, France; (R.D.); (Y.F.)
- LabEx IGO “Immunotherapy, Graft, Oncology”, F-44000 Nantes, France
- Correspondence: ; Tel.: +33-240-087-842
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Hernández-Quiles M, Baak R, Borgman A, den Haan S, Sobrevals Alcaraz P, van Es R, Kiss-Toth E, Vos H, Kalkhoven E. Comprehensive Profiling of Mammalian Tribbles Interactomes Implicates TRIB3 in Gene Repression. Cancers (Basel) 2021; 13:6318. [PMID: 34944947 PMCID: PMC8699236 DOI: 10.3390/cancers13246318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
The three human Tribbles (TRIB) pseudokinases have been implicated in a plethora of signaling and metabolic processes linked to cancer initiation and progression and can potentially be used as biomarkers of disease and prognosis. While their modes of action reported so far center around protein-protein interactions, the comprehensive profiling of TRIB interactomes has not been reported yet. Here, we have developed a robust mass spectrometry (MS)-based proteomics approach to characterize Tribbles' interactomes and report a comprehensive assessment and comparison of the TRIB1, -2 and -3 interactomes, as well as domain-specific interactions for TRIB3. Interestingly, TRIB3, which is predominantly localized in the nucleus, interacts with multiple transcriptional regulators, including proteins involved in gene repression. Indeed, we found that TRIB3 repressed gene transcription when tethered to DNA in breast cancer cells. Taken together, our comprehensive proteomic assessment reveals previously unknown interacting partners and functions of Tribbles proteins that expand our understanding of this family of proteins. In addition, our findings show that MS-based proteomics provides a powerful tool to unravel novel pseudokinase biology.
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Affiliation(s)
- Miguel Hernández-Quiles
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Rosalie Baak
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Suzanne den Haan
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Paula Sobrevals Alcaraz
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Robert van Es
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Endre Kiss-Toth
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2TN, UK;
| | - Harmjan Vos
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
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