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Dennis M, Hurley A, Bray N, Cordero C, Ilagan J, Mertz TM, Roberts SA. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells. PLoS Genet 2024; 20:e1011293. [PMID: 38805570 PMCID: PMC11161071 DOI: 10.1371/journal.pgen.1011293] [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: 05/12/2023] [Revised: 06/07/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
APOBEC-induced mutations occur in 50% of sequenced human tumors, with APOBEC3A (A3A) being a major contributor to mutagenesis in breast cancer cells. The mechanisms that cause A3A activation and mutagenesis in breast cancers are still unknown. Here, we describe factors that influence basal A3A mRNA transcript levels in breast cancer cells. We found that basal A3A mRNA correlates with A3A protein levels and predicts the amount of APOBEC signature mutations in a panel of breast cancer cell lines, indicating that increased basal transcription may be one mechanism leading to breast cancer mutagenesis. We also show that alteration of ERBB2 expression can drive A3A mRNA levels, suggesting the enrichment of the APOBEC mutation signature in Her2-enriched breast cancer could in part result from elevated A3A transcription. Hierarchical clustering of transcripts in primary breast cancers determined that A3A mRNA was co-expressed with other genes functioning in viral restriction and interferon responses. However, reduction of STAT signaling via inhibitors or shRNA in breast cancer cell lines had only minor impact on A3A abundance. Analysis of single cell RNA-seq from primary tumors indicated that A3A mRNA was highest in infiltrating immune cells within the tumor, indicating that correlations of A3A with STAT signaling in primary tumors may be result from higher immune infiltrates and are not reflective of STAT signaling controlling A3A expression in breast cancer cells. Analysis of ATAC-seq data in multiple breast cancer cell lines identified two transcription factor sites in the APOBEC3A promoter region that could promote A3A transcription. We determined that Rel-A, and Bach1, which have binding sites in these peaks, elevated basal A3A expression. Our findings highlight a complex and variable set of transcriptional activators for A3A in breast cancer cells.
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Affiliation(s)
- Madeline Dennis
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Alyssa Hurley
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Nicholas Bray
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Cameron Cordero
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Jose Ilagan
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Tony M. Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
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2
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Zhang S, Guo Y, Hu Y, Gao X, Bai F, Ding Q, Hou K, Wang Z, Sun X, Zhao H, Qu Z, Xu Q. The role of APOBEC3C in modulating the tumor microenvironment and stemness properties of glioma: evidence from pancancer analysis. Front Immunol 2023; 14:1242972. [PMID: 37809064 PMCID: PMC10551170 DOI: 10.3389/fimmu.2023.1242972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background It is now understood that APOBEC3 family proteins (A3s) are essential in tumor progression, yet their involvement in tumor immunity and stemness across diverse cancer types remains poorly understood. Methods In the present study, comprehensive genome-wide statistical and bioinformatic analyses were conducted to elucidate A3 family expression patterns, establishing clinically relevant correlations with prognosis, the tumor microenvironment(TME), immune infiltration, checkpoint blockade, and stemness across cancers. Different experimental techniques were applied, including RT-qPCR, immunohistochemistry, sphere formation assays, Transwell migration assays, and wound-healing assays, to investigate the impact of A3C on low-grade glioma (LGG) and glioblastoma multiforme (GBM), as well as its function in glioma stem cells(GSCs). Results Dysregulated expression of A3s was observed in various human cancer tissues. The prognostic value of A3 expression differed across cancer types, with a link to particularly unfavorable outcomes in gliomas. A3s are associated with the the TME and stemness in multiple cancers. Additionally, we developed an independent prognostic model based on A3s expression, which may be an independent prognostic factor for OS in patients with glioma. Subsequent validation underscored a strong association between elevated A3C expression and adverse prognostic outcomes, higher tumor grades, and unfavorable histology in glioma. A potential connection between A3C and glioma progression was established. Notably, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses implicated A3C in immune system-related diseases, with heightened A3C levels contributing to an immunosuppressive tumor microenvironment (TME) in glioma. Furthermore, in vitro experiments substantiated the role of A3C in sustaining and renewing glioma stem cells, as A3C deletion led to diminished proliferation, invasion, and migration of glioma cells. Conclusion The A3 family exhibits heterogeneous expression across various cancer types, with its expression profile serving as a predictive marker for overall survival in glioma patients. A3C emerges as a regulator of glioma progression, exerting its influence through modulation of the tumor microenvironment and regulation of stemness.
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Affiliation(s)
- Shoudu Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yuanzheng Hu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Xiaofang Gao
- The Department of Science and Technology, Zhengzhou Revogene Ltd, Zhengzhou, Henan, China
| | - Fanghui Bai
- Department of Oncology, Nanyang central Hospital, Nanyang, Henan, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Kaiqi Hou
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Zongqing Wang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Xing Sun
- Department of Oncology, Nanyang central Hospital, Nanyang, Henan, China
| | - Hui Zhao
- The Department of Science and Technology, Zhengzhou Revogene Ltd, Zhengzhou, Henan, China
| | - Zhongyu Qu
- Department of Oncology, Nanyang central Hospital, Nanyang, Henan, China
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
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3
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De Gregorio C, Catalán E, Garrido G, Morandé P, Bennett JC, Muñoz C, Cofré G, Huang YL, Cuadra B, Murgas P, Calvo M, Altermatt F, Yubero MJ, Palisson F, South AP, Ezquer M, Fuentes I. Maintenance of chronicity signatures in fibroblasts isolated from recessive dystrophic epidermolysis bullosa chronic wound dressings under culture conditions. Biol Res 2023; 56:23. [PMID: 37161592 PMCID: PMC10170710 DOI: 10.1186/s40659-023-00437-2] [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] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Recessive Dystrophic Epidermolysis Bullosa (RDEB) is a rare inherited skin disease caused by variants in the COL7A1 gene, coding for type VII collagen (C7), an important component of anchoring fibrils in the basement membrane of the epidermis. RDEB patients suffer from skin fragility starting with blister formation and evolving into chronic wounds, inflammation and skin fibrosis, with a high risk of developing aggressive skin carcinomas. Restricted therapeutic options are limited by the lack of in vitro models of defective wound healing in RDEB patients. RESULTS In order to explore a more efficient, non-invasive in vitro model for RDEB studies, we obtained patient fibroblasts derived from discarded dressings) and examined their phenotypic features compared with fibroblasts derived from non-injured skin of RDEB and healthy-donor skin biopsies. Our results demonstrate that fibroblasts derived from RDEB chronic wounds (RDEB-CW) displayed characteristics of senescent cells, increased myofibroblast differentiation, and augmented levels of TGF-β1 signaling components compared to fibroblasts derived from RDEB acute wounds and unaffected RDEB skin as well as skin from healthy-donors. Furthermore, RDEB-CW fibroblasts exhibited an increased pattern of inflammatory cytokine secretion (IL-1β and IL-6) when compared with RDEB and control fibroblasts. Interestingly, these aberrant patterns were found specifically in RDEB-CW fibroblasts independent of the culturing method, since fibroblasts obtained from dressing of acute wounds displayed a phenotype more similar to fibroblasts obtained from RDEB normal skin biopsies. CONCLUSIONS Our results show that in vitro cultured RDEB-CW fibroblasts maintain distinctive cellular and molecular characteristics resembling the inflammatory and fibrotic microenvironment observed in RDEB patients' chronic wounds. This work describes a novel, non-invasive and painless strategy to obtain human fibroblasts chronically subjected to an inflammatory and fibrotic environment, supporting their use as an accessible model for in vitro studies of RDEB wound healing pathogenesis. As such, this approach is well suited to testing new therapeutic strategies under controlled laboratory conditions.
