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Zhang L, Sagan A, Qin B, Hu B, Osmanbeyoglu HU. STAN, a computational framework for inferring spatially informed transcription factor activity across cellular contexts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600782. [PMID: 38979296 PMCID: PMC11230390 DOI: 10.1101/2024.06.26.600782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Transcription factors (TFs) drive significant cellular changes in response to environmental cues and intercellular signaling. Neighboring cells influence TF activity and, consequently, cellular fate and function. Spatial transcriptomics (ST) captures mRNA expression patterns across tissue samples, enabling characterization of the local microenvironment. However, these datasets have not been fully leveraged to systematically estimate TF activity governing cell identity. Here, we present STAN ( S patially informed T ranscription factor A ctivity N etwork), a linear mixed-effects computational method that predicts spot-specific, spatially informed TF activities by integrating curated TF-target gene priors, mRNA expression, spatial coordinates, and morphological features from corresponding imaging data. We tested STAN using lymph node, breast cancer, and glioblastoma ST datasets to demonstrate its applicability by identifying TFs associated with specific cell types, spatial domains, pathological regions, and ligand-receptor pairs. STAN augments the utility of ST to reveal the intricate interplay between TFs and spatial organization across a spectrum of cellular contexts.
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A Comprehensive Analysis of Interferon Regulatory Factor Expression: Correlation with Immune Cell Infiltration and Patient Prognosis in Endometrial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7948898. [PMID: 35993041 PMCID: PMC9381850 DOI: 10.1155/2022/7948898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022]
Abstract
As a family of transcription factors, the correlations between expression pattern of nine interferon regulatory factor (IRF) family members, the immune invasion pattern, and the associated patient survival rate in endometrial carcinoma (EC) remain to be elucidated. Based on The Cancer Genome Atlas (TCGA), the expression profiles of the high and low IRF mRNA expression groups were analyzed using R (3.6.3) statistical software. Gene annotation and pathway analyses were performed using Metascape. GSEA was performed using the R package clusterProfiler (3.6.3). The single-sample gene set enrichment analysis (ssGSEA) was used to quantify the relative tumor infiltration levels of immune cell types. Immunohistochemistry data provided by HPA database was used to study the expression of the IRF proteins. Using the GEPIA dataset, the correlation between the expression of IRFs and the tumor stage of EC was analyzed. The correlations between the different IRFs were analyzed using cBioPortal. The expression of IRF2, IRF3, IRF5, IRF6, IRF7, IRF8, and IRF9 was different when comparing EC and normal endometrial samples. IRF2, IRF6, IRF7, and IRF8 were indicated to be potential diagnostic markers for EC. In combination with receiver operating characteristic analysis results, IRF2, IRF6, IRF7, and IRF8 were indicated to be potential diagnostic markers for EC. Levels of individual IRFs were associated with alternate outcomes, with the expression of IRF3 being correlated with the stage of EC and high expression of IRF4 being positively correlated with overall survival (OS); conversely, high expression of IRF5 was negatively correlated with OS. Additionally, high expression levels of both IRF2 and IRF4 were positively correlated with the disease-specific survival rate, and high expression of IRF4 was positively correlated with the progression-free interval. These data suggest a role for IRF2, IRF4, and IRF5 in the prognosis of EC. The expression of IRFs is associated with immune infiltration.
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Barlier C, Barriales D, Samosyuk A, Jung S, Ravichandran S, Medvedeva YA, Anguita J, Del Sol A. A Catalogus Immune Muris of the mouse immune responses to diverse pathogens. Cell Death Dis 2021; 12:798. [PMID: 34404761 PMCID: PMC8370971 DOI: 10.1038/s41419-021-04075-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/09/2022]
Abstract
Immunomodulation strategies are crucial for several biomedical applications. However, the immune system is highly heterogeneous and its functional responses to infections remains elusive. Indeed, the characterization of immune response particularities to different pathogens is needed to identify immunomodulatory candidates. To address this issue, we compiled a comprehensive map of functional immune cell states of mouse in response to 12 pathogens. To create this atlas, we developed a single-cell-based computational method that partitions heterogeneous cell types into functionally distinct states and simultaneously identifies modules of functionally relevant genes characterizing them. We identified 295 functional states using 114 datasets of six immune cell types, creating a Catalogus Immune Muris. As a result, we found common as well as pathogen-specific functional states and experimentally characterized the function of an unknown macrophage cell state that modulates the response to Salmonella Typhimurium infection. Thus, we expect our Catalogus Immune Muris to be an important resource for studies aiming at discovering new immunomodulatory candidates.
