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Fuertes T, Álvarez-Corrales E, Gómez-Escolar C, Ubieto-Capella P, Serrano-Navarro Á, de Molina A, Méndez J, Ramiro AR, de Yébenes VG. miR-28-based combination therapy impairs aggressive B cell lymphoma growth by rewiring DNA replication. Cell Death Dis 2023; 14:687. [PMID: 37852959 PMCID: PMC10585006 DOI: 10.1038/s41419-023-06178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common aggressive B cell lymphoma and accounts for nearly 40% of cases of B cell non-Hodgkin lymphoma. DLBCL is generally treated with R-CHOP chemotherapy, but many patients do not respond or relapse after treatment. Here, we analyzed the therapeutic potential of the tumor suppressor microRNA-28 (miR-28) for DLBCL, alone and in combination with the Bruton's tyrosine kinase inhibitor ibrutinib. Combination therapy with miR-28 plus ibrutinib potentiated the anti-tumor effects of monotherapy with either agent by inducing a specific transcriptional cell-cycle arrest program that impairs DNA replication. The molecular actions of miR-28 and ibrutinib synergistically impair DNA replication by simultaneous inhibition of origin activation and fork progression. Moreover, we found that downregulation of the miR-28-plus-ibrutinib gene signature correlates with better survival of ABC-DLBCL patients. These results provide evidence for the effectiveness of a new miRNA-based ibrutinib combination therapy for DLBCL and unveil the miR-28-plus-ibrutinib gene signature as a new predictor of outcome in ABC-DLBCL patients.
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Affiliation(s)
- Teresa Fuertes
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Emigdio Álvarez-Corrales
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Carmen Gómez-Escolar
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - Álvaro Serrano-Navarro
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Antonio de Molina
- Comparative Medicine Unit. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Juan Méndez
- DNA replication Group. Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
| | - Virginia G de Yébenes
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.
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2
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Bioinformatics Analysis of miRNAs Targeting TRAF5 in DLBCL Involving in NF- κB Signaling Pathway and Affecting the Apoptosis and Signal Transduction. Genet Res (Camb) 2022; 2022:3222253. [PMID: 36619898 PMCID: PMC9803564 DOI: 10.1155/2022/3222253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/13/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is an aggressive B-cell lymphoma with high heterogeneity. There is an unmet need to investigate valid indicators for the diagnosis and therapy of DLBCL. Methods GEO database was utilized to screen for differentially expressed genes (DEGs) and differential miRNAs in DLBCL tissues. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyse DEGs. Then multiple databases were searched for related miRNAs within DLBCL, TNF receptor-associated factor 5 (TRAF5) and NF-kappa B (NF-κB) signaling pathways. The KOBAS database was used to assist in the screening of miRNAs of interest and construct the regulatory network of miRNA-mRNA. Finally, the expression level and diagnostic performance of miRNAs were analyzed with GEO datasets, and DEGs were identified from the GEPIA database. Results DEGs were significantly concentrated in the NF-κB signaling pathway and cytokine-cytokine receptor interaction, and involved in the process of immune response and protein binding. MiR-15a-5p, miR-147a, miR-192-5p, miR-197-3p, miR-532-5p, and miR-650 were revealed to be targeting TRAF5 and participating in NF-κB signaling pathway and might impact the apoptosis and signal transduction of DLBCL. In the GEPIA database, TRAF5 was significantly overexpressed in DLBCL. The expression of miR-197-3p was upregulated within GEO datasets, while the rest of the miRNAs were downregulated in DLBCL. Conclusions Subsets of miRNAs may participate in the NF-κB signaling pathway by co-targeting TRAF5 and could be prospective biomarkers exploring the pathogenesis of DLBCL.
