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Kvach MV, Harjes S, Kurup HM, Jameson GB, Harjes E, Filichev VV. Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A. Beilstein J Org Chem 2024; 20:1088-1098. [PMID: 38774272 PMCID: PMC11106675 DOI: 10.3762/bjoc.20.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/26/2024] [Indexed: 05/24/2024] Open
Abstract
Nucleoside and polynucleotide cytidine deaminases (CDAs), such as CDA and APOBEC3, share a similar mechanism of cytosine to uracil conversion. In 1984, phosphapyrimidine riboside was characterised as the most potent inhibitor of human CDA, but the quick degradation in water limited the applicability as a potential therapeutic. To improve stability in water, we synthesised derivatives of phosphapyrimidine nucleoside having a CH2 group instead of the N3 atom in the nucleobase. A charge-neutral phosphinamide and a negatively charged phosphinic acid derivative had excellent stability in water at pH 7.4, but only the charge-neutral compound inhibited human CDA, similar to previously described 2'-deoxyzebularine (Ki = 8.0 ± 1.9 and 10.7 ± 0.5 µM, respectively). However, under basic conditions, the charge-neutral phosphinamide was unstable, which prevented the incorporation into DNA using conventional DNA chemistry. In contrast, the negatively charged phosphinic acid derivative was incorporated into DNA instead of the target 2'-deoxycytidine using an automated DNA synthesiser, but no inhibition of APOBEC3A was observed for modified DNAs. Although this shows that the negative charge is poorly accommodated in the active site of CDA and APOBEC3, the synthetic route reported here provides opportunities for the synthesis of other derivatives of phosphapyrimidine riboside for potential development of more potent CDA and APOBEC3 inhibitors.
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Affiliation(s)
- Maksim V Kvach
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Harikrishnan M Kurup
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Geoffrey B Jameson
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
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2
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Jang GM, Annan Sudarsan AK, Shayeganmehr A, Prando Munhoz E, Lao R, Gaba A, Granadillo Rodríguez M, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L. Protein Interaction Map of APOBEC3 Enzyme Family Reveals Deamination-Independent Role in Cellular Function. Mol Cell Proteomics 2024; 23:100755. [PMID: 38548018 PMCID: PMC11070599 DOI: 10.1016/j.mcpro.2024.100755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination-independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence are not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and mapped a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein-folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology. Data are available via ProteomeXchange with the identifier PXD044275.
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Affiliation(s)
- Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA; J. David Gladstone Institutes, Gladstone Institute for Data Science and Biotechnology, San Francisco, California, USA
| | - Arun Kumar Annan Sudarsan
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arzhang Shayeganmehr
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Erika Prando Munhoz
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Reanna Lao
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA; J. David Gladstone Institutes, Gladstone Institute for Data Science and Biotechnology, San Francisco, California, USA
| | - Amit Gaba
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Milaid Granadillo Rodríguez
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Robin P Love
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
| | - Yuan Zhou
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; J. David Gladstone Institutes, Gladstone Institute for Data Science and Biotechnology, San Francisco, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA; J. David Gladstone Institutes, Gladstone Institute for Data Science and Biotechnology, San Francisco, California, USA
| | - Robyn M Kaake
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA; J. David Gladstone Institutes, Gladstone Institute for Data Science and Biotechnology, San Francisco, California, USA.
| | - Linda Chelico
- College of Medicine, Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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3
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Pan JW, Ragu M, Chan WQ, Hasan SN, Islam T, Teoh LY, Jamaris S, See MH, Yip CH, Rajadurai P, Looi LM, Taib NAM, Rueda OM, Caldas C, Chin SF, Lim J, Teo SH. Clustering of HR + /HER2- breast cancer in an Asian cohort is driven by immune phenotypes. Breast Cancer Res 2024; 26:67. [PMID: 38649964 PMCID: PMC11035138 DOI: 10.1186/s13058-024-01826-5] [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: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Breast cancer exhibits significant heterogeneity, manifesting in various subtypes that are critical in guiding treatment decisions. This study aimed to investigate the existence of distinct subtypes of breast cancer within the Asian population, by analysing the transcriptomic profiles of 934 breast cancer patients from a Malaysian cohort. Our findings reveal that the HR + /HER2- breast cancer samples display a distinct clustering pattern based on immune phenotypes, rather than conforming to the conventional luminal A-luminal B paradigm previously reported in breast cancers from women of European descent. This suggests that the activation of the immune system may play a more important role in Asian HR + /HER2- breast cancer than has been previously recognized. Analysis of somatic mutations by whole exome sequencing showed that counter-intuitively, the cluster of HR + /HER2- samples exhibiting higher immune scores was associated with lower tumour mutational burden, lower homologous recombination deficiency scores, and fewer copy number aberrations, implicating the involvement of non-canonical tumour immune pathways. Further investigations are warranted to determine the underlying mechanisms of these pathways, with the potential to develop innovative immunotherapeutic approaches tailored to this specific patient population.
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Affiliation(s)
- Jia-Wern Pan
- Cancer Research Malaysia, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia.
| | - Mohana Ragu
- Cancer Research Malaysia, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia
| | - Wei-Qin Chan
- Cancer Research Malaysia, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia
| | | | - Tania Islam
- Department of Surgery, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Li-Ying Teoh
- Department of Surgery, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Suniza Jamaris
- Department of Surgery, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mee-Hoong See
- Department of Surgery, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Cheng-Har Yip
- Subang Jaya Medical Centre, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia
| | - Pathmanathan Rajadurai
- Subang Jaya Medical Centre, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Oscar M Rueda
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Department of Oncology, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Department of Oncology, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Joanna Lim
- Cancer Research Malaysia, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, No. 1, Jalan SS12/1A, 47500, Subang Jaya, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University Malaya, 50603, Kuala Lumpur, Malaysia
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4
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Schloissnig S, Pani S, Rodriguez-Martin B, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M, Hunt S, Rausch T, Marschall T, Korbel JO. Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590093. [PMID: 38659906 PMCID: PMC11042266 DOI: 10.1101/2024.04.18.590093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Structural variants (SVs) contribute significantly to human genetic diversity and disease 1-4 . Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution 5-7 . Here we leveraged nanopore sequencing 8 to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies 3,4 . Our analysis details diverse SV classes-deletions, duplications, insertions, and inversions-at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions 9,10 of unique sequences, with both mobile element classes transducing sequences at either the 3'- or 5'-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.
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5
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Jang GM, Sudarsan AKA, Shayeganmehr A, Munhoz EP, Lao R, Gaba A, Rodríguez MG, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L. Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579137. [PMID: 38370690 PMCID: PMC10871184 DOI: 10.1101/2024.02.06.579137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence is not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and map a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology.
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Affiliation(s)
- Gwendolyn M. Jang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Arun Kumar Annan Sudarsan
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
- Current Address: Centre for Commercialization of Regenerative Medicine (CCRM), 661 University Ave #1002, Toronto, ON M5G 1M1
| | - Arzhang Shayeganmehr
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
| | - Erika Prando Munhoz
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
- Current Address: Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW Calgary, AB T2N 4N1
| | - Reanna Lao
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amit Gaba
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
| | - Milaid Granadillo Rodríguez
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
| | - Robin P. Love
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
- Current Address: Faculty of Medicine & Dentistry, Department of Medicine, TB Program Evaluation & Research Unit, University of Alberta, 11402 University Avenue NW, Edmonton, AB, T6G 2J3
| | - Benjamin J. Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Robyn M. Kaake
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Linda Chelico
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
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Dananberg A, Striepen J, Rozowsky JS, Petljak M. APOBEC Mutagenesis in Cancer Development and Susceptibility. Cancers (Basel) 2024; 16:374. [PMID: 38254863 PMCID: PMC10814203 DOI: 10.3390/cancers16020374] [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: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
APOBEC cytosine deaminases are prominent mutators in cancer, mediating mutations in over 50% of cancers. APOBEC mutagenesis has been linked to tumor heterogeneity, persistent cell evolution, and therapy responses. While emerging evidence supports the impact of APOBEC mutagenesis on cancer progression, the understanding of its contribution to cancer susceptibility and malignant transformation is limited. We examine the existing evidence for the role of APOBEC mutagenesis in carcinogenesis on the basis of the reported associations between germline polymorphisms in genes encoding APOBEC enzymes and cancer risk, insights into APOBEC activities from sequencing efforts of both malignant and non-malignant human tissues, and in vivo studies. We discuss key knowledge gaps and highlight possible ways to gain a deeper understanding of the contribution of APOBEC mutagenesis to cancer development.