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Affiliation(s)
- Céline Barlier
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Diego Barriales
- Inflammation and Macrophage Plasticity laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Alexey Samosyuk
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Sascha Jung
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Srikanth Ravichandran
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Yulia A Medvedeva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, Russian Federation
- Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russian Federation
| | - Juan Anguita
- Inflammation and Macrophage Plasticity laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, 48012, Spain
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, 48012, Spain.
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Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors. Nat Commun 2020; 11:6318. [PMID: 33298918 PMCID: PMC7726151 DOI: 10.1038/s41467-020-20136-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Primary effusion lymphoma (PEL) has a very poor prognosis. To evaluate the contributions of enhancers/promoters interactions to PEL cell growth and survival, here we produce H3K27ac HiChIP datasets in PEL cells. This allows us to generate the PEL enhancer connectome, which links enhancers and promoters in PEL genome-wide. We identify more than 8000 genomic interactions in each PEL cell line. By incorporating HiChIP data with H3K27ac ChIP-seq data, we identify interactions between enhancers/enhancers, enhancers/promoters, and promoters/promoters. HiChIP further links PEL super-enhancers to PEL dependency factors MYC, IRF4, MCL1, CCND2, MDM2, and CFLAR. CRISPR knock out of MEF2C and IRF4 significantly reduces MYC and IRF4 super-enhancer H3K27ac signal. Knock out also reduces MYC and IRF4 expression. CRISPRi perturbation of these super-enhancers by tethering transcription repressors to enhancers significantly reduces target gene expression and reduces PEL cell growth. These data provide insights into PEL molecular pathogenesis.
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Antonczyk A, Krist B, Sajek M, Michalska A, Piaszyk-Borychowska A, Plens-Galaska M, Wesoly J, Bluyssen HAR. Direct Inhibition of IRF-Dependent Transcriptional Regulatory Mechanisms Associated With Disease. Front Immunol 2019; 10:1176. [PMID: 31178872 PMCID: PMC6543449 DOI: 10.3389/fimmu.2019.01176] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Interferon regulatory factors (IRFs) are a family of homologous proteins that regulate the transcription of interferons (IFNs) and IFN-induced gene expression. As such they are important modulating proteins in the Toll-like receptor (TLR) and IFN signaling pathways, which are vital elements of the innate immune system. IRFs have a multi-domain structure, with the N-terminal part acting as a DNA binding domain (DBD) that recognizes a DNA-binding motif similar to the IFN-stimulated response element (ISRE). The C-terminal part contains the IRF-association domain (IAD), with which they can self-associate, bind to IRF family members or interact with other transcription factors. This complex formation is crucial for DNA binding and the commencing of target-gene expression. IRFs bind DNA and exert their activating potential as homo or heterodimers with other IRFs. Moreover, they can form complexes (e.g., with Signal transducers and activators of transcription, STATs) and collaborate with other co-acting transcription factors such as Nuclear factor-κB (NF-κB) and PU.1. In time, more of these IRF co-activating mechanisms have been discovered, which may play a key role in the pathogenesis of many diseases, such as acute and chronic inflammation, autoimmune diseases, and cancer. Detailed knowledge of IRFs structure and activating mechanisms predisposes IRFs as potential targets for inhibition in therapeutic strategies connected to numerous immune system-originated diseases. Until now only indirect IRF modulation has been studied in terms of antiviral response regulation and cancer treatment, using mainly antisense oligonucleotides and siRNA knockdown strategies. However, none of these approaches so far entered clinical trials. Moreover, no direct IRF-inhibitory strategies have been reported. In this review, we summarize current knowledge of the different IRF-mediated transcriptional regulatory mechanisms and how they reflect the diverse functions of IRFs in homeostasis and in TLR and IFN signaling. Moreover, we present IRFs as promising inhibitory targets and propose a novel direct IRF-modulating strategy employing a pipeline approach that combines comparative in silico docking to the IRF-DBD with in vitro validation of IRF inhibition. We hypothesize that our methodology will enable the efficient identification of IRF-specific and pan-IRF inhibitors that can be used for the treatment of IRF-dependent disorders and malignancies.