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Affiliation(s)
- Cristian De Gregorio
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, 7610658, Chile
| | - Evelyng Catalán
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | - Gabriel Garrido
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | - Pilar Morandé
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | | | - Catalina Muñoz
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | - Glenda Cofré
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | - Ya-Lin Huang
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, 7610658, Chile
| | - Bárbara Cuadra
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, 7610658, Chile
| | - Paola Murgas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Margarita Calvo
- Facultad de Ciencias Biológicas y División de Anestesiología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Núcleo milenio para el estudio del dolor MINUSPAIN, Santiago, Chile
| | - Fernando Altermatt
- División de Anestesiología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Joao Yubero
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
- Pediatrics and Pediatric Infectious Diseases of Clínica Alemana, Facultad de Medicina Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Francis Palisson
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
- Servicio de Dermatología, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrew P South
- Department of Dermatology & Cutaneous Biology, Thomas Jefferson University, Philadelphia, USA
| | - Marcelo Ezquer
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, 7610658, Chile.
| | - Ignacia Fuentes
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile.
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, 7610658, Chile.
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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4
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Dudley JP. APOBECs: Our fickle friends? PLoS Pathog 2023; 19:e1011364. [PMID: 37200235 DOI: 10.1371/journal.ppat.1011364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Jaquelin P Dudley
- Department of Molecular Biosciences and LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
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5
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Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
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Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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6
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Olah C, Reis H, Hoffmann MJ, Mairinger F, Ting S, Hadaschik B, Krafft U, Grünwald V, Nyirady P, Varadi M, Győrffy B, Kiss A, Szekely E, Sjödahl G, Szarvas T. Predictive value of molecular subtypes and APOBEC3G for adjuvant chemotherapy in urothelial bladder cancer. Cancer Med 2023; 12:5222-5232. [PMID: 36204983 PMCID: PMC10028049 DOI: 10.1002/cam4.5324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVE Although targeted approaches have become available in second- and third-line settings, platinum-based chemotherapy remains the standard first-line treatment for advanced muscle-invasive bladder cancer (MIBC). Therefore, the prediction of platinum resistance is of utmost clinical importance. METHODS In this study, we established a routine compatible method for the molecular classification of MIBC samples according to various classification systems and applied this method to evaluate the impact of subtypes on survival after adjuvant chemotherapy. This retrospective study included 191 patients with advanced MIBC (pT≥3 or pN+) who underwent radical cystectomy, with or without adjuvant chemotherapy. A 48-gene panel and classifier rule set were established to determine molecular subtypes according to TCGA, MDA, LundTax, and Consensus classifications. Additionally, 12 single platinum-predictive candidate genes were assessed. The results were correlated with patients' clinicopathological and follow-up data and were validated using independent data sets. RESULTS Our final evaluation of 159 patients demonstrated better survival in the luminal groups for those who received chemotherapy compared with those who did not. In contrast, no such differences were observed in basal subtypes. The use of chemotherapy was associated with better survival in patients with high APOBEC3G expression (p < 0.002). This association was confirmed using an independent data set of patients who received neoadjuvant platinum therapy. CONCLUSIONS The proposed method robustly replicates the most commonly used transcriptome-based subtype classifications from paraffin-embedded tissue samples. The luminal, but not basal, molecular subtypes had the greatest benefit from adjuvant platinum therapy. We identified and validated APOBEC3G as a novel predictive marker for platinum-treated patients.