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Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jacob S Rozowsky
- Medical Scientist Training Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mia Petljak
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
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7
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Karousis ED, Schubert K, Ban N. Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. EMBO J 2024; 43:151-167. [PMID: 38200146 PMCID: PMC10897431 DOI: 10.1038/s44318-023-00019-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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8
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McGuinness CF, Black MA, Dunbier AK. Restriction site associated DNA sequencing for tumour mutation burden estimation and mutation signature analysis. Cancer Med 2023; 12:21545-21560. [PMID: 37974533 PMCID: PMC10726921 DOI: 10.1002/cam4.6711] [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: 07/27/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Genome-wide measures of genetic disruption such as tumour mutation burden (TMB) and mutation signatures are emerging as useful biomarkers to stratify patients for treatment. Clinicians commonly use cancer gene panels for tumour mutation burden estimation, and whole genome sequencing is the gold standard for mutation signature analysis. However, the accuracy and cost associated with these assays limits their utility at scale. METHODS WGS data from 560 breast cancer patients was used for in silico library simulations to evaluate the accuracy of an FDA approved cancer gene panel as well as restriction enzyme associated DNA sequencing (RADseq) libraries for TMB estimation and mutation signature analysis. We also transfected a mouse mammary cell line with APOBEC enzymes and sequenced resulting clones to evaluate the efficacy of RADseq in an experimental setting. RESULTS RADseq had improved accuracy of TMB estimation and derivation of mutation profiles when compared to the FDA approved cancer panel. Using simulated immune checkpoint blockade (ICB) trials, we show that inaccurate TMB estimation leads to a reduction in power for deriving an optimal TMB cutoff to stratify patients for immune checkpoint blockade treatment. Additionally, prioritisation of APOBEC hypermutated tumours in these trials optimises TMB cutoff determination for breast cancer. The utility of RADseq in an experimental setting was also demonstrated, based on characterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. CONCLUSION In conclusion, our work demonstrates that RADseq has the potential to be used as a cost-effective, accurate solution for TMB estimation and mutation signature analysis by both clinicians and basic researchers.
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Affiliation(s)
- Conor F. McGuinness
- Department of BiochemistryUniversity of OtagoDunedinNew Zealand
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
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9
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Kim SH, Im SA, Suh KJ, Lee KH, Kim MH, Sohn J, Park YH, Kim JY, Jeong JH, Lee KE, Choi IS, Park KH, Kim HJ, Cho EK, Park SY, Kim M, Kim JH. Clinical activity of nivolumab in combination with eribulin in HER2-negative metastatic breast cancer: A phase IB/II study (KCSG BR18-16). Eur J Cancer 2023; 195:113386. [PMID: 37890351 DOI: 10.1016/j.ejca.2023.113386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/13/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
AIM We evaluated the efficacy and safety of nivolumab and eribulin combination therapy for metastatic breast cancer (BC) in Asian populations. METHODS In this parallel phase II study, adult patients with histologically confirmed recurrent/metastatic hormone receptor-positive/HER2-negative (HR+HER2-) or triple-negative BC (TNBC) were prospectively enroled from 10 academic hospitals in Korea (ClinicalTrials.gov Identifier: NCT04061863). They received nivolumab (360 mg) on day 1 plus eribulin (1.4 mg/m2) on days 1 and 8 every 3 weeks until disease progression or intolerable toxicity. The primary endpoint was the investigator-assessed 6-month progression-free survival (PFS) rate in each subtype. Secondary endpoints included investigator-assessed objective response rate (ORR) as per Response Evaluation Criteria in Advanced Solid Tumors version 1.1, disease control rate, overall survival, and treatment toxicity. The association between PD-L1 expression and efficacy was investigated. RESULTS Forty-five patients with HR+HER2- BC and 45 with TNBC were enroled. Their median age was 51 (range, 31-71) years, and 74 (82.2%) received one or two prior treatments before enrolment. Six-month PFS was 47.2% and 25.1% in the HR+HER2- and TNBC cohorts, respectively. Median PFS was 5.6 (95% confidence interval [CI]: 5.3-7.4) and 3.0 (95% CI: 2.1-5.2) months in the HR+HER2- and TNBC groups, respectively. ORRs were 53.3% (complete response [CR]: 0, partial response [PR]: 24) and 28.9% (CR: 1, PR: 12). Patients with PD-L1+ tumours (PD-L1 expression ≥1%) and PD-L1- tumours (ORR 50% versus 53.8% in HR+HER2-, 30.8% versus 29.0% in TNBC) had similar ORRs. Neutropenia was the most common grade 3/4 adverse event; the most common immune-related adverse events (AEs) were grades 1/2 hypothyroidism and pruritus. Five patients discontinued therapy because of immune-related AEs. CONCLUSION Nivolumab plus eribulin showed promising efficacy and tolerable safety in previously treated HER2- metastatic BC. TRIAL REGISTRATION NCT04061863.
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Affiliation(s)
- Se Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University Hospital, Cancer Research Institute, Seoul National University, College of Medicine, Seoul, South Korea
| | - Koung Jin Suh
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Kyung-Hun Lee
- Department of Internal Medicine, Seoul National University Hospital, Cancer Research Institute, Seoul National University, College of Medicine, Seoul, South Korea
| | - Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Joohyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Yeon Hee Park
- Hematology-Oncology, Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ji-Yeon Kim
- Hematology-Oncology, Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyoung Eun Lee
- Department of Hematology and Oncology, Ewha Womans University Hospital, Seoul, South Korea
| | - In Sil Choi
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Kyong Hwa Park
- Division of Medical Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Seoul, South Korea
| | - Hee-Jun Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Eun Kyung Cho
- Division of Medical Oncology, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon, South Korea
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Milim Kim
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea; Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jee Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea.
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10
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McCann JL, Cristini A, Law EK, Lee SY, Tellier M, Carpenter MA, Beghè C, Kim JJ, Sanchez A, Jarvis MC, Stefanovska B, Temiz NA, Bergstrom EN, Salamango DJ, Brown MR, Murphy S, Alexandrov LB, Miller KM, Gromak N, Harris RS. APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer. Nat Genet 2023; 55:1721-1734. [PMID: 37735199 PMCID: PMC10562255 DOI: 10.1038/s41588-023-01504-w] [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: 07/12/2020] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
The single-stranded DNA cytosine-to-uracil deaminase APOBEC3B is an antiviral protein implicated in cancer. However, its substrates in cells are not fully delineated. Here APOBEC3B proteomics reveal interactions with a surprising number of R-loop factors. Biochemical experiments show APOBEC3B binding to R-loops in cells and in vitro. Genetic experiments demonstrate R-loop increases in cells lacking APOBEC3B and decreases in cells overexpressing APOBEC3B. Genome-wide analyses show major changes in the overall landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions, as well as binding of APOBEC3B to many of these sites. APOBEC3 mutagenesis impacts genes overexpressed in tumors and splice factor mutant tumors preferentially, and APOBEC3-attributed kataegis are enriched in RTCW motifs consistent with APOBEC3B deamination. Taken together with the fact that APOBEC3B binds single-stranded DNA and RNA and preferentially deaminates DNA, these results support a mechanism in which APOBEC3B regulates R-loops and contributes to R-loop mutagenesis in cancer.
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Affiliation(s)
- Jennifer L McCann
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Emily K Law
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Seo Yun Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Michael A Carpenter
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Biochemistry and Structural Biology Department, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Chiara Beghè
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jae Jin Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea
| | - Anthony Sanchez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Matthew C Jarvis
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Bojana Stefanovska
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Biochemistry and Structural Biology Department, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Daniel J Salamango
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Margaret R Brown
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
- Biochemistry and Structural Biology Department, University of Texas Health San Antonio, San Antonio, TX, USA.
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA.
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11
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Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty S, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181 Suppl 76:118-144. [PMID: 36794631 PMCID: PMC10329998 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
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Affiliation(s)
- Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Sean McGinty
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
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12
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Pužar Dominkuš P, Hudler P. Mutational Signatures in Gastric Cancer and Their Clinical Implications. Cancers (Basel) 2023; 15:3788. [PMID: 37568604 PMCID: PMC10416847 DOI: 10.3390/cancers15153788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Gastric cancer is characterised by high inter- and intratumour heterogeneity. The majority of patients are older than 65 years and the global burden of this disease is increasing due to the aging of the population. The disease is usually diagnosed at advanced stages, which is a consequence of nonspecific symptoms. Few improvements have been made at the level of noninvasive molecular diagnosis of sporadic gastric cancer, and therefore the mortality rate remains high. A new field of mutational signatures has emerged in the past decade with advances in the genome sequencing technology. These distinct mutational patterns in the genome, caused by exogenous and endogenous mutational processes, can be associated with tumour aetiology and disease progression, and could provide novel perception on the treatment possibilities. This review assesses the mutational signatures found in gastric cancer and summarises their potential for use in clinical setting as diagnostic or prognostic biomarkers. Associated treatment options and biomarkers already implemented in clinical use are discussed, together with those that are still being explored or are in clinical studies.
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Affiliation(s)
- Pia Pužar Dominkuš
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Petra Hudler
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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13
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Kurup HM, Kvach MV, Harjes S, Jameson GB, Harjes E, Filichev VV. Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A. Org Biomol Chem 2023; 21:5117-5128. [PMID: 37282621 PMCID: PMC10282898 DOI: 10.1039/d3ob00392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2'-deoxycytidine providing a Ki of 290 ± 40 nM, which is only slightly weaker than the Ki of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2'-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors.
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Affiliation(s)
- Harikrishnan M Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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14
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Granadillo Rodríguez M, Wong L, Chelico L. Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells. Front Genome Ed 2023; 5:1196697. [PMID: 37324648 PMCID: PMC10267419 DOI: 10.3389/fgeed.2023.1196697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and in vitro deamination. Cell migration and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activities in vitro. Notably, in nuclear lysates, the in vitro deaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to that of A3B and A3H in whole-cell lysates. Their similar activities in cells, nonetheless, resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show that in vitro deamination data do not always reflect cell DNA damage, all three A3s induce DNA damage, and the impact of each is different.