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3
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Yu F, He H, Nastoupil LJ, Xu-Monette ZY, Pham K, Liang Y, Chen G, Fowler NH, Yin CC, Tan D, Yang Y, Hu S, Young KH, Pham LV, You MJ. Targetable vulnerability of deregulated FOXM1/PLK1 signaling axis in diffuse large B cell lymphoma. Am J Cancer Res 2022; 12:4666-4679. [PMID: 36381323 PMCID: PMC9641390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023] Open
Abstract
FOXM1 is a transcription factor that controls cell cycle regulation, cell proliferation, and differentiation. Overexpression of FOXM1 has been implicated in various cancer types. However, the activation status and functional significance of FOXM1 in diffuse large B cell lymphoma (DLBCL) have not been well investigated. Using proteomic approaches, we discovered that the protein expression levels of FOXM1 and PLK1 were positively correlated in DLBCL cell lines and primary DLBCL. Expression levels of FOXM1 and PLK1 mRNAs were also significantly higher in DLBCL than in normal human B cells and could predict poor prognosis of DLBCL, particularly in patients with germinal center B cell-like (GCB) DLBCL. Furthermore, proteomic studies defined a FOXM1-PLK1 signature that consisted of proteins upstream and downstream of that axis involved in the p38-MAPK-AKT pathway, cell cycle, and DNA damage/repair. Further studies demonstrated a mechanistic function of the FOXM1/PLK1 axis in connection with the DNA damage response pathways regulating the S/G2 checkpoint of the cell cycle. Therapeutic targeting of FOXM1/PLK1 using a FOXM1 or PLK1 inhibitor, as well as other clinically relevant small-molecule inhibitors targeting ATR-CHK1, was highly effective in DLBCL in vitro models. These findings are instrumental for lymphoma drug discovery aiming at the FOXM1/PLK1/ATR/CHK1 axis.
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Affiliation(s)
- Fang Yu
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Department of Pathology, The First Affiliated Hospital of Zhejiang UniversityHangzhou, Zhejiang, China
| | - Hua He
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - Loretta J Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - Zijun Y Xu-Monette
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Division of Hematopathology, Duke University Medical Center and Duke Cancer InstituteDurham, NC, USA
| | - Ky Pham
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Department of Neurology, McGovern Medical School, University of Texas Health Science CenterHouston, TX, USA
| | - Yong Liang
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Taizhou University College of MedicineTaizhou, Zhejiang, China
| | - Guang Chen
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Taizhou University College of MedicineTaizhou, Zhejiang, China
| | - Nathan H Fowler
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - C Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - Dongfeng Tan
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - Yaling Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - Shimin Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Division of Hematopathology, Duke University Medical Center and Duke Cancer InstituteDurham, NC, USA
| | - Lan V Pham
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- Oncology Discovery, AbbVie Inc.South San Francisco, CA, USA
| | - M James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX, USA
- The University of Texas MD Anderson Cancer Center and UTHealth Graduate School of Biomedical SciencesHouston, TX, USA
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4
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Hornick EL, Stunz LL, Sabree S, Wu X, Witzig TE, Bishop GA. The Tumor Suppressor Protein TRAF3 Modulates GSK3 Activity and Susceptibility of B Lymphoma Cells to GSK3 Inhibition. Cancers (Basel) 2022; 14:cancers14205029. [PMID: 36291813 PMCID: PMC9599470 DOI: 10.3390/cancers14205029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 01/28/2023] Open
Abstract
TNF receptor-associated factor 3 (TRAF3) is an adapter protein that inhibits many signals that promote B cell survival and activation. Mice with a B cell-specific TRAF3 deficiency and humans with a rare haploinsufficiency in TRAF3 have enhanced development of BCLs as they age. Loss-of-function mutations in TRAF3 are common in B cell malignancies. Recent studies show that pharmacological inhibition of the enzyme glycogen synthase kinase 3 (GSK3), which regulates cellular growth, survival, and metabolism, inhibits growth and survival of BCL-derived B cells. In this study, we found that TRAF3 and GSK3 associated in B cells. The relative levels of TRAF3 in BCL cell lines correlated positively with the ratio of inactive to total GSK3β, and negatively correlated with susceptibility to GSK3 inhibition by the GSK3 inhibitory drug 9-ING-41, currently in clinical trials. Uniquely in BCLs with low TRAF3, GSK3 inhibition caused increased loss of the TRAF3-regulated, anti-apoptotic protein Mcl-1. GSK3 inhibition also blocked hyperresponsiveness to IL-6 receptor signaling in TRAF3-deficient BCL cells. Together, these results support the utility of 9-ING-41 as a treatment for BCL, and suggest that a decrease or loss of TRAF3 in BCLs could act as a biomarker for increased susceptibility to GSK3 inhibitor treatment.