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Affiliation(s)
- Aleksandra Antonczyk
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Bart Krist
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Malgorzata Sajek
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Agata Michalska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Piaszyk-Borychowska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Martyna Plens-Galaska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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Li S, Alvarez RV, Sharan R, Landsman D, Ovcharenko I. Quantifying deleterious effects of regulatory variants. Nucleic Acids Res 2017; 45:2307-2317. [PMID: 27980060 PMCID: PMC5389506 DOI: 10.1093/nar/gkw1263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/05/2016] [Indexed: 12/13/2022] Open
Abstract
The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed CAPE, which calculates the likelihood of a genetic variant deactivating enhancers by disrupting the binding of transcription factors (TFs) in a given cellular context. CAPE learns sequence signatures associated with putative enhancers originating from large-scale sequencing experiments (such as ChIP-seq or DNase-seq) and models the change in enhancer signature upon a single nucleotide substitution. CAPE accurately identifies causative cis-regulatory variation including expression quantitative trait loci (eQTLs) and DNase I sensitivity quantitative trait loci (dsQTLs) in a tissue-specific manner with precision superior to several currently available methods. The presented method can be trained on any tissue-specific dataset of enhancers and known functional variants and applied to prioritize disease-associated variants in the corresponding tissue.
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Affiliation(s)
- Shan Li
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roberto Vera Alvarez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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MicroRNA-18a-5p functions as an oncogene by directly targeting IRF2 in lung cancer. Cell Death Dis 2017; 8:e2764. [PMID: 28471447 PMCID: PMC5520692 DOI: 10.1038/cddis.2017.145] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Lung cancer is the major form of cancer resulting in cancer-related mortality around the world. MicroRNAs are endogenous small non-coding single-stranded RNAs, which can engage in the regulation of gene expression. In this study, miR-18a-5p significantly upregulated in non-small cell lung cancer (NSCLC) tissues and NSCLC cell lines, suggesting an oncogenic function in lung cancer. Additionally, miR-18a-5p can promote carcinogenesis by directly targeting interferon regulatory factor 2 (IRF2). Further experiments indicated that IRF2 can increase cell apoptosis, inhibit cell proliferation and migration ability. Our study demonstrates that miR-18a-5p promotes autophagy in NSCLC. Collectively, these results indicate that miR-18a-5p can not only promote NSCLC by suppressing IRF2, but also will be a promising target in the near future.
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Li MMH, Bozzacco L, Hoffmann HH, Breton G, Loschko J, Xiao JW, Monette S, Rice CM, MacDonald MR. Interferon regulatory factor 2 protects mice from lethal viral neuroinvasion. J Exp Med 2016; 213:2931-2947. [PMID: 27899441 PMCID: PMC5154937 DOI: 10.1084/jem.20160303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 09/09/2016] [Accepted: 11/01/2016] [Indexed: 01/08/2023] Open
Abstract
Li et al. describe a novel role for IRF2, previously known as a negative regulator of type I IFN signaling, in protection of mice from lethal viral neuroinvasion by facilitating the proper localization of B cells and antibodies to the central nervous system. The host responds to virus infection by activating type I interferon (IFN) signaling leading to expression of IFN-stimulated genes (ISGs). Dysregulation of the IFN response results in inflammatory diseases and chronic infections. In this study, we demonstrate that IFN regulatory factor 2 (IRF2), an ISG and a negative regulator of IFN signaling, influences alphavirus neuroinvasion and pathogenesis. A Sindbis virus strain that in wild-type (WT) mice only causes disease when injected into the brain leads to lethal encephalitis in Irf2−/− mice after peripheral inoculation. Irf2−/− mice fail to control virus replication and recruit immune infiltrates into the brain. Reduced B cells and virus-specific IgG are observed in the Irf2−/− mouse brains despite the presence of peripheral neutralizing antibodies, suggesting a defect in B cell trafficking to the central nervous system (CNS). B cell–deficient μMT mice are significantly more susceptible to viral infection, yet WT B cells and serum are unable to rescue the Irf2−/− mice. Collectively, our data demonstrate that proper localization of B cells and local production of antibodies in the CNS are required for protection. The work advances our understanding of host mechanisms that affect viral neuroinvasion and their contribution to immunity against CNS infections.