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15
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Roelofs PA, Martens JW, Harris RS, Span PN. Clinical Implications of APOBEC3-Mediated Mutagenesis in Breast Cancer. Clin Cancer Res 2023; 29:1658-1669. [PMID: 36478188 PMCID: PMC10159886 DOI: 10.1158/1078-0432.ccr-22-2861] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Over recent years, members of the APOBEC3 family of cytosine deaminases have been implicated in increased cancer genome mutagenesis, thereby contributing to intratumor and intertumor genomic heterogeneity and therapy resistance in, among others, breast cancer. Understanding the available methods for clinical detection of these enzymes, the conditions required for their (dysregulated) expression, the clinical impact they have, and the clinical implications they may offer is crucial in understanding the current impact of APOBEC3-mediated mutagenesis in breast cancer. Here, we provide a comprehensive review of recent developments in the detection of APOBEC3-mediated mutagenesis and responsible APOBEC3 enzymes, summarize the pathways that control their expression, and explore the clinical ramifications and opportunities they pose. We propose that APOBEC3-mediated mutagenesis can function as a helpful predictive biomarker in several standard-of-care breast cancer treatment plans and may be a novel target for treatment.
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Affiliation(s)
- Pieter A. Roelofs
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - John W.M. Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul N. Span
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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16
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Castilha EP, Curti RRDJ, de Oliveira JN, Vitiello GAF, Guembarovski RL, Couto-Filho JD, Oliveira KBD. APOBEC3A/B Polymorphism Is Not Associated with Human Papillomavirus Infection and Cervical Carcinogenesis. Pathogens 2023; 12:pathogens12050636. [PMID: 37242306 DOI: 10.3390/pathogens12050636] [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: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The persistence of a high-risk Human papillomavirus (HPV-HR) infection of the cervix results in different manifestations of lesions depending on the immunologic capacity of the host. Variations in apolipoprotein B mRNA editing enzyme catalytic polypeptide (APOBEC)-like genes, such as the APOBEC3A/B deletion hybrid polymorphism (A3A/B), may contribute to cervical malignancy in the presence of HPV. The aim of this study was to investigate the association between the A3A/B polymorphism and HPV infection and the development of cervical intraepithelial lesions and cervical cancer in Brazilian women. The study enrolled 369 women, who were categorized according to the presence of infection and subdivided according to the degree of intraepithelial lesion and cervical cancer. APOBEC3A/B was genotyped by allele-specific polymerase chain reaction (PCR). As for the A3A/B polymorphism, the distribution of genotypes was similar between groups and among the analyzed subgroups. There were no significant differences in the presence of infection or development of lesions, even after exclusion of confounding factors. This is the first study to show that the A3A/B polymorphism is not associated with HPV infection and the development of intraepithelial lesions and cervical cancer in Brazilian women.
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Affiliation(s)
- Eliza Pizarro Castilha
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | - Rafaela Roberta de Jaime Curti
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | - Janaina Nicolau de Oliveira
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | | | - Roberta Losi Guembarovski
- Department of Biological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | | | - Karen Brajão de Oliveira
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
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17
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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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18
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Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
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Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
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19
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Nakata Y, Ode H, Kubota M, Kasahara T, Matsuoka K, Sugimoto A, Imahashi M, Yokomaku Y, Iwatani Y. Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome. Nucleic Acids Res 2023; 51:783-795. [PMID: 36610792 PMCID: PMC9881129 DOI: 10.1093/nar/gkac1238] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The number of genetic variations in the SARS-CoV-2 genome has been increasing primarily due to continuous viral mutations. Here, we report that the human APOBEC3A (A3A) cytidine deaminase plays a critical role in the induction of C-to-U substitutions in the SARS-CoV-2 genome. Bioinformatic analysis of the chronological genetic changes in a sequence database indicated that the largest UC-to-UU mutation signature, consistent with APOBEC-recognized nucleotide motifs, was predominant in single-stranded RNA regions of the viral genome. In SARS-CoV-2-infected cells, exogenous expression of A3A but not expression of other APOBEC proteins induced UC-to-UU mutations in viral RNA (vRNA). Additionally, the mutated C bases were often located at the tips in bulge or loop regions in the vRNA secondary structure. Interestingly, A3A mRNA expression was drastically increased by interferons (IFNs) and tumour necrosis factor-α (TNF-α) in epithelial cells derived from the respiratory system, a site of efficient SARS-CoV-2 replication. Moreover, the UC-to-UU mutation rate was increased in SARS-CoV-2 produced from lung epithelial cells treated with IFN-ß and TNF-α, but not from CRISPR/Cas9-based A3A knockout cells. Collectively, these findings demonstrate that A3A is a primary host factor that drives mutations in the SARS-CoV-2 RNA genome via RNA editing.
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Affiliation(s)
- Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan,Department of AIDS Research, Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Takaaki Kasahara
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan,Department of Respiratory Medicine, Division of Internal Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yasumasa Iwatani
- To whom correspondence should be addressed. Tel: +81 52 951 1111; Fax: +81 52 963 3970;
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20
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Sofiyeva N, Krakstad C, Halle MK, O'Mara TA, Romundstad P, Hveem K, Vatten L, Lønning PE, Gansmo LB, Knappskog S.
APOBEC3A
/B
deletion polymorphism and endometrial cancer risk. Cancer Med 2022; 12:6659-6667. [PMID: 36394079 PMCID: PMC10067079 DOI: 10.1002/cam4.5448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A common 30 kb deletion affecting the APOBEC3A and APOBEC3B genes has been linked to increased APOBEC activity and APOBEC-related mutational signatures in human cancers. The role of this deletion as a cancer risk factor remains controversial. MATERIALS AND METHODS We genotyped the APOBEC3A/B deletion in a sample of 1,470 Norwegian endometrial cancer cases and compared to 1,918 healthy controls. For assessment across Caucasian populations, we mined genotypes of the SNP rs12628403, which is in strong linkage disequilibrium with the deletion, in a GWAS dataset of 4,274 cases and 18,125 healthy controls, through the ECAC consortium. RESULTS We found the APOBEC3A/B deletion variant to be significantly associated with reduced risk of endometrial cancer among Norwegian women (OR = 0.75; 95% CI = 0.62-0.91; p = 0.003; dominant model). Similar results were found in the subgroup of endometrioid endometrial cancer (OR = 0.64; 95% CI = 0.51-0.79; p = 3.6 × 10-5 ; dominant model). The observed risk reduction was particularly strong among individuals in the range of 50-60 years of age (OR = 0.51; 95% CI = 0.33-0.78; p = 0.002; dominant model). In the different populations included in the ECAC dataset, the ORs varied from 0.85 to 1.05. Although five out of six populations revealed ORs <1.0, the overall estimate was nonsignificant and, as such, did not formally validate the findings in the Norwegian cohort. CONCLUSION The APOBEC3A/B deletion polymorphism is associated with a decreased risk of endometrial cancer in the Norwegian population.
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Affiliation(s)
- Nigar Sofiyeva
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
| | - Camilla Krakstad
- Department of Clinical Science, Centre for Cancer Biomarkers University of Bergen Bergen Norway
- Department of Obstetrics and Gynaecology Haukeland University Hospital Bergen Norway
| | - Mari K. Halle
- Department of Clinical Science, Centre for Cancer Biomarkers University of Bergen Bergen Norway
- Department of Obstetrics and Gynaecology Haukeland University Hospital Bergen Norway
| | - Tracy A. O'Mara
- Cancer Program QIMR Berghofer Medical Research Institute Brisbane Australia
| | - Pål Romundstad
- Department of Public Health, Faculty of Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Faculty of Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Lars Vatten
- Department of Public Health, Faculty of Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Per E. Lønning
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
| | - Liv B. Gansmo
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
| | - Stian Knappskog
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
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21
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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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22
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Kurup HM, Kvach MV, Harjes S, Barzak FM, Jameson GB, Harjes E, Filichev VV. Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A. Biochemistry 2022; 61:2568-2578. [DOI: 10.1021/acs.biochem.2c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harikrishnan M. Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V. Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Fareeda M. Barzak
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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23
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Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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24
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Chen CH, Wei KC, Liao WC, Lin YY, Chen HC, Feng LY, Liu CH, Huang CY, Chen KT, Wu CS, Chang YS, Yu JS, Chang IYF. Prognostic value of an APOBEC3 deletion polymorphism for glioma patients in Taiwan. J Neurosurg 2022; 138:1325-1337. [PMID: 36152319 DOI: 10.3171/2022.7.jns2250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/20/2022] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The molecular pathogenesis of malignant gliomas, characterized by diverse tumor histology with differential prognosis, remains largely unelucidated. An APOBEC3 deletion polymorphism, with a deletion in APOBEC3B, has been correlated to risk and prognosis in several cancers, but its role in glioma is unclear. The authors aimed to examine the clinical relevance of the APOBEC3 deletion polymorphism to glioma risk and survival in a glioma patient cohort in Taiwan. METHODS The authors detected deletion genotypes in 403 glioma patients and 1365 healthy individuals in Taiwan and correlated the genotypes with glioma risk, clinicopathological factors, patient survival, and patient sex. APOBEC3 gene family expression was measured and correlated to the germline deletion. A nomogram model was constructed to predict patient survival in glioma. RESULTS The proportion of APOBEC3B-/- and APOBEC3B+/- genotypes was higher in glioblastoma (GBM) patients than healthy individuals and correlated with higher GBM risk in males. A higher percentage of cases with APOBEC3B- was observed in male than female glioma patients. The presence of APOBEC3B-/- was correlated with better overall survival (OS) in male astrocytic glioma patients. No significant correlation of the genotypes to glioma risk and survival was observed in the female patient cohort. Lower APOBEC3B expression was observed in astrocytic glioma patients with APOBEC3B-/- and was positively correlated with better OS. A 5-factor nomogram model was constructed based on male patients with astrocytic gliomas in the study cohort and worked efficiently for predicting patient OS. CONCLUSIONS The germline APOBEC3 deletion was associated with increased GBM risk and better OS in astrocytic glioma patients in the Taiwan male population. The APOBEC3B deletion homozygote was a potential independent prognostic factor predicting better survival in male astrocytic glioma patients.