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Affiliation(s)
- Emma L. Hornick
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, USA
| | - Laura L. Stunz
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, USA
- Veterans Administration Medical Center, Iowa City, IA 52242, USA
| | - Shakoora Sabree
- Graduate Program in Immunology and MSTP Program, The University of Iowa, Iowa City, IA 52242, USA
| | - Xiaosheng Wu
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas E. Witzig
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Gail A. Bishop
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, USA
- Veterans Administration Medical Center, Iowa City, IA 52242, USA
- Graduate Program in Immunology and MSTP Program, The University of Iowa, Iowa City, IA 52242, USA
- Correspondence:
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5
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Whillock AL, Ybarra TK, Bishop GA. TNF receptor-associated factor 3 restrains B-cell receptor signaling in normal and malignant B cells. J Biol Chem 2021; 296:100465. [PMID: 33639170 PMCID: PMC8042179 DOI: 10.1016/j.jbc.2021.100465] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/20/2022] Open
Abstract
TRAF3 has diverse signaling functions, which vary by cell type. Uniquely in B lymphocytes, TRAF3 inhibits homeostatic survival. Highlighting the role of TRAF3 as a tumor suppressor, loss-of-function TRAF3 mutations are associated with human B-cell malignancies, while B-cell-specific deletion of TRAF3 in mice leads to autoimmunity and lymphoma development. The role of TRAF3 in inhibiting noncanonical NF-κB activation, CD40 and BAFF-R signaling to B cells is well documented. In contrast, TRAF3 enhances many T-cell effector functions, through associating with and enhancing signaling by the T-cell receptor (TCR)-CD28 complex. The present study was designed to determine the role of TRAF3 in signaling via the B-cell antigen receptor (BCR). The BCR is crucial for antigen recognition, survival, proliferation, and antibody production, and defects in BCR signaling can promote abnormal survival of malignant B cells. Here, we show that TRAF3 is associated with both CD79B and the BCR-activated kinases Syk and Btk following BCR stimulation. BCR-induced phosphorylation of Syk and additional downstream kinases was increased in TRAF3−/− B cells, with regulation observed in both follicular and marginal zone B-cell subsets. BCR stimulation of TRAF3−/− B cells resulted in increased surface expression of MHC-II, CD80, and CD86 molecules. Interestingly, increased survival of TRAF3−/− primary B cells was resistant to inhibition of Btk, while TRAF3-deficient malignant B-cell lines showed enhanced sensitivity. TRAF3 serves to restrain normal and malignant BCR signaling, with important implications for its role in normal B-cell biology and abnormal survival of malignant B cells.
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Affiliation(s)
- Amy L Whillock
- Department of Microbiology & Immunology, University of Iowa, Iowa City, Iowa, USA; Immunology Graduate Program, University of Iowa, Iowa City, Iowa, USA; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Tiffany K Ybarra
- Department of Microbiology & Immunology, University of Iowa, Iowa City, Iowa, USA; Immunology Graduate Program, University of Iowa, Iowa City, Iowa, USA
| | - Gail A Bishop
- Department of Microbiology & Immunology, University of Iowa, Iowa City, Iowa, USA; Immunology Graduate Program, University of Iowa, Iowa City, Iowa, USA; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA; Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA; VA Medical Center, Iowa City, Iowa, USA.