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Affiliation(s)
- Melody M H Li
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Leonia Bozzacco
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Jakob Loschko
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Jing W Xiao
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Sébastien Monette
- Tri-Institutional Laboratory of Comparative Pathology, Memorial Sloan-Kettering Cancer Center, The Rockefeller University, Weill Cornell Medical College, New York, NY 10065
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
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Exploring the effects of homeopathic Apis mellifica preparations on human gene expression profiles. HOMEOPATHY 2014; 103:127-32. [DOI: 10.1016/j.homp.2014.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 01/16/2014] [Accepted: 01/20/2014] [Indexed: 01/15/2023]
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Smith N, Tierney R, Wei W, Vockerodt M, Murray PG, Woodman CB, Rowe M. Induction of interferon-stimulated genes on the IL-4 response axis by Epstein-Barr virus infected human b cells; relevance to cellular transformation. PLoS One 2013; 8:e64868. [PMID: 23724103 PMCID: PMC3664578 DOI: 10.1371/journal.pone.0064868] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/19/2013] [Indexed: 11/19/2022] Open
Abstract
Epstein-Barr virus (EBV) is an oncogenic virus that is associated with the pathogenesis of several human lymphoid malignancies, including Hodgkin's lymphoma. Infection of normal resting B cells with EBV results in activation to lymphoblasts that are phenotypically similar to those generated by physiological stimulation with CD40L plus IL-4. One important difference is that infection leads to the establishment of permanently growing lymphoblastoid cell lines, whereas CD40L/IL-4 blasts have finite proliferation lifespans. To identify early events which might later determine why EBV infected blasts go on to establish transformed cell lines, we performed global transcriptome analyses on resting B cells and on EBV and CD40L/IL-4 blasts after 7 days culture. As anticipated there was considerable overlap in the transcriptomes of the two types of lymphoblasts when compared to the original resting B cells, reflecting common changes associated with lymphocyte activation and proliferation. Of interest to us was a subset of 255 genes that were differentially expressed between EBV and CD40L/IL-4 blasts. Genes which were more highly expressed in EBV blasts were substantially and significantly enriched for a set of interferon-stimulated genes which on further in silico analyses were found to be repressed by IL-4 in other cell contexts and to be up-regulated in micro-dissected malignant cells from Hodgkin's lymphoma biopsies when compared to their normal germinal center cell counterparts. We hypothesized that EBV and IL-4 were targeting and discordantly regulating a common set of genes. This was supported experimentally in our B cell model where IL-4 stimulation partially reversed transcriptional changes which follow EBV infection and it impaired the efficiency of EBV-induced B cell transformation. Taken together, these data suggest that the discordant regulation of interferon and IL-4 pathway genes by EBV that occurs early following infection of B cells has relevance to the development or maintenance of an EBV-associated malignancy.
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Affiliation(s)
- Nikki Smith
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
| | - Rosemary Tierney
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
| | - Wenbin Wei
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
| | - Martina Vockerodt
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
| | - Paul G. Murray
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
| | - Ciaran B. Woodman
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
| | - Martin Rowe
- School of Cancer Sciences, Birmingham Cancer Research UK Centre, and Birmingham Centre for Human Virology, University of Birmingham College of Medical and Dental Sciences, Birmingham, United Kingdom
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