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Affiliation(s)
| | - Kuo-Chen Wei
- 2School of Medicine, and.,5Department of Neurosurgery.,7Neuroscience Research Center, and.,11Department of Neurosurgery, New Taipei Municipal Tucheng Hospital, New Taipei City
| | - Wei-Chao Liao
- 1Molecular Medicine Research Center.,4Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Taoyuan
| | - You-Yu Lin
- 9Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei.,10Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei
| | | | - Li-Ying Feng
- 11Department of Neurosurgery, New Taipei Municipal Tucheng Hospital, New Taipei City
| | - Chiung-Hui Liu
- 12Department of Post-Baccalaureate Medicine and.,13PhD Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung City, Taiwan
| | - Chiung-Yin Huang
- 7Neuroscience Research Center, and.,11Department of Neurosurgery, New Taipei Municipal Tucheng Hospital, New Taipei City
| | - Ko-Ting Chen
- 2School of Medicine, and.,5Department of Neurosurgery.,7Neuroscience Research Center, and
| | - Chi-Sheng Wu
- 1Molecular Medicine Research Center.,6Department of Otolaryngology-Head & Neck Surgery
| | | | - Jau-Song Yu
- 1Molecular Medicine Research Center.,3Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan.,8Liver Research Center, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan
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25
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McIlroy D, Peltier C, Nguyen ML, Manceau L, Mobuchon L, Le Baut N, Nguyen NK, Tran MC, Nguyen TC, Bressollette-Bodin C. Quantification of APOBEC3 Mutation Rates Affecting the VP1 Gene of BK Polyomavirus In Vivo. Viruses 2022; 14:v14092077. [PMID: 36146883 PMCID: PMC9504301 DOI: 10.3390/v14092077] [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: 08/11/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in the BK polyomavirus (BKPyV) capsid accumulate in kidney transplant (KTx) recipients with persistent virus replication. They are associated with neutralization escape and appear to arise as a result of cytosine deamination by host cell APOBEC3A/B enzymes. To study the mutagenic processes occurring in patients, we amplified the typing region of the VP1 gene, sequenced the amplicons to a depth of 5000–10,000×, and identified rare mutations, which were fitted to COSMIC mutational signatures. Background mutations were identified in amplicons from plasmids carrying the BKPyV genome and compared to mutations observed in 148 samples from 23 KTx recipients in France and in Vietnam. Three mutational signatures were consistently observed in urine, serum, and kidney biopsy samples, two of which, SBS2 and SBS13, corresponded to APOBEC3A/B activity. In addition, a third signature with no known etiology, SBS89, was detected both in patient samples, and in cells infected in vitro with BKPyV. Quantitatively, APOBEC3A/B mutation rates in urine samples were strongly correlated with urine viral load, and also appeared to vary between individuals. These results confirm that APOBEC3A/B is a major, but not the only, source of BKPyV genome mutations in patients.
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Affiliation(s)
- Dorian McIlroy
- Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes Université, CHU Nantes, INSERM, F-44000 Nantes, France
- Faculté des Sciences et des Techniques, Nantes Université, 44093 Nantes, France
- Correspondence: ; Tel.: +33-02-44-76-81-82
| | - Cécile Peltier
- Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes Université, CHU Nantes, INSERM, F-44000 Nantes, France
| | - My-Linh Nguyen
- Department of Medical Microbiology, Hanoi Medical University, Hanoi 116001, Vietnam
| | - Louise Manceau
- Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes Université, CHU Nantes, INSERM, F-44000 Nantes, France
- CHU Nantes, Nantes Université, Service de Virologie, 44093 Nantes, France
| | - Lenha Mobuchon
- Molecular Biology and Sequencing Services, CHU Nantes, 44000 Nantes, France
| | - Nicolas Le Baut
- Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes Université, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Ngoc-Khanh Nguyen
- Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes Université, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Minh-Chau Tran
- Department of Kidney Diseases and Dialysis, Vietduc University Hospital, Hanoi 110214, Vietnam
| | - The-Cuong Nguyen
- Department of Medical Microbiology, Hanoi Medical University, Hanoi 116001, Vietnam
| | - Céline Bressollette-Bodin
- Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes Université, CHU Nantes, INSERM, F-44000 Nantes, France
- CHU Nantes, Nantes Université, Service de Virologie, 44093 Nantes, France
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26
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Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res 2022; 50:1551-1561. [PMID: 35048970 PMCID: PMC8860616 DOI: 10.1093/nar/gkab1297] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Affiliation(s)
- Ankit K Pathak
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Bharathram Uppili
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Safal Walia
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Saman Fatihi
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tahseen Abbas
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sofia Banu
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | | | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Sana Fatma
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Shifu Aggarwal
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mahesh Shanker Dhar
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Rahul C Bhoyar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohit Kumar Divakar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohammed Faruq
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Lipi Thukral
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sunil K Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mitali Mukerji
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Indian Institute of Technology (IIT), Jodhpur, India
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27
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Liu W, Ji H, Zhao J, Song J, Zheng S, Chen L, Li P, Tan X, Ding Y, Pu R, Yin J, Han X, Cao G. Transcriptional repression and apoptosis influence the effect of APOBEC3A/3B functional polymorphisms on biliary tract cancer risk. Int J Cancer 2022; 150:1825-1837. [PMID: 35020946 DOI: 10.1002/ijc.33930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/08/2022]
Abstract
APOBEC3-related somatic mutations are predominant in biliary tract cancers (BTCs). We aimed to elucidate the roles of APOBEC3A/3B functional polymorphisms and their influencing factors on the development of cholangiocarcinoma and gallbladder cancer (GBC). Polymorphisms at the promoter regions of APOBEC3A and APOBEC3B were genotyped in 3231 participants using quantitative PCR. Dual-luciferase reporter assay was applied to investigate the promoter activity. The difference in gene accessibility between cholangiocarcinoma cells and GBC cells was analyzed through single-cell transposase accessible chromatin sequencing. The effect of APOBEC3A on apoptosis was examined by cytometry. It's found that rs2267401-G at the APOBEC3B promoter decreases cholangiocarcinoma risk (age-, gender-adjusted odds ratio [AOR], 0.69; 95% confidence interval [CI], 0.51-0.94) but increases GBC risk (AOR, 2.04; 95% CI, 1.35-3.10). rs2267401-G confers a decreased APOBEC3B promoter activity in cholangiocarcinoma cells but an increased activity in GBC cells, possibly because the transcriptional repressor TFAP2A is over-expressed in cholangiocarcinoma. Tumor necrosis factor-α (TNF-α) increases the level of APOBEC3B via inhibiting TFAP2A expression rather than directly increasing the accessibility of APOBEC3B promoter. APOBEC3A promoter rs12157810-C decreased the risks of cholangiocarcinoma and GBC, with an AOR (95% CI) of 0.80 (0.66-0.97) and 0.75 (0.59-0.95), respectively. rs12157810-C upregulated the promoter activity in both cholangiocarcinoma and GBC cells. TNF-α upregulated the activity of the APOBEC3A promoter with rs12157810-C via increasing the accessibility of Ets-1 p68. APOBEC3A overexpression attenuates cancer evolution by causing apoptosis, in contrast to APOBEC3B. The heterogeneity in the transcriptional regulation of APOBEC3B affects the evolutionary potential of cancer cells in the inflammatory microenvironment. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenbin Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongxiang Ji
- Department of Liver Cancer Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Jun Zhao
- Department of Liver Cancer Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Jiahui Song
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Shaoling Zheng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Lei Chen
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Peng Li
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xiaojie Tan
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yibo Ding
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Rui Pu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jianhua Yin
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xue Han
- Department of Chronic Disease, Center for Disease Control and Prevention of Yangpu District, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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28
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APOBEC mediated mutagenesis drives genomic heterogeneity in endometriosis. J Hum Genet 2022; 67:323-329. [PMID: 35017684 DOI: 10.1038/s10038-021-01003-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022]
Abstract
Endometriosis is a benign gynecologic condition, acting as a precursor of certain histological subtypes of ovarian cancers. The epithelial cells of endometriotic tissues and normal uterine endometrium accumulated somatic mutations in cancer-associated genes such as phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and Kirsten rat sarcoma (KRAS) proto-oncogene. To determine the genomic characteristic of endometriotic epithelial cells and normal uterine endometrium and to identify the predominant mutational process acting on them, we studied the somatic mutation profiles obtained from whole exome sequencing of 14 endometriotic epithelium and 11 normal uterine endometrium tissues and classified them into mutational signatures. We observed that single base substitutions 2/13 (SBS), attributed to Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit (APOBEC) induced mutagenesis, were significant in endometriotic tissues, but not in the normal uterine endometrium. Additionally, the larger number and wider allele frequency distribution of APOBEC signature mutations, compared to cancer-associated driver mutations in endometriotic epithelium suggested APOBEC mutagenesis as an important source of mutational burden and heterogeneity in endometriosis. Further, the relative risk of enriched APOBEC signature mutations was higher in endometriosis patients who were carriers of APOBEC3A/3B germline deletion, a common polymorphism in East Asians which involves the complete loss of APOBEC3B coding region. Our results illustrate the significance of APOBEC induced mutagenesis in driving the genomic heterogeneity of endometriosis.