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6
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Zhou L, Ding L, Gong Y, Zhao J, Xin G, Zhou R, Zhang W. Identification of hub genes associated with the pathogenesis of diffuse large B-cell lymphoma subtype one characterized by host response via integrated bioinformatic analyses. PeerJ 2020; 8:e10269. [PMID: 33240622 PMCID: PMC7682441 DOI: 10.7717/peerj.10269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background Host response diffuse large B-cell lymphoma (HR DLBCL) shares features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities, frequent splenic and bone marrow involvement, and younger age at presentation. HR DLBCL is inherently less responsive to the standard treatment for DLBCL. Moreover, the mechanism of infiltration of HR DLBCL with preexisting abundant T-cells and dendritic cells is unknown, and their associated underlying immune responses incompletely defined. Here, hub genes and pathogenesis associated with HR DLBCL were explored to reveal molecular mechanisms and treatment targets. Methods Differentially expressed genes were identified in three datasets (GSE25638, GSE44337, GSE56315). The expression profile of the genes in the GSE53786 dataset was used to constructed a co-expression network. Protein-protein interactions analysis in the modules of interest identified candidate hub genes. Then screening of real hub genes was carried out by survival analysis within the GSE53786 and GSE10846 datasets. Expression of hub genes was validated in the Gene expression profiling interactive analysis, Oncomine databases and human tissue specimens. Functional enrichment analysis and Gene set enrichment analysis were utilized to investigate the potential mechanisms. Tumor Immune Estimation Resource and The Cancer Genome Atlas were used to mine the association of the hub gene with tumor immunity, potential upstream regulators were predicted using bioinformatics tools. Results A total of 274 common differentially expressed genes were identified. Within the key module, we identified CXCL10 as a real hub gene. The validation of upregulated expression level of CXCL10 was consistent with our study. CXCL10 might have a regulatory effect on tumor immunity. The predicted miRNA (hsa-mir-6849-3p) and transcription factor (IRF9) might regulate gene expression in the hub module.
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Affiliation(s)
- Lingna Zhou
- Department of Pathology and Physiology, Cancer Institute, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liya Ding
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology and Pathophysiology, Institute of Pathology and Forensic Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuqi Gong
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology and Pathophysiology, Institute of Pathology and Forensic Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jing Zhao
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Gong Xin
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China, Hangzhou, Zhejiang, China
| | - Ren Zhou
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology and Pathophysiology, Institute of Pathology and Forensic Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Zhang
- Department of Pathology and Physiology, Cancer Institute, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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7
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Sertorio M, Nowrouzi A, Akbarpour M, Chetal K, Salomonis N, Brons S, Mascia A, Ionascu D, McCauley S, Kupneski T, Köthe A, Debus J, Perentesis JP, Abdollahi A, Zheng Y, Wells SI. Differential transcriptome response to proton versus X-ray radiation reveals novel candidate targets for combinatorial PT therapy in lymphoma. Radiother Oncol 2020; 155:293-303. [PMID: 33096164 DOI: 10.1016/j.radonc.2020.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND PURPOSE Knowledge of biological responses to proton therapy (PT) in comparison to X-ray remains in its infancy. Identification of PT specific molecular signals is an important opportunity for the discovery of biomarkers and synergistic drugs to advance clinical application. Since PT is used for the treatment of lymphoma, we report here transcriptomic responses of lymphoma cell lines to PT vs X-ray and identify potential therapeutic targets. MATERIALS AND METHODS Two lymphoma cell lines of human (BL41) and murine (J3D) origin were irradiated by X-ray and PT. Differential transcriptome regulation was quantified by RNA sequencing for each radiation type at 12 hours post irradiation. Gene-set enrichment analysis revealed deregulated molecular pathways and putative targets for lymphoma cell sensitization to PT. RESULTS Transcriptomic gene set enrichment analyses uncovered pathways that contribute to the unfolded protein response (UPR) and mitochondrial transport. Functional validation at multiple time points demonstrated increased UPR activation and decreased protein translation, perhaps due to increased oxidative stress and oxidative protein damage after PT. PPARgamma was identified as a potential regulator of the PT transcriptomic response. Inhibition of PPARgamma by two compounds, T0070907 and SR2595, sensitized lymphoma cells to PT. CONCLUSIONS Proton vs X-ray radiation leads to the transcriptional regulation of a specific subset of genes in line with diminished protein translation and UPR activation that may be due to oxidative stress. This study demonstrates that different radiation qualities trigger distinct cellular responses in lymphoma cells, and identifies PPARgamma inhibition as a potential strategy for the sensitization of lymphoma to PT.