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Affiliation(s)
- Csilla Olah
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Henning Reis
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michèle J Hoffmann
- Department of Urology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Fabian Mairinger
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | - Saskia Ting
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | - Boris Hadaschik
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Krafft
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Viktor Grünwald
- Department of Medical Oncology, University of Duisburg-Essen, Essen, Germany
| | - Peter Nyirady
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Melinda Varadi
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Balázs Győrffy
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
- 2nd Department of Pediatrics and Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Andras Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Eszter Szekely
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Gottfrid Sjödahl
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Tibor Szarvas
- Department of Urology, University of Duisburg-Essen, Essen, Germany
- Department of Urology, Semmelweis University, Budapest, Hungary
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7
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Fanourakis G, Kyrodimos E, Papanikolaou V, Chrysovergis A, Kafiri G, Papanikolaou N, Verykokakis M, Tosios K, Vastardis H. APOBEC3B Is Co-Expressed with PKCα/NF-κB in Oral and Oropharyngeal Squamous Cell Carcinomas. Diagnostics (Basel) 2023; 13:diagnostics13030569. [PMID: 36766673 PMCID: PMC9914863 DOI: 10.3390/diagnostics13030569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
The enzymatic activity of APOBEC3B (A3B) has been implicated as a prime source of mutagenesis in head and neck squamous cell carcinoma (HNSCC). The expression of Protein Kinase C α (PKCα) and Nuclear Factor-κΒ p65 (NF-κΒ p65) has been linked to the activation of the classical and the non-canonical NF-κB signaling pathways, respectively, both of which have been shown to lead to the upregulation of A3B. Accordingly, the aim of the present study was to evaluate the expression of PKCα, NF-κΒ p65 and A3B in non-HPV related oral and oropharyngeal squamous cell carcinomas (SCC), by means of immunohistochemistry and in silico methods. PKCα was expressed in 29/36 (80%) cases of oral and oropharyngeal SCCs, with 25 (69%) cases showing a PKCα+/A3B+ phenotype and only 6/36 (17%) cases showing a PKCα-/A3B+ phenotype. Εxpression of NF-κB p65 was seen in 33/35 (94%) cases of oral and oropharyngeal SCCs, with 30/35 (86%) cases showing an NF-κB p65+/A3B+ phenotype and only 2/35 (6%) cases showing an NF-κB p65-/A3B+ phenotype. In addition, mRNA expression analysis, using the UALCAN database, revealed strong expression of all three genes. These findings indicate that the expression of A3B is associated with PKCα/NF-κB p65 expression and suggest a potential role for the PKC/NF-κB signaling pathway in the development of oral and oropharyngeal cancer.
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Affiliation(s)
- Galinos Fanourakis
- Department of Oral Biology, School of Dentistry, National and Kapodistrian University of Athens, 2 Thivon Str., 11527 Athens, Greece
- Correspondence:
| | - Efthymios Kyrodimos
- 1st ENT Department, Hippokration Hospital, School of Medicine, National and Kapodistrian University of Athens, 114 Vasilissis Sophias Ave., 11527 Athens, Greece
| | - Vasileios Papanikolaou
- 1st ENT Department, Hippokration Hospital, School of Medicine, National and Kapodistrian University of Athens, 114 Vasilissis Sophias Ave., 11527 Athens, Greece
| | - Aristeidis Chrysovergis
- 1st ENT Department, Hippokration Hospital, School of Medicine, National and Kapodistrian University of Athens, 114 Vasilissis Sophias Ave., 11527 Athens, Greece
| | - Georgia Kafiri
- Department of Pathology, Hippokration Hospital, 114 Vasilissis Sophias Ave., 11527 Athens, Greece
| | - Nikolaos Papanikolaou
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira Str., Vassilika Vouton, 70013 Heraklion, Greece
| | - Mihalis Verykokakis
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, 34 Fleming Str., 16672 Vari, Greece
| | - Konstantinos Tosios
- Department of Oral Pathology, Medicine and Hospital Dentistry, School of Dentistry, National and Kapodistrian University of Athens, 2 Thivon Str., 11527 Athens, Greece
| | - Heleni Vastardis
- Department of Orthodontics, School of Dentistry, National and Kapodistrian University of Athens, 2 Thivon Str., 11527 Athens, Greece
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8
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Timmerman AL, Kaczorowska J, Deijs M, Bakker M, van der Hoek L. Control of Human Anelloviruses by Cytosine to Uracil Genome Editing. mSphere 2022; 7:e0050622. [PMID: 36374042 PMCID: PMC9769745 DOI: 10.1128/msphere.00506-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Anelloviruses are the most common viruses infecting humans. Every human carries a nonpathogenic personal anellovirus virome (anellome), yet it is unknown which mechanisms contribute to its stability. Here, we assessed the dynamics and impact of a host antiviral defense mechanism-cytidine deaminase activity leading to C to U editing in anelloviruses-on the stability of the anellome. We investigated anellome sequence data obtained from serum samples collected every 6 months from two healthy subjects followed for more than 30 years. The subjects were infected by a total of 64 anellovirus lineages. Minus-stranded C to U editing was observed in lineages belonging to the Alpha-, Beta-, and Gammatorquevirus genera. The edited genomes were present within virus particles, therefore editing must have occurred at the late stages of the virus life cycle. Editing was favored by 5'-TC contexts in the virus genome, indicating that apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like, catalytic subunit 3 or A3 (APOBEC3) proteins are involved. Within a lineage, mutational dynamics varied over time and few fixations of mutations were detected, indicating that C to U editing is a dead end for a virus genome. We detected an editing coldspot in the GC-rich regions, suggesting that the GC-rich region is crucial for genome packaging, since only packaged virus particles were included in the analysis. Finally, we noticed a lineage-specific reduced concentration after an editing event, yet no clearance. In conclusion, cytidine deaminase activity does not clear anelloviruses, nor does it play a major role in virus evolution, but it does contribute to the stability of the anellome. IMPORTANCE Despite significant attention on anellovirus research, the interaction between the anellovirus virome and the human host remains unknown. We show the dynamics of APOBEC3-mediated cytidine deaminase activity on anelloviruses during a 30-year period of chronic infection and postulate that this antiviral mechanism controls anelloviruses. These results expand our knowledge of anellovirus-host interactions, which may be important for the design of gene therapies.