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29
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Impact of the APOBEC3A/B deletion polymorphism on risk of ovarian cancer. Sci Rep 2021; 11:23463. [PMID: 34873230 PMCID: PMC8648731 DOI: 10.1038/s41598-021-02820-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
A germline 29.5-kb deletion variant removes the 3’ end of the APOBEC3A gene and a large part of APOBEC3B, creating a hybrid gene that has been linked to increased APOBEC3 activity and DNA damage in human cancers. We genotyped the APOBEC3A/B deletion in hospital-based samples of 1398 Norwegian epithelial ovarian cancer patients without detected BRCA1/2 germline mutations and compared to 1,918 healthy female controls, to assess the potential cancer risk associated with the deletion. We observed an association between APOBEC3A/B status and reduced risk for ovarian cancer (OR = 0.75; CI = 0.61–0.91; p = 0.003) applying the dominant model. Similar results were found in other models. The association was observed both in non-serous and serous cases (dominant model: OR = 0.69; CI = 0.50–0.95; p = 0.018 and OR = 0.77; CI = 0.62–0.96; p = 0.019, respectively) as well as within high-grade serous cases (dominant model: OR = 0.79; CI = 0.59–1.05). For validation purposes, we mined an available large multinational GWAS-based data set of > 18,000 cases and > 26,000 controls for SNP rs12628403, known to be in linkage disequilibrium with the APOBEC3A/B deletion. We found a non-significant trend for SNP rs12628403 being linked to reduced risk of ovarian cancer in general and similar trends for all subtypes. For clear cell cancers, the risk reduction reached significance (OR = 0.85; CI = 0.69–1.00).
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30
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Fenton TR. Accumulation of host cell genetic errors following high-risk HPV infection. Curr Opin Virol 2021; 51:1-8. [PMID: 34543805 DOI: 10.1016/j.coviro.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Tim R Fenton
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK; School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
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31
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Liu W, Deng Y, Li Z, Chen Y, Zhu X, Tan X, Cao G. Cancer Evo-Dev: A Theory of Inflammation-Induced Oncogenesis. Front Immunol 2021; 12:768098. [PMID: 34880864 PMCID: PMC8645856 DOI: 10.3389/fimmu.2021.768098] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic inflammation is a prerequisite for the development of cancers. Here, we present the framework of a novel theory termed as Cancer Evolution-Development (Cancer Evo-Dev) based on the current understanding of inflammation-related carcinogenesis, especially hepatocarcinogenesis induced by chronic infection with hepatitis B virus. The interaction between genetic predispositions and environmental exposures, such as viral infection, maintains chronic non-resolving inflammation. Pollution, metabolic syndrome, physical inactivity, ageing, and adverse psychosocial exposure also increase the risk of cancer via inducing chronic low-grade smoldering inflammation. Under the microenvironment of non-resolving inflammation, pro-inflammatory factors facilitate the generation of somatic mutations and viral mutations by inducing the imbalance between the mutagenic forces such as cytidine deaminases and mutation-correcting forces including uracil-DNA glycosylase. Most cells with somatic mutations and mutated viruses are eliminated in survival competition. Only a small percentage of mutated cells survive, adapt to the hostile environment, retro-differentiate, and function as cancer-initiating cells via altering signaling pathways. These cancer-initiating cells acquire stem-ness, reprogram metabolic patterns, and affect the microenvironment. The carcinogenic process follows the law of "mutation-selection-adaptation". Chronic physical activity reduces the levels of inflammation via upregulating the activity and numbers of NK cells and lymphocytes and lengthening leukocyte telomere; downregulating proinflammatory cytokines including interleukin-6 and senescent lymphocytes especially in aged population. Anti-inflammation medication reduces the occurrence and recurrence of cancers. Targeting cancer stemness signaling pathways might lead to cancer eradication. Cancer Evo-Dev not only helps understand the mechanisms by which inflammation promotes the development of cancers, but also lays the foundation for effective prophylaxis and targeted therapy of various cancers.
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Affiliation(s)
- Wenbin Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yang Deng
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai’an, China
| | - Zishuai Li
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yifan Chen
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xiaoqiong Zhu
- Department of Nutrition, School of Public Health, Anhui Medical University, Hefei, China
| | - Xiaojie Tan
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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32
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Moody S, Senkin S, Islam SMA, Wang J, Nasrollahzadeh D, Cortez Cardoso Penha R, Fitzgerald S, Bergstrom EN, Atkins J, He Y, Khandekar A, Smith-Byrne K, Carreira C, Gaborieau V, Latimer C, Thomas E, Abnizova I, Bucciarelli PE, Jones D, Teague JW, Abedi-Ardekani B, Serra S, Scoazec JY, Saffar H, Azmoudeh-Ardalan F, Sotoudeh M, Nikmanesh A, Poustchi H, Niavarani A, Gharavi S, Eden M, Richman P, Campos LS, Fitzgerald RC, Ribeiro LF, Soares-Lima SC, Dzamalala C, Mmbaga BT, Shibata T, Menya D, Goldstein AM, Hu N, Malekzadeh R, Fazel A, McCormack V, McKay J, Perdomo S, Scelo G, Chanudet E, Humphreys L, Alexandrov LB, Brennan P, Stratton MR. Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence. Nat Genet 2021; 53:1553-1563. [PMID: 34663923 DOI: 10.1038/s41588-021-00928-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/28/2021] [Indexed: 12/28/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence that is not fully explained by known lifestyle and environmental risk factors. It has been speculated that an unknown exogenous exposure(s) could be responsible. Here we combine the fields of mutational signature analysis with cancer epidemiology to study 552 ESCC genomes from eight countries with varying incidence rates. Mutational profiles were similar across all countries studied. Associations between specific mutational signatures and ESCC risk factors were identified for tobacco, alcohol, opium and germline variants, with modest impacts on mutation burden. We find no evidence of a mutational signature indicative of an exogenous exposure capable of explaining differences in ESCC incidence. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC)-associated mutational signatures single-base substitution (SBS)2 and SBS13 were present in 88% and 91% of cases, respectively, and accounted for 25% of the mutation burden on average, indicating that APOBEC activation is a crucial step in ESCC tumor development.
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Affiliation(s)
- Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sergey Senkin
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - S M Ashiqul Islam
- Moores Cancer Centre, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, La Jolla, CA, USA
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Dariush Nasrollahzadeh
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | | | - Stephen Fitzgerald
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Erik N Bergstrom
- Moores Cancer Centre, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, La Jolla, CA, USA
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Joshua Atkins
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Yudou He
- Moores Cancer Centre, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, La Jolla, CA, USA
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Azhar Khandekar
- Moores Cancer Centre, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, La Jolla, CA, USA
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Karl Smith-Byrne
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Christine Carreira
- Evidence Synthesis and Classification Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Valerie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Emily Thomas
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Irina Abnizova
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Pauline E Bucciarelli
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Jean-Yves Scoazec
- Department Laboratory Medicine and Pathology, Gustave Roussy, Paris, France
| | - Hiva Saffar
- Department of Pathology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Farid Azmoudeh-Ardalan
- Liver Transplantation Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Arash Nikmanesh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Ahmadreza Niavarani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Samad Gharavi
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Michael Eden
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul Richman
- Histopathology Department, Hemel Hempstead General Hospital, Hemel Hempstead, UK
| | - Lia S Campos
- West Suffolk NHS Foundation Trust, Bury St Edmunds, UK
| | | | | | | | | | - Blandina Theophil Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre & Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Centre Research Institute, Tokyo, Japan
| | | | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Abdolreza Fazel
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Valerie McCormack
- Environment and Lifestyle Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ghislaine Scelo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Estelle Chanudet
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ludmil B Alexandrov
- Moores Cancer Centre, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, La Jolla, CA, USA
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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33
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Brasó-Maristany F, Sansó M, Chic N, Martínez D, González-Farré B, Sanfeliu E, Ghiglione L, Carcelero E, Garcia-Corbacho J, Sánchez M, Soy D, Jares P, Peg V, Saura C, Muñoz M, Prat A, Vivancos A. Case Report: A Case Study Documenting the Activity of Atezolizumab in a PD-L1-Negative Triple-Negative Breast Cancer. Front Oncol 2021; 11:710596. [PMID: 34616675 PMCID: PMC8489403 DOI: 10.3389/fonc.2021.710596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/31/2021] [Indexed: 12/02/2022] Open
Abstract
The immune checkpoint inhibitor atezolizumab is approved for PD-L1-positive triple-negative breast cancer (TNBC). However, no activity of atezolizumab in PD-L1-negative TNBC has been reported to date. Here, we present the case study of a woman with TNBC with low tumor infiltrating lymphocytes and PD-L1-negative disease, which achieved a significant response to atezolizumab monotherapy and durable response after the combination of atezolizumab and nab-paclitaxel. The comprehensive genomic analysis that we performed in her tumor and plasma samples revealed high tumor mutational burden (TMB), presence of the APOBEC genetic signatures, high expression of the tumor inflammation signature, and a HER2-enriched subtype by the PAM50 assay. Some of these biomarkers have been shown to independently predict response to immunotherapy in other tumors and may explain the durable response in our patient. Our work warrants further translational studies to identify biomarkers of response to immune checkpoint inhibitors in TNBC beyond PD-L1 expression and to better select patients that will benefit from immunotherapy.