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Affiliation(s)
- Mathieu Sertorio
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA.
| | - Ali Nowrouzi
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Germany; German Cancer Consortium (DKTK) Core Center, Clinical Cooperation Units (CCU) Translational Radiation Oncology and Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Germany; Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty (HDMF), Heidelberg University, Germany
| | - Mahdi Akbarpour
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Germany; German Cancer Consortium (DKTK) Core Center, Clinical Cooperation Units (CCU) Translational Radiation Oncology and Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Germany; Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty (HDMF), Heidelberg University, Germany
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Stephan Brons
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Germany
| | - Anthony Mascia
- Department of Radiation Oncology, University of Cincinnati College of Medicine, USA
| | - Dan Ionascu
- Department of Radiation Oncology, University of Cincinnati College of Medicine, USA
| | - Shelby McCauley
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Taylor Kupneski
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Andreas Köthe
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Jürgen Debus
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Germany; German Cancer Consortium (DKTK) Core Center, Clinical Cooperation Units (CCU) Translational Radiation Oncology and Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Germany; Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty (HDMF), Heidelberg University, Germany
| | - John P Perentesis
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Amir Abdollahi
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Germany; German Cancer Consortium (DKTK) Core Center, Clinical Cooperation Units (CCU) Translational Radiation Oncology and Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Germany; Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty (HDMF), Heidelberg University, Germany
| | - Yi Zheng
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA.
| | - Susanne I Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA.
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8
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Sulfiredoxin as a Potential Therapeutic Target for Advanced and Metastatic Prostate Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:2148562. [PMID: 32411320 PMCID: PMC7201699 DOI: 10.1155/2020/2148562] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/09/2019] [Indexed: 12/28/2022]
Abstract
The incidence of prostate cancer (PCa) is increasing, and it is currently the second most frequent cause of death by cancer in men. Despite advancements in cancer therapies, new therapeutic approaches are still needed for treatment-refractory advanced metastatic PCa. Cross-species analysis presents a robust strategy for the discovery of new potential therapeutic targets. This strategy involves the integration of genomic data from genetically engineered mouse models (GEMMs) and human PCa datasets. Considering the role of antioxidant pathways in tumor initiation and progression, we searched oxidative stress-related genes for a potential therapeutic target for PCa. First, we analyzed RNA-sequencing data from Pb-Cre4; Ptenf/f mice and discovered an increase in sulfiredoxin (Srxn1) mRNA expression in high-grade prostatic intraepithelial neoplasia (PIN), well-differentiated adenocarcinoma (medium-stage tumors), and poor-differentiated adenocarcinoma (advanced-stage prostate tumors). The increase of SRXN1 protein expression was confirmed by immunohistochemistry in mouse prostate tumor paraffin samples. Analyses of human databases and prostate tissue microarrays demonstrated that SRXN1 is overexpressed in a subset of high-grade prostate tumors and correlates with aggressive PCa with worse prognosis and decreased survival. Analyses in vitro showed that SRXN1 expression is also higher in most PCa cell lines compared to normal cell lines. Furthermore, siRNA-mediated downregulation of SRXN1 led to decreased viability of PCa cells LNCaP. In conclusion, we identified the antioxidant enzyme SRXN1 as a potential therapeutic target for PCa. Our results suggest that the use of specific SRXN1 inhibitors may be an effective strategy for the adjuvant treatment of castration-resistant PCa with SRXN1 overexpression.
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Jurmeister S, Ramos-Montoya A, Sandi C, Pértega-Gomes N, Wadhwa K, Lamb AD, Dunning MJ, Attig J, Carroll JS, Fryer LG, Felisbino SL, Neal DE. Identification of potential therapeutic targets in prostate cancer through a cross-species approach. EMBO Mol Med 2018; 10:e8274. [PMID: 29437778 PMCID: PMC5840539 DOI: 10.15252/emmm.201708274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 01/01/2018] [Accepted: 01/08/2018] [Indexed: 12/14/2022] Open
Abstract
Genetically engineered mouse models of cancer can be used to filter genome-wide expression datasets generated from human tumours and to identify gene expression alterations that are functionally important to cancer development and progression. In this study, we have generated RNAseq data from tumours arising in two established mouse models of prostate cancer, PB-Cre/PtenloxP/loxP and p53loxP/loxPRbloxP/loxP, and integrated this with published human prostate cancer expression data to pinpoint cancer-associated gene expression changes that are conserved between the two species. To identify potential therapeutic targets, we then filtered this information for genes that are either known or predicted to be druggable. Using this approach, we revealed a functional role for the kinase MELK as a driver and potential therapeutic target in prostate cancer. We found that MELK expression was required for cell survival, affected the expression of genes associated with prostate cancer progression and was associated with biochemical recurrence.