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Affiliation(s)
- Anne L. Timmerman
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Joanna Kaczorowska
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Margreet Bakker
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
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9
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Petljak M, Green AM, Maciejowski J, Weitzman MD. Addressing the benefits of inhibiting APOBEC3-dependent mutagenesis in cancer. Nat Genet 2022; 54:1599-1608. [PMID: 36280735 PMCID: PMC9700387 DOI: 10.1038/s41588-022-01196-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/29/2022] [Indexed: 01/21/2023]
Abstract
Mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC)3 cytosine deaminase activity have been found in over half of cancer types, including some therapy-resistant and metastatic tumors. Driver mutations can occur in APOBEC3-favored sequence contexts, suggesting that mutagenesis by APOBEC3 enzymes may drive cancer evolution. The APOBEC3-mediated signatures are often detected in subclonal branches of tumor phylogenies and are acquired in cancer cell lines over long periods of time, indicating that APOBEC3 mutagenesis can be ongoing in cancer. Collectively, these and other observations have led to the proposal that APOBEC3 mutagenesis represents a disease-modifying process that could be inhibited to limit tumor heterogeneity, metastasis and drug resistance. However, critical aspects of APOBEC3 biology in cancer and in healthy tissues have not been clearly defined, limiting well-grounded predictions regarding the benefits of inhibiting APOBEC3 mutagenesis in different settings in cancer. We discuss the relevant mechanistic gaps and strategies to address them to investigate whether inhibiting APOBEC3 mutagenesis may confer clinical benefits in cancer.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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10
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Tsukimoto S, Hakata Y, Tsuji-Kawahara S, Enya T, Tsukamoto T, Mizuno S, Takahashi S, Nakao S, Miyazawa M. Distinctive High Expression of Antiretroviral APOBEC3 Protein in Mouse Germinal Center B Cells. Viruses 2022; 14:v14040832. [PMID: 35458563 PMCID: PMC9029289 DOI: 10.3390/v14040832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/07/2022] [Accepted: 04/13/2022] [Indexed: 12/04/2022] Open
Abstract
Tissue and subcellular localization and its changes upon cell activation of virus-restricting APOBEC3 at protein levels are important to understanding physiological functions of this cytidine deaminase, but have not been thoroughly analyzed in vivo. To precisely follow the possible activation-induced changes in expression levels of APOBEC3 protein in different mouse tissues and cell populations, genome editing was utilized to establish knock-in mice that express APOBEC3 protein with an in-frame FLAG tag. Flow cytometry and immunohistochemical analyses were performed prior to and after an immunological stimulation. Cultured B cells expressed higher levels of APOBEC3 protein than T cells. All differentiation and activation stages of freshly prepared B cells expressed significant levels of APOBEC3 protein, but germinal center cells possessed the highest levels of APOBEC3 protein localized in their cytoplasm. Upon immunological stimulation with sheep red blood cells in vivo, germinal center cells with high levels of APOBEC3 protein expression increased in their number, but FLAG-specific fluorescence intensity in each cell did not change. T cells, even those in germinal centers, did not express significant levels of APOBEC3 protein. Thus, mouse APOBEC3 protein is expressed at distinctively high levels in germinal center B cells. Antigenic stimulation did not affect expression levels of cellular APOBEC3 protein despite increased numbers of germinal center cells.
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Affiliation(s)
- Shota Tsukimoto
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan; (S.T.); (Y.H.); (S.T.-K.); (T.E.); or (T.T.)
- Department of Anesthesiology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan;
| | - Yoshiyuki Hakata
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan; (S.T.); (Y.H.); (S.T.-K.); (T.E.); or (T.T.)
| | - Sachiyo Tsuji-Kawahara
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan; (S.T.); (Y.H.); (S.T.-K.); (T.E.); or (T.T.)
| | - Takuji Enya
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan; (S.T.); (Y.H.); (S.T.-K.); (T.E.); or (T.T.)
- Department of Pediatrics, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan
| | - Tetsuo Tsukamoto
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan; (S.T.); (Y.H.); (S.T.-K.); (T.E.); or (T.T.)
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Transborder Medical Research Center, Department of Laboratory Animal Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan;
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan;
| | - Shinichi Nakao
- Department of Anesthesiology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan;
| | - Masaaki Miyazawa
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan; (S.T.); (Y.H.); (S.T.-K.); (T.E.); or (T.T.)
- Anti-Aging Center, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Osaka, Japan
- Correspondence:
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11
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Shilova ON, Tsyba DL, Shilov ES. Mutagenic Activity of AID/APOBEC Deaminases in Antiviral Defense and Carcinogenesis. Mol Biol 2022; 56:46-58. [PMID: 35194245 PMCID: PMC8852905 DOI: 10.1134/s002689332201006x] [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: 12/28/2020] [Revised: 04/23/2021] [Accepted: 06/01/2021] [Indexed: 01/02/2023]
Abstract
Proteins of the AID/APOBEC family are capable of cytidine deamination in nucleic acids forming uracil. These enzymes are involved in mRNA editing, protection against viruses, the introduction of point mutations into DNA during somatic hypermutation, and antibody isotype switching. Since these deaminases, especially AID, are potent mutagens, their expression, activity, and specificity are regulated by several intracellular mechanisms. In this review, we discuss the mechanisms of impaired expression and activation of AID/APOBEC proteins in human tumors and their role in carcinogenesis and tumor progression. Also, the diagnostic and potential therapeutic value of increased expression of AID/APOBEC in different types of tumors is analyzed. We assume that in the case of solid tumors, increased expression of endogenous deaminases can serve as a marker of response to immunotherapy since multiple point mutations in host DNA could lead to amino acid substitutions in tumor proteins and thereby increase the frequency of neoepitopes.
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Affiliation(s)
- O. N. Shilova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - D. L. Tsyba
- Pavlov First State Medical University, 197022 St. Petersburg, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - E. S. Shilov
- Faculty of Biology, Moscow State University, 119234 Moscow, Russia
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12
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Scholtes GK, Sawyer AM, Vaca CC, Clerc I, Roh M, Song C, D'Aquila RT. The von Hippel-Lindau Cullin-RING E3 ubiquitin ligase regulates APOBEC3 cytidine deaminases. Transl Res 2021; 237:1-15. [PMID: 34004371 PMCID: PMC8440357 DOI: 10.1016/j.trsl.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
The 7 members of the A3 family of cytidine deaminases (A3A to A3H) share a conserved catalytic activity that converts cytidines in single-stranded (ss) DNA into uridines, thereby inducing mutations. After their initial identification as cell-intrinsic defenses against HIV and other retroviruses, A3s were also found to impair many additional viruses. Moreover, some of the A3 proteins (A3A, A3B, and A3H haplotype I) are dysregulated in cancer cells, thereby causing chromosomal mutations that can be selected to fuel progression of malignancy. Viral mechanisms that increase transcription of A3 genes or induce proteasomal degradation of A3 proteins have been characterized. However, only a few underlying biological mechanisms regulating levels of A3s in uninfected cells have been described. Here, we characterize that the von Hippel-Lindau tumor suppressor (pVHL), via its CRLpVHL, induces degradation of all 7 A3 proteins. Two independent lines of evidence supported the conclusion that the multiprotein CRLpVHL complex is necessary for A3 degradation. CRLpVHL more effectively induced degradation of nuclear, procancer A3 (A3B) than the cytoplasmic, antiretroviral A3 (A3G). These results identify specific cellular factors that regulate A3s post-translationally.