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Affiliation(s)
- Fara Brasó-Maristany
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Miriam Sansó
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Oncology and Hematology, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Nuria Chic
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Débora Martínez
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Blanca González-Farré
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Pathology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Esther Sanfeliu
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Pathology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Lucio Ghiglione
- Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Esther Carcelero
- Department of Pharmacy, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Javier Garcia-Corbacho
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Marcelo Sánchez
- Department of Radiology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Dolors Soy
- Department of Pharmacy, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Molecular Biology Core, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Vicente Peg
- Vall d'Hebron University Hospital and Vall d'Hebron Institute of Oncology (VHIO), Medical Oncology Service, Barcelona, Spain
| | - Cristina Saura
- Vall d'Hebron University Hospital and Vall d'Hebron Institute of Oncology (VHIO), Medical Oncology Service, Barcelona, Spain.,SOLTI Cooperative Group, Barcelona, Spain.,Department of Oncology, Institut Oncològic Baselga (IOB) Institute of Oncology, Quironsalud Group, Barcelona, Spain
| | - Montserrat Muñoz
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,SOLTI Cooperative Group, Barcelona, Spain.,Department of Oncology, Institut Oncològic Baselga (IOB) Institute of Oncology, Quironsalud Group, Barcelona, Spain.,Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
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34
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Caval V, Suspène R, Khalfi P, Gaillard J, Caignard G, Vitour D, Roingeard P, Vartanian JP, Wain-Hobson S. Frame-shifted APOBEC3A encodes two alternative proapoptotic proteins that target the mitochondrial network. J Biol Chem 2021; 297:101081. [PMID: 34403699 PMCID: PMC8424220 DOI: 10.1016/j.jbc.2021.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/02/2022] Open
Abstract
The human APOBEC3A (A3A) cytidine deaminase is a powerful DNA mutator enzyme recognized as a major source of somatic mutations in tumor cell genomes. However, there is a discrepancy between APOBEC3A mRNA levels after interferon stimulation in myeloid cells and A3A detection at the protein level. To understand this difference, we investigated the expression of two novel alternative “A3Alt” proteins encoded in the +1-shifted reading frame of the APOBEC3A gene. A3Alt-L and its shorter isoform A3Alt-S appear to be transmembrane proteins targeted to the mitochondrial compartment that induce membrane depolarization and apoptosis. Thus, the APOBEC3A gene represents a new example wherein a single gene encodes two proapoptotic proteins, A3A cytidine deaminases that target the genome and A3Alt proteins that target mitochondria.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France.
| | | | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France; Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Julien Gaillard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
| | - Grégory Caignard
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Damien Vitour
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Philippe Roingeard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
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35
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Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses 2021; 13:1366. [PMID: 34372572 PMCID: PMC8310219 DOI: 10.3390/v13071366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) enzymes are capable of inhibiting a wide range of endogenous and exogenous viruses using deaminase and deaminase-independent mechanisms. These enzymes are essential components of our innate immune system, as evidenced by (a) their strong positive selection and expansion in primates, (b) the evolution of viral counter-defense mechanisms, such as proteasomal degradation mediated by HIV Vif, and (c) hypermutation and inactivation of a large number of integrated HIV-1 proviruses. Numerous APOBEC3 single nucleotide polymorphisms, haplotypes, and splice variants have been identified in humans. Several of these variants have been reported to be associated with differential antiviral immunity. This review focuses on the current knowledge in the field about these natural variations and their roles in infectious diseases.
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Affiliation(s)
- Shiva Sadeghpour
- Department of Biological Science, University of California Irvine, Irvine, CA 92697, USA;
| | - Saeideh Khodaee
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran;
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA;
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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36
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Meshcheryakova A, Pietschmann P, Zimmermann P, Rogozin IB, Mechtcheriakova D. AID and APOBECs as Multifaceted Intrinsic Virus-Restricting Factors: Emerging Concepts in the Light of COVID-19. Front Immunol 2021; 12:690416. [PMID: 34276680 PMCID: PMC8282206 DOI: 10.3389/fimmu.2021.690416] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
The AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme catalytic subunit) family with its multifaceted mode of action emerges as potent intrinsic host antiviral system that acts against a variety of DNA and RNA viruses including coronaviruses. All family members are cytosine-to-uracil deaminases that either have a profound role in driving a strong and specific humoral immune response (AID) or restricting the virus itself by a plethora of mechanisms (APOBECs). In this article, we highlight some of the key aspects apparently linking the AID/APOBECs and SARS-CoV-2. Among those is our discovery that APOBEC4 shows high expression in cell types and anatomical parts targeted by SARS-CoV-2. Additional focus is given by us to the lymphoid structures and AID as the master regulator of germinal center reactions, which result in antibody production by plasma and memory B cells. We propose the dissection of the AID/APOBECs gene signature towards decisive determinants of the patient-specific and/or the patient group-specific antiviral response. Finally, the patient-specific mapping of the AID/APOBEC polymorphisms should be considered in the light of COVID-19.
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Affiliation(s)
- Anastasia Meshcheryakova
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Peter Pietschmann
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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37
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Pan JW, Zabidi MMA, Chong BK, Meng MY, Ng PS, Hasan SN, Sandey B, Bahnu S, Rajadurai P, Yip CH, Rueda OM, Caldas C, Chin SF, Teo SH. Germline APOBEC3B deletion increases somatic hypermutation in Asian breast cancer that is associated with Her2 subtype, PIK3CA mutations and immune activation. Int J Cancer 2021; 148:2489-2501. [PMID: 33423300 DOI: 10.1002/ijc.33463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022]
Abstract
A 30-kb deletion that eliminates the coding region of APOBEC3B (A3B) is >5 times more common in women of Asian descent compared to European descent. This polymorphism creates a chimera with the APOBEC3A (A3A) coding region and A3B 3'UTR, and it is associated with an increased risk for breast cancer in Asian women. Here, we explored the relationship between the A3B deletion polymorphism with tumour characteristics in Asian women. Using whole exome and whole transcriptome sequencing data of 527 breast tumours, we report that germline A3B deletion polymorphism leads to expression of the A3A-B hybrid isoform and increased APOBEC-associated somatic hypermutation. Hypermutated tumours, regardless of A3B germline status, were associated with the Her2 molecular subtype and PIK3CA mutations. Compared to nonhypermutated tumours, hypermutated tumours also had higher neoantigen burden, tumour heterogeneity and immune activation. Taken together, our results suggest that the germline A3B deletion polymorphism, via the A3A-B hybrid isoform, contributes to APOBEC mutagenesis in a significant proportion of Asian breast cancers. In addition, APOBEC somatic hypermutation, regardless of A3B background, may be an important clinical biomarker for Asian breast cancers.
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Affiliation(s)
- Jia-Wern Pan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | - Boon-Keat Chong
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Mei-Yee Meng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Pei-Sze Ng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Siti Norhidayu Hasan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Bethan Sandey
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Saira Bahnu
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | | | - Cheng-Har Yip
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
- Cambridge Breast Cancer Research Unit, CRUK Cambridge Cancer Centre, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Soo-Hwang Teo
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
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Ben X, Tian D, Liang J, Wu M, Xie F, Zheng J, Chen J, Fei Q, Guo X, Weng X, Liu S, Xie X, Ying Y, Qiao G, Jing C. APOBEC3B deletion polymorphism and lung cancer risk in the southern Chinese population. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:656. [PMID: 33987354 PMCID: PMC8105993 DOI: 10.21037/atm-21-989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Approximately 80–85% of lung cancer is the non-small cell lung cancer (NSCLC) subtype, which ranks as the leading cause of cancer deaths worldwide. APOBEC3B (A3B) was reported to be a key source of mutations in NSCLC. However, the role of the A3B deletion polymorphism in the etiology of NSCLC has not been well-documented. Methods A case-control study with 317 NSCLC patients and 334 healthy controls was conducted to explore the association between the A3B deletion polymorphism and the risk of NSCLC. The unconditional logistic regression model was performed to calculate the odds ratio (OR) and the 95% confidence interval (CI), and the confounding factors were adjusted, including age, gender, and smoking status, to estimate the risk. An analysis of gene-environment interactions was performed using multifactor dimensionality reduction (MDR) software. Results We found that the del/del genotype of A3B deletion significantly increased NSCLC risk. Compared with individuals carrying the ins/ins genotype of A3B deletion, individuals with the del/del genotype had a 2.36 times increased risk of developing NSCLC after adjusting for confounding factors (OR =2.71, 95% CI: 1.67–4.42, P<0.001). A 3-factor gene-environment (A3B deletion, gender, and smoking) interaction model was found for NSCLC (OR =4.407, 95% CI: 1.174–16.549, P=0.028). Conclusions We propose that the A3B deletion polymorphism can increase the risk of developing NSCLC, and their interactions with gender and smoking may contribute to the risk of NSCLC in the southern Chinese population.