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Affiliation(s)
- Sarah Jurmeister
- Uro-oncology Research Group, CRUK Cambridge Institute, Cambridge, UK
| | | | - Chiranjeevi Sandi
- Uro-oncology Research Group, CRUK Cambridge Institute, Cambridge, UK
| | - Nelma Pértega-Gomes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Karan Wadhwa
- Uro-oncology Research Group, CRUK Cambridge Institute, Cambridge, UK
| | - Alastair D Lamb
- Uro-oncology Research Group, CRUK Cambridge Institute, Cambridge, UK
- Department of Urology, University of Cambridge, Cambridge, UK
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Mark J Dunning
- Bioinformatics Core Facility, CRUK Cambridge Institute, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lee Gd Fryer
- Uro-oncology Research Group, CRUK Cambridge Institute, Cambridge, UK
| | - Sérgio L Felisbino
- Department of Morphology, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Sao Paulo, Brazil
| | - David E Neal
- Uro-oncology Research Group, CRUK Cambridge Institute, Cambridge, UK
- Department of Urology, University of Cambridge, Cambridge, UK
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
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10
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Gu C, Yang Y, Sompallae R, Xu H, Tompkins VS, Holman C, Hose D, Goldschmidt H, Tricot G, Zhan F, Janz S. FOXM1 is a therapeutic target for high-risk multiple myeloma. Leukemia 2016; 30:873-82. [PMID: 26648534 PMCID: PMC4826574 DOI: 10.1038/leu.2015.334] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/05/2015] [Accepted: 11/24/2015] [Indexed: 12/23/2022]
Abstract
The transcription factor forkhead box M1 (FOXM1) is a validated oncoprotein in solid cancers, but its role in malignant plasma cell tumors such as multiple myeloma (MM) is unknown. We analyzed publicly available MM data sets and found that overexpression of FOXM1 prognosticates inferior outcome in a subset (~15%) of newly diagnosed cases, particularly patients with high-risk disease based on global gene expression changes. Follow-up studies using human myeloma cell lines (HMCLs) as the principal experimental model system demonstrated that enforced expression of FOXM1 increased growth, survival and clonogenicity of myeloma cells, whereas knockdown of FOXM1 abolished these features. In agreement with that, constitutive upregulation of FOXM1 promoted HMCL xenografts in laboratory mice, whereas inducible knockdown of FOXM1 led to growth inhibition. Expression of cyclin-dependent kinase 6 (CDK6) and NIMA-related kinase 2 (NEK2) was coregulated with FOXM1 in both HMCLs and myeloma patient samples, suggesting interaction of these three genes in a genetic network that may lend itself to targeting with small-drug inhibitors for new approaches to myeloma therapy and prevention. These results establish FOXM1 as high-risk myeloma gene and provide support for the design and testing of FOXM1-targeted therapies specifically for the FOXM1(High) subset of myeloma.