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Affiliation(s)
- Gael K Scholtes
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Aubrey M Sawyer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cristina C Vaca
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Isabelle Clerc
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Meejeon Roh
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Chisu Song
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard T D'Aquila
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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13
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Faure-Dupuy S, Riedl T, Rolland M, Hizir Z, Reisinger F, Neuhaus K, Schuehle S, Remouchamps C, Gillet N, Schönung M, Stadler M, Wettengel J, Barnault R, Parent R, Schuster LC, Farhat R, Prokosch S, Leuchtenberger C, Öllinger R, Engleitner T, Rippe K, Rad R, Unger K, Tscharahganeh D, Lipka DB, Protzer U, Durantel D, Lucifora J, Dejardin E, Heikenwälder M. Control of APOBEC3B induction and cccDNA decay by NF-κB and miR-138-5p. JHEP Rep 2021; 3:100354. [PMID: 34704004 PMCID: PMC8523871 DOI: 10.1016/j.jhepr.2021.100354] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/28/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background & Aims Immune-mediated induction of cytidine deaminase APOBEC3B (A3B) expression leads to HBV covalently closed circular DNA (cccDNA) decay. Here, we aimed to decipher the signalling pathway(s) and regulatory mechanism(s) involved in A3B induction and related HBV control. Methods Differentiated HepaRG cells (dHepaRG) knocked-down for NF-κB signalling components, transfected with siRNA or micro RNAs (miRNA), and primary human hepatocytes ± HBV or HBVΔX or HBV-RFP, were treated with lymphotoxin beta receptor (LTβR)-agonist (BS1). The biological outcomes were analysed by reverse transcriptase-qPCR, immunoblotting, luciferase activity, chromatin immune precipitation, electrophoretic mobility-shift assay, targeted-bisulfite-, miRNA-, RNA-, genome-sequencing, and mass-spectrometry. Results We found that canonical and non-canonical NF-κB signalling pathways are mandatory for A3B induction and anti-HBV effects. The degree of immune-mediated A3B production is independent of A3B promoter demethylation but is controlled post-transcriptionally by the miRNA 138-5p expression (hsa-miR-138-5p), promoting A3B mRNA decay. Hsa-miR-138-5p over-expression reduced A3B levels and its antiviral effects. Of note, established infection inhibited BS1-induced A3B expression through epigenetic modulation of A3B promoter. Twelve days of treatment with a LTβR-specific agonist BS1 is sufficient to reduce the cccDNA pool by 80% without inducing significant damages to a subset of cancer-related host genes. Interestingly, the A3B-mediated effect on HBV is independent of the transcriptional activity of cccDNA as well as on rcDNA synthesis. Conclusions Altogether, A3B represents the only described enzyme to target both transcriptionally active and inactive cccDNA. Thus, inhibiting hsa-miR-138-5p expression should be considered in the combinatorial design of new therapies against HBV, especially in the context of immune-mediated A3B induction. Lay summary Immune-mediated induction of cytidine deaminase APOBEC3B is transcriptionally regulated by NF-κB signalling and post-transcriptionally downregulated by hsa-miR-138-5p expression, leading to cccDNA decay. Timely controlled APOBEC3B-mediated cccDNA decay occurs independently of cccDNA transcriptional activity and without damage to a subset of cancer-related genes. Thus, APOBEC3B-mediated cccDNA decay could offer an efficient therapeutic alternative to target hepatitis B virus chronic infection. Impairment of NF-κB signalling prevents APOBEC3B induction and cccDNA decay. APOBEC3B is post-transcriptionally regulated by the hsa-miR-138-5p. Over-expression of the hsa-miR-138-5p inhibits APOBEC3B expression and cccDNA decay. A3B timely induces cccDNA decay without damage to cancer-related genes. APOBEC3B-mediated cccDNA decay is independent of cccDNA transcriptional activity.
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Key Words
- A20, tumour necrosis factor alpha-induced protein 3
- APOBEC3A/A3A, apolipoprotein B mRNA editing catalytic polypeptide-like A
- APOBEC3B
- APOBEC3B/A3B, apolipoprotein B mRNA editing catalytic polypeptide-like B
- APOBEC3G/A3G, apolipoprotein B mRNA editing catalytic polypeptide-like G
- BCA, bicinchoninic acid assay
- CHB, chronic hepatitis B
- CXCL10, C-X-C motif chemokine ligand 10
- ChIP, chromatin immune precipitation
- EMSA, electrophoretic mobility-shift assay
- H3K4Me3, histone 3 lysine 4 trimethylation
- HBx
- Hepatitis B virus
- IFNα/γ, interferon alpha/gamma
- IKKα/β, IκB kinase alpha/beta
- JMJD8, jumonji domain containing 8
- LPS, lipopolysaccharide
- LTβR, lymphotoxin beta receptor
- MAPK, mitogen-activated protein kinase
- NEMO, NF-κB essential modulator
- NF-κB
- NF-κB, nuclear factor kappa B
- NIK, NF-κB inducing kinase
- NT, non-treated
- RT-qPCR, reverse transcription-quantitative PCR
- RelA, NF-κB p65 subunit
- TNF, tumour necrosis factor
- UBE2V1, ubiquitin conjugating enzyme E2 V1
- UTR, untranslated region
- cccDNA
- cccDNA, covalently closed circular DNA
- d.p.i., days post infection
- miRNA
- miRNA, micro RNA
- siCTRL, siRNA control
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Affiliation(s)
- Suzanne Faure-Dupuy
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maude Rolland
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Zoheir Hizir
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Florian Reisinger
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Katharina Neuhaus
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Svenja Schuehle
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Caroline Remouchamps
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Nicolas Gillet
- Integrated Veterinary Research Unit, Namur Research Institute for Life Sciences, Namur, Belgium
| | - Maximilian Schönung
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Mira Stadler
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jochen Wettengel
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Romain Barnault
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Romain Parent
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Linda Christina Schuster
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rayan Farhat
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Sandra Prokosch
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Leuchtenberger
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Darjus Tscharahganeh
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, Heidelberg, Germany
| | - Daniel B. Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - David Durantel
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Julie Lucifora
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
- Corresponding authors. Addresses: Laboratory of Molecular Immunology and Signal Transduction, University of Liège, GIGA-Institute, Avenue de l'Hôpital, 1, CHU, B34, 4000 Liege, Belgium. Tel.: +32 4 366 4472; fax: +32 4 366 4534
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany. Tel.: +49 6221 42 3891; Fax: +49 6221 42 3899
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14