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Affiliation(s)
- Xiaosong Ben
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dan Tian
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiayu Liang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Min Wu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Fan Xie
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jinlong Zheng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jingmin Chen
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Qiaoyuan Fei
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xinrong Guo
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xueqiong Weng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shan Liu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xin Xie
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yuting Ying
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chunxia Jing
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China.,Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
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Cheng AZ, Moraes SN, Shaban NM, Fanunza E, Bierle CJ, Southern PJ, Bresnahan WA, Rice SA, Harris RS. APOBECs and Herpesviruses. Viruses 2021; 13:v13030390. [PMID: 33671095 PMCID: PMC7998176 DOI: 10.3390/v13030390] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022] Open
Abstract
The apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of DNA cytosine deaminases provides a broad and overlapping defense against viral infections. Successful viral pathogens, by definition, have evolved strategies to escape restriction by the APOBEC enzymes of their hosts. HIV-1 and related retroviruses are thought to be the predominant natural substrates of APOBEC enzymes due to obligate single-stranded (ss)DNA replication intermediates, abundant evidence for cDNA strand C-to-U editing (genomic strand G-to-A hypermutation), and a potent APOBEC degradation mechanism. In contrast, much lower mutation rates are observed in double-stranded DNA herpesviruses and the evidence for APOBEC mutation has been less compelling. However, recent work has revealed that Epstein-Barr virus (EBV), Kaposi’s sarcoma-associated herpesvirus (KSHV), and herpes simplex virus-1 (HSV-1) are potential substrates for cellular APOBEC enzymes. To prevent APOBEC-mediated restriction these viruses have repurposed their ribonucleotide reductase (RNR) large subunits to directly bind, inhibit, and relocalize at least two distinct APOBEC enzymes—APOBEC3B and APOBEC3A. The importance of this interaction is evidenced by genetic inactivation of the EBV RNR (BORF2), which results in lower viral infectivity and higher levels of C/G-to-T/A hypermutation. This RNR-mediated mechanism therefore likely functions to protect lytic phase viral DNA replication intermediates from APOBEC-catalyzed DNA C-to-U deamination. The RNR-APOBEC interaction defines a new pathogen-host conflict that the virus must win in real-time for transmission and pathogenesis. However, partial losses over evolutionary time may also benefit the virus by providing mutational fuel for adaptation.
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Affiliation(s)
- Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (A.Z.C.); (R.S.H.)
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nadine M. Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elisa Fanunza
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Craig J. Bierle
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Peter J. Southern
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wade A. Bresnahan
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen A. Rice
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (A.Z.C.); (R.S.H.)
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Granadillo Rodríguez M, Flath B, Chelico L. The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead. Open Biol 2020; 10:200188. [PMID: 33292100 PMCID: PMC7776566 DOI: 10.1098/rsob.200188] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse 'off-target' cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the APOBEC 'off-target' activity are overexpression in a non-normal cell type, nuclear localization and replication stress. The resulting uracil-induced mutations contribute to genomic variation, which may result in neutral, beneficial or harmful consequences for the cancer. This review summarizes the functional and biochemical basis of the APOBEC3 enzyme activity and highlights their relationship with the most well-studied cancers in this particular context such as breast, lung, bladder, and human papillomavirus-associated cancers. We focus on APOBEC3A, APOBEC3B and APOBEC3H haplotype I because they are the leading candidates as sources of somatic mutations in these and other cancers. Also, we discuss the prognostic value of the APOBEC3 expression in drug resistance and response to therapies.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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41
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Revathidevi S, Murugan AK, Nakaoka H, Inoue I, Munirajan AK. APOBEC: A molecular driver in cervical cancer pathogenesis. Cancer Lett 2020; 496:104-116. [PMID: 33038491 PMCID: PMC7539941 DOI: 10.1016/j.canlet.2020.10.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/16/2020] [Accepted: 10/04/2020] [Indexed: 02/09/2023]
Abstract
Cervical cancer is one of the foremost common cancers in women. Human papillomavirus (HPV) infection remains a major risk factor of cervical cancer. In addition, numerous other genetic and epigenetic factors also are involved in the underlying pathogenesis of cervical cancer. Recently, it has been reported that apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC), DNA-editing protein plays an important role in the molecular pathogenesis of cancer. Particularly, the APOBEC3 family was shown to induce tumor mutations by aberrant DNA editing mechanism. In general, APOBEC3 enzymes play a pivotal role in the deamination of cytidine to uridine in DNA and RNA to control diverse biological processes such as regulation of protein expression, innate immunity, and embryonic development. Innate antiviral activity of the APOBEC3 family members restrict retroviruses, endogenous retro-element, and DNA viruses including the HPV that is the leading risk factor for cervical cancer. This review briefly describes the pathogenesis of cervical cancer and discusses in detail the recent findings on the role of APOBEC in the molecular pathogenesis of cervical cancer. APOBEC enzymes deaminate cytidine to uridine and control diverse biological processes including viral restriction. APOBEC3, DNA/RNA-editing enzyme plays an important role in the molecular pathogenesis of cervical cancer. APOBEC3-mediated DNA editing leads to the accumulation of somatic mutations in tumors and HPV genome. Deregulation of APOBEC3 family genes cause genomic instability and result in drug resistance, and immune-evasion in tumors.
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Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India; Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India.
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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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Roelofs PA, Goh CY, Chua BH, Jarvis MC, Stewart TA, McCann JL, McDougle RM, Carpenter MA, Martens JW, Span PN, Kappei D, Harris RS. Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B. eLife 2020; 9:61287. [PMID: 32985974 PMCID: PMC7553775 DOI: 10.7554/elife.61287] [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: 05/05/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible for A3B upregulation in cancer are poorly understood. Here we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenous A3B gene. The same E2F site is required for A3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate the binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E2F6 and DREAM/E2F4 complexes. Knockdown and overexpression studies confirm the involvement of these repressive complexes in regulating A3B expression. Altogether, these studies demonstrate that A3B expression is suppressed in normal cells by repressive E2F complexes and that viral or mutational disruption of this regulatory network triggers overexpression in breast cancer and provides fuel for tumor evolution.
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Affiliation(s)
- Pieter A Roelofs
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Chai Yeen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States
| | - Teneale A Stewart
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Mater Research Institute, The University of Queensland, Faculty of Medicine, Brisbane, Australia
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - Rebecca M McDougle
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Hennepin Healthcare, Minneapolis, United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - John Wm Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
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Hix MA, Wong L, Flath B, Chelico L, Cisneros GA. Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer. NAR Cancer 2020; 2:zcaa023. [PMID: 32984821 PMCID: PMC7503452 DOI: 10.1093/narcan/zcaa023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022] Open
Abstract
A number of APOBEC family DNA cytosine deaminases can induce mutations in tumor cells. APOBEC3H haplotype I is one of the deaminases that has been proposed to cause mutations in lung cancer. Here, we confirmed that APOBEC3H haplotype I can cause uracil-induced DNA damage in lung cancer cells that results in γH2AX foci. Interestingly, the database of cancer biomarkers in DNA repair genes (DNArCdb) identified a single-nucleotide polymorphism (rs139298) of APOBEC3H haplotype I that is involved in lung cancer. While we thought this may increase the activity of APOBEC3H haplotype I, instead we found through computational modeling and cell-based experiments that this single-nucleotide polymorphism causes the destabilization of APOBEC3H Haplotype I. Computational analysis suggests that the resulting K121E change affects the structure of APOBEC3H leading to active site disruption and destabilization of the RNA-mediated dimer interface. A K117E mutation in a K121E background stabilized the APOBEC3H haplotype I, thus enabling biochemical study. Subsequent analysis showed that K121E affected catalytic activity, single-stranded DNA binding and oligomerization on single-stranded DNA. The destabilization of a DNA mutator associated with lung cancer supports the model that too much APOBEC3-induced mutation could result in immune recognition or death of tumor cells.
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Affiliation(s)
- Mark A Hix
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - Lai Wong
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Ben Flath
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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Di Giorgio S, Martignano F, Torcia MG, Mattiuz G, Conticello SG. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. SCIENCE ADVANCES 2020; 6:eabb5813. [PMID: 32596474 PMCID: PMC7299625 DOI: 10.1126/sciadv.abb5813] [Citation(s) in RCA: 244] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/05/2020] [Indexed: 05/13/2023]
Abstract
The COVID-19 outbreak has become a global health risk, and understanding the response of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host deaminases is an innate restriction process to counter virus infection, but it is not yet known whether this process operates against coronaviruses. Here, we analyze RNA sequences from bronchoalveolar lavage fluids obtained from coronavirus-infected patients. We identify nucleotide changes that may be signatures of RNA editing: adenosine-to-inosine changes from ADAR deaminases and cytosine-to-uracil changes from APOBEC deaminases. Mutational analysis of genomes from different strains of Coronaviridae from human hosts reveals mutational patterns consistent with those observed in the transcriptomic data. However, the reduced ADAR signature in these data raises the possibility that ADARs might be more effective than APOBECs in restricting viral propagation. Our results thus suggest that both APOBECs and ADARs are involved in coronavirus genome editing, a process that may shape the fate of both virus and patient.