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Affiliation(s)
- Chunyan Gu
- Basic Medical College, Nanjing University of Chinese Medicine, 210046 Nanjing, People’s Republic of China
- Department of Pathology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Ye Yang
- Basic Medical College, Nanjing University of Chinese Medicine, 210046 Nanjing, People’s Republic of China
- Department of Internal Medicine, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Ramakrishna Sompallae
- Basic Medical College, Nanjing University of Chinese Medicine, 210046 Nanjing, People’s Republic of China
- Department of Bioinformatics Core Facility, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Hongwei Xu
- Department of Internal Medicine, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Van S. Tompkins
- Department of Pathology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Carol Holman
- Department of Pathology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Dirk Hose
- Medizinische Klinik V, Universitätsklinikum Heidelberg
- Nationales Centrum für Tumorerkrankungen, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Medizinische Klinik V, Universitätsklinikum Heidelberg
- Nationales Centrum für Tumorerkrankungen, Heidelberg, Germany
| | - Guido Tricot
- Department of Internal Medicine, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
- Holden Comprehensive Cancer Center, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Fenghuang Zhan
- Department of Internal Medicine, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
- Holden Comprehensive Cancer Center, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
| | - Siegfried Janz
- Department of Pathology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
- Holden Comprehensive Cancer Center, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242 Iowa, USA
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11
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Szedlak A, Paternostro G, Piermarocchi C. Control of asymmetric Hopfield networks and application to cancer attractors. PLoS One 2014; 9:e105842. [PMID: 25170874 PMCID: PMC4149479 DOI: 10.1371/journal.pone.0105842] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/24/2014] [Indexed: 12/20/2022] Open
Abstract
The asymmetric Hopfield model is used to simulate signaling dynamics in gene regulatory networks. The model allows for a direct mapping of a gene expression pattern into attractor states. We analyze different control strategies aimed at disrupting attractor patterns using selective local fields representing therapeutic interventions. The control strategies are based on the identification of signaling bottlenecks, which are single nodes or strongly connected clusters of nodes that have a large impact on the signaling. We provide a theorem with bounds on the minimum number of nodes that guarantee control of bottlenecks consisting of strongly connected components. The control strategies are applied to the identification of sets of proteins that, when inhibited, selectively disrupt the signaling of cancer cells while preserving the signaling of normal cells. We use an experimentally validated non-specific and an algorithmically-assembled specific B cell gene regulatory network reconstructed from gene expression data to model cancer signaling in lung and B cells, respectively. Among the potential targets identified here are TP53, FOXM1, BCL6 and SRC. This model could help in the rational design of novel robust therapeutic interventions based on our increasing knowledge of complex gene signaling networks.
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Affiliation(s)
- Anthony Szedlak
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
| | - Giovanni Paternostro
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- Salgomed Inc., Del Mar, California, United States of America
| | - Carlo Piermarocchi
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
- Salgomed Inc., Del Mar, California, United States of America
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12
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Zhao B, Barrera LA, Ersing I, Willox B, Schmidt SCS, Greenfeld H, Zhou H, Mollo SB, Shi TT, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, Gewurz BE. The NF-κB genomic landscape in lymphoblastoid B cells. Cell Rep 2014; 8:1595-606. [PMID: 25159142 DOI: 10.1016/j.celrep.2014.07.037] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 06/09/2014] [Accepted: 07/21/2014] [Indexed: 01/17/2023] Open
Abstract
The nuclear factor κB (NF-κΒ) subunits RelA, RelB, cRel, p50, and p52 are each critical for B cell development and function. To systematically characterize their responses to canonical and noncanonical NF-κB pathway activity, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) analysis in lymphoblastoid B cell lines (LCLs). We found a complex NF-κB-binding landscape, which did not readily reflect the two NF-κB pathway paradigms. Instead, 10 subunit-binding patterns were observed at promoters and 11 at enhancers. Nearly one-third of NF-κB-binding sites lacked κB motifs and were instead enriched for alternative motifs. The oncogenic forkhead box protein FOXM1 co-occupied nearly half of NF-κB-binding sites and was identified in protein complexes with NF-κB on DNA. FOXM1 knockdown decreased NF-κB target gene expression and ultimately induced apoptosis, highlighting FOXM1 as a synthetic lethal target in B cell malignancy. These studies provide a resource for understanding mechanisms that underlie NF-κB nuclear activity and highlight opportunities for selective NF-κB blockade.
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Affiliation(s)
- Bo Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Luis A Barrera
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ina Ersing
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Bradford Willox
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stefanie C S Schmidt
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Greenfeld
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hufeng Zhou
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah B Mollo
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tommy T Shi
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kaoru Takasaki
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sizun Jiang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Cahir-McFarland
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Elliott Kieff
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin E Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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