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Riedl T, Faure-Dupuy S, Rolland M, Schuehle S, Hizir Z, Calderazzo S, Zhuang X, Wettengel J, Lopez AM, Barnault R, Mirakaj V, Prokosch S, Heide D, Leuchtenbergeg C, Schneider M, Heßling B, Stottmeier B, Wessbecher IM, Schirmacher P, McKeating JA, Protzer U, Durantel D, Lucifora J, Dejardin E, Heikenwalder M. Hypoxia-Inducible Factor 1 Alpha-Mediated RelB/APOBEC3B Down-regulation Allows Hepatitis B Virus Persistence. Hepatology 2021; 74:1766-1781. [PMID: 33991110 PMCID: PMC7611739 DOI: 10.1002/hep.31902] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Therapeutic strategies against HBV focus, among others, on the activation of the immune system to enable the infected host to eliminate HBV. Hypoxia-inducible factor 1 alpha (HIF1α) stabilization has been associated with impaired immune responses. HBV pathogenesis triggers chronic hepatitis-related scaring, leading inter alia to modulation of liver oxygenation and transient immune activation, both factors playing a role in HIF1α stabilization. APPROACH AND RESULTS We addressed whether HIF1α interferes with immune-mediated induction of the cytidine deaminase, apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B; A3B), and subsequent covalently closed circular DNA (cccDNA) decay. Liver biopsies of chronic HBV (CHB) patients were analyzed by immunohistochemistry and in situ hybridization. The effect of HIF1α induction/stabilization on differentiated HepaRG or mice ± HBV ± LTβR-agonist (BS1) was assessed in vitro and in vivo. Induction of A3B and subsequent effects were analyzed by RT-qPCR, immunoblotting, chromatin immunoprecipitation, immunocytochemistry, and mass spectrometry. Analyzing CHB highlighted that areas with high HIF1α levels and low A3B expression correlated with high HBcAg, potentially representing a reservoir for HBV survival in immune-active patients. In vitro, HIF1α stabilization strongly impaired A3B expression and anti-HBV effect. Interestingly, HIF1α knockdown was sufficient to rescue the inhibition of A3B up-regulation and -mediated antiviral effects, whereas HIF2α knockdown had no effect. HIF1α stabilization decreased the level of v-rel reticuloendotheliosis viral oncogene homolog B protein, but not its mRNA, which was confirmed in vivo. Noteworthy, this function of HIF1α was independent of its partner, aryl hydrocarbon receptor nuclear translocator. CONCLUSIONS In conclusion, inhibiting HIF1α expression or stabilization represents an anti-HBV strategy in the context of immune-mediated A3B induction. High HIF1α, mediated by hypoxia or inflammation, offers a reservoir for HBV survival in vivo and should be considered as a restricting factor in the development of immune therapies.
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Affiliation(s)
- Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Suzanne Faure-Dupuy
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Maude Rolland
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Svenja Schuehle
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Zohier Hizir
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Silvia Calderazzo
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, and Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jochen Wettengel
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Alexander Martin Lopez
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Romain Barnault
- Departement of Anesthesiology and Intensive Care Medecine, Molecular Intensive Care Medicine, University Hospital Tübingen, Eberhard-Karls-University, DE-72076, Tuebingen, Germany
| | - Valbona Mirakaj
- Departement of Anesthesiology and Intensive Care Medecine, Molecular Intensive Care Medicine, University Hospital Tübingen, Eberhard-Karls-University, DE-72076, Tuebingen, Germany
| | - Sandra Prokosch
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Leuchtenbergeg
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Mass spectrometry based Protein Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bernd Heßling
- Mass spectrometry based Protein Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Stottmeier
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany,German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Isabel M. Wessbecher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany,Tissue Bank of the German Center for Infection Research (DZIF), Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany,Tissue Bank of the German Center for Infection Research (DZIF), Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, and Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Ulrike Protzer
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - David Durantel
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Julie Lucifora
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium,Corresponding authors: Prof. Dr. Mathias Heikenwälder, Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany. Tel.: +49 6221 42-3891, Fax: +49 6221 42-3899, ; Dr. Dejardin Emmanuel, Laboratory of Molecular Immunology and Signal Transduction, University of Liège, GIGA Institute, Avenue de hôpital, 1, CHU, B34, 4000 Liege, Belgium, Tel: +32 4 3664472, Fax: +32 4 3664534,
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany,Corresponding authors: Prof. Dr. Mathias Heikenwälder, Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany. Tel.: +49 6221 42-3891, Fax: +49 6221 42-3899, ; Dr. Dejardin Emmanuel, Laboratory of Molecular Immunology and Signal Transduction, University of Liège, GIGA Institute, Avenue de hôpital, 1, CHU, B34, 4000 Liege, Belgium, Tel: +32 4 3664472, Fax: +32 4 3664534,
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15
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Zhao K, Zhang Q, Flanagan SA, Lang X, Jiang L, Parsels LA, Parsels JD, Zou W, Lawrence TS, Buisson R, Green MD, Morgan MA. Cytidine Deaminase APOBEC3A Regulates PD-L1 Expression in Cancer Cells in a JNK/c-JUN-Dependent Manner. Mol Cancer Res 2021; 19:1571-1582. [PMID: 34045311 DOI: 10.1158/1541-7786.mcr-21-0219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/21/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022]
Abstract
Programmed death-ligand 1 (PD-L1) promotes tumor immune evasion by engaging the PD-1 receptor and inhibiting T-cell activity. While the regulation of PD-L1 expression is not fully understood, its expression is associated with tumor mutational burden and response to immune checkpoint therapy. Here, we report that Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A) is an important regulator of PD-L1 expression. Using an APOBEC3A inducible expression system as well as siRNA against endogenous APOBEC3A, we found that APOBEC3A regulates PD-L1 mRNA and protein levels as well as PD-L1 cell surface expression in cancer. Mechanistically, APOBEC3A-induced PD-L1 expression was dependent on APOBEC3A catalytic activity as catalytically dead APOBEC3A mutant (E72A) failed to induce PD-L1 expression. Furthermore, APOBEC3A-induced PD-L1 expression was dependent on replication-associated DNA damage and JNK/c-JUN signaling but not interferon signaling. In addition, we confirmed the relevance of these finding in patient tumors as APOBEC3A expression and mutational signature correlated with PD-L1 expression in multiple patient cancer types. These data provide a novel link between APOBEC3A, its DNA mutagenic activity and PD-L1-mediated antitumoral immunity. This work nominates APOBEC3A as a mechanism of immune evasion and a potential biomarker for the therapeutic efficacy of immune checkpoint blockade. IMPLICATIONS: APOBEC3A catalytic activity induces replication-associated DNA damage to promote PD-L1 expression implying that APOBEC3A-driven mutagenesis represents both a mechanism of tumor immune evasion and a therapeutically targetable vulnerability in cancer cells.