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Affiliation(s)
- Salvatore Di Giorgio
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Filippo Martignano
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Maria Gabriella Torcia
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy
| | - Giorgio Mattiuz
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
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Trancoso I, Morimoto R, Boehm T. Co-evolution of mutagenic genome editors and vertebrate adaptive immunity. Curr Opin Immunol 2020; 65:32-41. [PMID: 32353821 PMCID: PMC7768089 DOI: 10.1016/j.coi.2020.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022]
Abstract
The adaptive immune systems of all vertebrates rely on self-DNA mutating enzymes to assemble their antigen receptors in lymphocytes of their two principal lineages. In jawed vertebrates, the RAG1/2 recombinase directs V(D)J recombination of B cell and T cell receptor genes, whereas the activation-induced cytidine deaminase AID engages in their secondary modification. The recombination activating genes (RAG) 1 and 2 evolved from an ancient transposon-encoded genome modifier into a self-DNA mutator serving adaptive immunity; this was possible as a result of domestication, involving several changes in RAG1 and RAG2 proteins suppressing transposition and instead facilitating-coupled cleavage and recombination. By contrast, recent evidence supports the notion that the antigen receptors of T-like and B-like cells of jawless vertebrates, designated variable lymphocyte receptors (VLRs), are somatically assembled through a process akin to gene conversion that is believed to be dependent on the activities of distant relatives of AID, the cytidine deaminases CDA1 and CDA2, respectively. It appears, therefore, that the precursors of AID and CDAs underwent a domestication process that changed their target range from foreign nucleic acids to self-DNA; this multi-step evolutionary process ensured that the threat to host genome integrity was minimized. Here, we review recent findings illuminating the evolutionary steps associated with the domestication of the two groups of genome editors, RAG1/2 and cytidine deaminases, indicating how they became the driving forces underlying the emergence of vertebrate adaptive immune systems.
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Affiliation(s)
- Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ryo Morimoto
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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Germline APOBEC3B deletion influences clinicopathological parameters in luminal-A breast cancer: evidences from a southern Brazilian cohort. J Cancer Res Clin Oncol 2020; 146:1523-1532. [PMID: 32285256 DOI: 10.1007/s00432-020-03208-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE APOBEC3A and APOBEC3B cytidine deaminases have been implicated in the pathogenesis of multiple cancers, including breast cancer (BC). A germline deletion linking APOBEC3A and APOBEC3B loci (A3A/B) has been associated with higher APOBEC-mediated mutational burden, but its association with BC risk have been controversial. Therefore, this study investigated the association between A3A/B and BC susceptibility and clinical presentation in a Brazilian cohort. METHODS A3A/B deletion was evaluated through allele-specific PCR in 341 BC patients and 397 women without familial or personal history of neoplasia from Brazil and associations with susceptibility to BC subtypes were tested through age-adjusted logistic models while correlations with clinicopathological parameters were tested using Kendall's tests. RESULTS No association was found between A3A/B and BC susceptibility; however, in Luminal-A BCs, it was positively correlated with tumor size (Tau-c = 0.125) and Ki67 (Tau-c = 0.116) and negatively correlated with lymph node metastasis (LNM) (Tau-c = - 0.162). The negative association between A3A/B with LNM in Luminal-A BCs remained significant even after adjusting for tumor size and Ki67 in logistic models (OR = 0.22; p = 0.008). CONCLUSION These results show that although A3A/B may not modify BC susceptibility in Brazilian population, it may affect clinicopathological features in BC subtypes, promoting tumor cell proliferation while being negatively associated with LNM in Luminal-A BCs.
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Hsieh P, Vollger MR, Dang V, Porubsky D, Baker C, Cantsilieris S, Hoekzema K, Lewis AP, Munson KM, Sorensen M, Kronenberg ZN, Murali S, Nelson BJ, Chiatante G, Maggiolini FAM, Blanché H, Underwood JG, Antonacci F, Deleuze JF, Eichler EE. Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes. Science 2020; 366:366/6463/eaax2083. [PMID: 31624180 DOI: 10.1126/science.aax2083] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/05/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.
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Affiliation(s)
- PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Vy Dang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Shwetha Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Giorgia Chiatante
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari, Italy
| | | | - Hélène Blanché
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Pacific Biosciences (PacBio) of California, Inc., Menlo Park, CA, USA
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari, Italy
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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Kim YS, Sun DS, Yoon JS, Ko YH, Won HS, Kim JS. Clinical implications of APOBEC3A and 3B expression in patients with breast cancer. PLoS One 2020; 15:e0230261. [PMID: 32176735 PMCID: PMC7075570 DOI: 10.1371/journal.pone.0230261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
Background We aimed to evaluate the expression of APOBEC3A (A3A), 3B (A3B) mRNA, and germline APOBEC3A/B deletion polymorphism in patients with breast cancers and to investigate the correlation between their expressions and clinicopathological characteristics. Methods RNA and DNA samples were extracted from 138 breast cancer tissues and adjacent normal breast tissues. The levels of A3A and A3B mRNA transcripts were determined using quantitative real-time polymerase chain reaction. Insertion and deletion PCR assays were performed to detect the A3B deletion allele. The serum concentrations of soluble programmed death-ligand 1 (sPD-L1) and interferon gamma were determined using enzyme-linked immunosorbent assays. Results A3B mRNA expression levels were significantly higher in triple-negative breast cancers compared to hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancers. Older age of the patient and high ki-67 expression were associated with increased expression levels of A3A and A3B mRNA. Advanced tumor stage, presence of lymph node involvement, and high histological grade were associated with increased expression levels of A3A mRNA. The APOBEC3A/B deletion allele was found in 77 (55.8%) patients. TP53 and PIK3CA mutations were detected in 62 (44.9%) and 31 (22.5%) patients, respectively. The presence of a PIK3CA mutation was associated with lower A3A mRNA expression levels. There was a weak positive relationship between A3A mRNA expression levels and serum sPD-L1 levels. Conclusions There was a difference in A3B mRNA expression levels according to breast cancer subtypes, and high levels of A3A and A3B mRNA expressions were associated with an aggressive phenotype. There was a high incidence of APOBEC3A/B deletion allele. Further studies are needed to identify the clinical significance of APOBEC in Asian patients with breast cancer.
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Affiliation(s)
- Yong-seok Kim
- Department of Surgery, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Der Sheng Sun
- Division of Medical Oncology, Department of Internal Medicine, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung-sook Yoon
- Clinical Research Laboratory, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon Ho Ko
- Division of Medical Oncology, Department of Internal Medicine, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hye Sung Won
- Division of Medical Oncology, Department of Internal Medicine, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- * E-mail: (JSK); (HSW)
| | - Jeong Soo Kim
- Department of Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- * E-mail: (JSK); (HSW)
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50
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Zhang XL, Luo MT, Song JH, Pang W, Zheng YT. An Alu Element Insertion in Intron 1 Results in Aberrant Alternative Splicing of APOBEC3G Pre-mRNA in Northern Pig-Tailed Macaques ( Macaca leonina) That May Reduce APOBEC3G-Mediated Hypermutation Pressure on HIV-1. J Virol 2020; 94:e01722-19. [PMID: 31776266 PMCID: PMC6997765 DOI: 10.1128/jvi.01722-19] [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: 10/08/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
APOBEC3 family members, particularly APOBEC3F and APOBEC3G, inhibit the replication and spread of various retroviruses by inducing hypermutation in newly synthesized viral DNA. Viral hypermutation by APOBEC3 is associated with viral evolution, viral transmission, and disease progression. In recent years, increasing attention has been paid to targeting APOBEC3G for AIDS therapy. Thus, a controllable model system using species such as macaques, which provide a relatively ideal in vivo system, is needed for the study of APOBEC3-related issues. To appropriately utilize this animal model for biomedical research, important differences between human and macaque APOBEC3s must be considered. In this study, we found that the ratio of APOBEC3G-mediated/APOBEC3-mediated HIV-1 hypermutation footprints was much lower in peripheral blood mononuclear cells (PBMCs) from northern pig-tailed macaques than in PBMCs from humans. Next, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and resulted from an Alu element insertion into macaque APOBEC3G gene intron 1. This alternative splicing pattern generating an aberrant APOBEC3G mRNA isoform may significantly dilute full-length APOBEC3G and reduce APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques, which was supported by the elimination of other possibilities accounting for this hypermutation difference between the two hosts.IMPORTANCE APOBEC3 family members, particularly APOBEC3F and APOBEC3G, are important cellular antiviral factors. Recently, more attention has been paid to targeting APOBEC3G for AIDS therapy. To appropriately utilize macaque animal models for the study of APOBEC3-related issues, it is important that the differences between human and macaque APOBEC3s are clarified. In this study, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and which may reduce the APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques (NPMs). Our work provides important information for the proper application of macaque animal models for APOBEC3-related issues in AIDS research and a better understanding of the biological functions of APOBEC3 proteins.
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Affiliation(s)
- Xiao-Liang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Meng-Ting Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jia-Hao Song
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Institute of Health Sciences, Anhui University, Hefei, Anhui, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
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