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Affiliation(s)
- Kailiang Zhao
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan.,Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qiang Zhang
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Sheryl A Flanagan
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Xueting Lang
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Long Jiang
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Leslie A Parsels
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Joshua D Parsels
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Weiping Zou
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan School of Medicine, Ann Arbor, Michigan.,Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan.,Department of Pathology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan.,Graduate Program in Immunology, University of Michigan School of Medicine, Ann Arbor, Michigan.,Graduate Program in Cancer Biology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Rémi Buisson
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, California.,Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, California
| | - Michael D Green
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan. .,Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan School of Medicine, Ann Arbor, Michigan.,Department of Radiation Oncology, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan.
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16
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Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations. Microorganisms 2020; 8:microorganisms8121965. [PMID: 33322320 PMCID: PMC7764263 DOI: 10.3390/microorganisms8121965] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
The evolutionary conflict between retroviruses and their vertebrate hosts over millions of years has led to the emergence of cellular innate immune proteins termed restriction factors as well as their viral antagonists. Evidence accumulated in the last two decades has substantially increased our understanding of the elaborate mechanisms utilized by these restriction factors to inhibit retroviral replication, mechanisms that either directly block viral proteins or interfere with the cellular pathways hijacked by the viruses. Analyses of these complex interactions describe patterns of accelerated evolution for these restriction factors as well as the acquisition and evolution of their virus-encoded antagonists. Evidence is also mounting that many restriction factors identified for their inhibition of specific retroviruses have broader antiviral activity against additional retroviruses as well as against other viruses, and that exposure to these multiple virus challenges has shaped their adaptive evolution. In this review, we provide an overview of the restriction factors that interfere with different steps of the retroviral life cycle, describing their mechanisms of action, adaptive evolution, viral targets and the viral antagonists that evolved to counter these factors.
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17
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The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
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18
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Petljak M, Maciejowski J. Molecular origins of APOBEC-associated mutations in cancer. DNA Repair (Amst) 2020; 94:102905. [PMID: 32818816 PMCID: PMC7494591 DOI: 10.1016/j.dnarep.2020.102905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 01/03/2023]
Abstract
The APOBEC family of cytidine deaminases has been proposed to represent a major enzymatic source of mutations in cancer. Here, we summarize available evidence that links APOBEC deaminases to cancer mutagenesis. We also highlight newly identified human cell models of APOBEC mutagenesis, including cancer cell lines with suspected endogenous APOBEC activity and a cell system of telomere crisis-associated mutations. Finally, we draw on recent data to propose potential causes of APOBEC misregulation in cancer, including the instigating factors, the relevant mutator(s), and the mechanisms underlying generation of the genome-dispersed and clustered APOBEC-induced mutations.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 , USA.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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19
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Covino DA, Kaczor-Urbanowicz KE, Lu J, Chiantore MV, Fiorucci G, Vescio MF, Catapano L, Purificato C, Galluzzo CM, Amici R, Andreotti M, Gauzzi MC, Pellegrini M, Fantuzzi L. Transcriptome Profiling of Human Monocyte-Derived Macrophages Upon CCL2 Neutralization Reveals an Association Between Activation of Innate Immune Pathways and Restriction of HIV-1 Gene Expression. Front Immunol 2020; 11:2129. [PMID: 33072075 PMCID: PMC7531389 DOI: 10.3389/fimmu.2020.02129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/05/2020] [Indexed: 01/01/2023] Open
Abstract
Macrophages are key targets of human immunodeficiency virus type 1 (HIV-1) infection and main producers of the proinflammatory chemokine CC chemokine ligand 2 (CCL2), whose expression is induced by HIV-1 both in vitro and in vivo. We previously found that CCL2 neutralization in monocyte-derived macrophages (MDMs) strongly inhibited HIV-1 replication affecting post-entry steps of the viral life cycle. Here, we used RNA-sequencing to deeply characterize the cellular factors and pathways modulated by CCL2 blocking in MDMs and involved in HIV-1 replication restriction. We report that exposure to CCL2 neutralizing antibody profoundly affected the MDM transcriptome. Functional annotation clustering of up-regulated genes identified two clusters enriched for antiviral defense and immune response pathways, comprising several interferon-stimulated, and restriction factor coding genes. Transcripts in the clusters were enriched for RELA and NFKB1 targets, suggesting the activation of the canonical nuclear factor κB pathway as part of a regulatory network involving miR-155 up-regulation. Furthermore, while HIV-1 infection caused small changes to the MDM transcriptome, with no evidence of host defense gene expression and type I interferon signature, CCL2 blocking enabled the activation of a strong host innate response in infected macrophage cultures, and potently inhibited viral genes expression. Notably, an inverse correlation was found between levels of viral transcripts and of the restriction factors APOBEC3A (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 A), ISG15, and MX1. These findings highlight an association between activation of innate immune pathways and HIV-1 restriction upon CCL2 blocking and identify this chemokine as an endogenous factor contributing to the defective macrophage response to HIV-1. Therapeutic targeting of CCL2 may thus strengthen host innate immunity and restrict HIV-1 replication.
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Affiliation(s)
| | - Karolina Elżbieta Kaczor-Urbanowicz
- UCLA Section of Oral Biology, Division of Oral Biology & Medicine, Center for Oral and Head/Neck Oncology Research, Center for the Health Sciences, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, United States.,UCLA Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, United States
| | - Jing Lu
- UCLA Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, United States
| | | | - Gianna Fiorucci
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.,Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | | | - Laura Catapano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Cristina Purificato
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Roberta Amici
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Matteo Pellegrini
- UCLA Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, United States
| | - Laura Fantuzzi
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
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20
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Lau KCK, Joshi SS, Mahoney DJ, Mason AL, van Marle G, Osiowy C, Coffin CS. Differences in HBV Replication, APOBEC3 Family Expression, and Inflammatory Cytokine Levels Between Wild-Type HBV and Pre-core (G1896A) or Basal Core Promoter (A1762T/G1764A) Mutants. Front Microbiol 2020; 11:1653. [PMID: 32760388 PMCID: PMC7372132 DOI: 10.3389/fmicb.2020.01653] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
Background Chronic hepatitis B virus (HBV) infection is the leading cause of hepatocellular carcinoma (HCC) world-wide. HBV variants, particularly the G1896A pre-core (PC) and A1762T/G1764A basal core promoter (BCP) mutations, are established risk factors for cirrhosis and HCC, but the molecular biological basis is unclear. We hypothesized that these variants result in differential HBV replication, APOBEC3 family expression, and cytokine/chemokine expression. Methods HepG2 cells were transfected with monomeric full-length containing wild-type, PC, or BCP HBV. Cells and supernatant were collected to analyze viral infection markers (i.e., HBsAg, HBeAg, HBV DNA, and RNA). Cellular APOBEC3 expression and activity was assessed by quantitative real-time (qRT)-PCR, immunoblot, differential DNA denaturation PCR, and sequencing. Cytokine/chemokines in the supernatant and in serum from 11 CHB carriers (4 non-cirrhotic; 7 cirrhotic and/or HCC) with predominantly wild-type, PC, or BCP variants were evaluated by Luminex. Results HBeAg expression was reduced in PC and BCP variants, and higher supernatant HBV DNA and HBV RNA levels were found with A1762T/G1764A vs. G1896A mutant (p < 0.05). Increased APOBEC3G protein levels in wild-type vs. mutant were not associated with HBV covalently closed circular DNA G-to-A hypermutations. Differences in cytokine/chemokine expression in culture supernatants, especially IL-13 were observed amongst the variants analyzed. Noticeable increases of numerous cytokines/chemokines, including IL-4 and IL-8, were observed in ex vivo serum collected from CHB carriers with PC mutant. Conclusion HBV sequence variation leads to differences in HBV protein production (HBeAg) and viral replication in addition to altered host innate antiviral restriction factor (APOBEC3) and cytokine/chemokine expression.
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Affiliation(s)
- Keith C K Lau
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Shivali S Joshi
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Douglas J Mahoney
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Andrew L Mason
- Department of Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Carla Osiowy
- Viral Hepatitis and Bloodborne Pathogens, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Carla S Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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21
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Green AM, Weitzman MD. The spectrum of APOBEC3 activity: From anti-viral agents to anti-cancer opportunities. DNA Repair (Amst) 2019; 83:102700. [PMID: 31563041 PMCID: PMC6876854 DOI: 10.1016/j.dnarep.2019.102700] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
The APOBEC3 family of cytosine deaminases are part of the innate immune response to viral infection, but also have the capacity to damage cellular DNA. Detection of mutational signatures consistent with APOBEC3 activity, together with elevated APOBEC3 expression in cancer cells, has raised the possibility that these enzymes contribute to oncogenesis. Genome deamination by APOBEC3 enzymes also elicits DNA damage response signaling and presents therapeutic vulnerabilities for cancer cells. Here, we discuss implications of APOBEC3 activity in cancer and the potential to exploit their mutagenic activity for targeted cancer therapies.
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Affiliation(s)
- Abby M Green
- Division of Oncology, Children's Hospital of Philadelphia, United States; Division of Infectious Diseases, Children's Hospital of Philadelphia, United States; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, United States; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, United States; Department of Pediatrics, Washington University School of Medicine, United States.
| | - Matthew D Weitzman
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, United States; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, United States; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, United States.
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22
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Covino DA, Purificato C, Catapano L, Galluzzo CM, Gauzzi MC, Vella S, Lefebvre E, Seyedkazemi S, Andreotti M, Fantuzzi L. APOBEC3G/3A Expression in Human Immunodeficiency Virus Type 1-Infected Individuals Following Initiation of Antiretroviral Therapy Containing Cenicriviroc or Efavirenz. Front Immunol 2018; 9:1839. [PMID: 30135687 PMCID: PMC6092507 DOI: 10.3389/fimmu.2018.01839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/25/2018] [Indexed: 01/09/2023] Open
Abstract
Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3) family members are cytidine deaminases that play crucial roles in innate responses to retrovirus infection. The mechanisms by which some of these enzymes restrict human immunodeficiency virus type 1 (HIV-1) replication have been extensively investigated in vitro. However, little is known regarding how APOBEC3 proteins affect the pathogenesis of HIV-1 infection in vivo and how antiretroviral therapy influences their expression. In this work, a longitudinal analysis was performed to evaluate APOBEC3G/3A expression in peripheral blood mononuclear cells of antiretroviral-naive HIV-1-infected individuals treated with cenicriviroc (CVC) or efavirenz (EFV) at baseline and 4, 12, 24, and 48 weeks post-treatment follow-up. While APOBEC3G expression was unaffected by therapy, APOBEC3A levels increased in CVC but not EFV arm at week 48 of treatment. APOBEC3G expression correlated directly with CD4+ cell count and CD4+/CD8+ cell ratio, whereas APOBEC3A levels inversely correlated with plasma soluble CD14. These findings suggest that higher APOBEC3G/3A levels may be associated with protective effects against HIV-1 disease progression and chronic inflammation and warrant further studies.
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Affiliation(s)
- Daniela A Covino
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Cristina Purificato
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Catapano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Stefano Vella
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Eric Lefebvre
- Allergan plc, South San Francisco, CA, United States
| | | | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Fantuzzi
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
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