1
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Fingerman DF, O'Leary DR, Hansen AR, Tran T, Harris BR, DeWeerd RA, Hayer KE, Fan J, Chen E, Tennakoon M, Meroni A, Szeto JH, Devenport J, LaVigne D, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. EMBO J 2024; 43:3240-3255. [PMID: 38886582 PMCID: PMC11294446 DOI: 10.1038/s44318-024-00137-x] [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: 01/22/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
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Affiliation(s)
- Dylan F Fingerman
- 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
| | - David R O'Leary
- 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
| | - Ava R Hansen
- 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
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Thi Tran
- 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
| | - Brooke R Harris
- 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
| | - Rachel A DeWeerd
- 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
| | - Katharina E Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiayi Fan
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Chen
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- School of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Mithila Tennakoon
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alice Meroni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Julia H Szeto
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica Devenport
- 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
| | - Danielle LaVigne
- 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
| | - Matthew D Weitzman
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ophir Shalem
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeffrey Bednarski
- 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
| | - Alessandro Vindigni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 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.
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2
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Kawale AS, Zou L. Regulation, functional impact, and therapeutic targeting of APOBEC3A in cancer. DNA Repair (Amst) 2024; 141:103734. [PMID: 39047499 DOI: 10.1016/j.dnarep.2024.103734] [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: 05/02/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Enzymes of the apolipoprotein B mRNA editing catalytic polypeptide like (APOBEC) family are cytosine deaminases that convert cytosine to uracil in DNA and RNA. Among these proteins, APOBEC3 sub-family members, APOBEC3A (A3A) and APOBEC3B (A3B), are prominent sources of mutagenesis in cancer cells. The aberrant expression of A3A and A3B in cancer cells leads to accumulation of mutations with specific single-base substitution (SBS) signatures, characterized by C→T and C→G changes, in a number of tumor types. In addition to fueling mutagenesis, A3A and A3B, particularly A3A, induce DNA replication stress, DNA damage, and chromosomal instability through their catalytic activities, triggering a range of cellular responses. Thus, A3A/B have emerged as key drivers of genome evolution during cancer development, contributing to tumorigenesis, tumor heterogeneity, and therapeutic resistance. Yet, the expression of A3A/B in cancer cells presents a cancer vulnerability that can be exploited therapeutically. In this review, we discuss the recent studies that shed light on the mechanisms regulating A3A expression and the impact of A3A in cancer. We also review recent advances in the development of A3A inhibitors and provide perspectives on the future directions of A3A research.
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Affiliation(s)
- Ajinkya S Kawale
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
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3
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Belica CA, Carpenter MA, Chen Y, Brown WL, Moeller NH, Boylan IT, Harris RS, Aihara H. A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination. J Biol Chem 2024; 300:107410. [PMID: 38796062 PMCID: PMC11234013 DOI: 10.1016/j.jbc.2024.107410] [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: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024] Open
Abstract
Over the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a need for biochemical tools that can be used to identify and characterize potential inhibitors of this enzyme family. In response to this challenge, we have developed a Real-time APOBEC3-mediated DNA Deamination assay. This assay offers a single-step set-up and real-time fluorescent read-out, and it is capable of providing insights into enzyme kinetics. The assay also offers a high-sensitivity and easily scalable method for identifying APOBEC3 inhibitors. This assay serves as a crucial addition to the existing APOBEC3 biochemical and cellular toolkit and possesses the versatility to be readily adapted into a high-throughput format for inhibitor discovery.
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Affiliation(s)
- Christopher A Belica
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael A Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Nicholas H Moeller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ian T Boylan
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA.
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.
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4
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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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5
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Belica CA, Carpenter MA, Chen Y, Brown WL, Moeller NH, Boylan IT, Harris RS, Aihara H. A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593688. [PMID: 38766133 PMCID: PMC11100776 DOI: 10.1101/2024.05.11.593688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Over the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a need for biochemical tools that can be used to identify and characterize potential inhibitors of this enzyme family. In response to this challenge, we have developed a Real-time APOBEC3-mediated DNA Deamination (RADD) assay. This assay offers a single-step set-up and real-time fluorescent read-out, and it is capable of providing insights into enzyme kinetics and also offering a high-sensitivity and easily scalable method for identifying APOBEC3 inhibitors. This assay serves as a crucial addition to the existing APOBEC3 biochemical and cellular toolkit and possesses the versatility to be readily adapted into a high-throughput format for inhibitor discovery.
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Affiliation(s)
- Christopher A. Belica
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Nicholas H. Moeller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Ian T. Boylan
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA
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6
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Gupta A, Gazzo A, Selenica P, Safonov A, Pareja F, da Silva EM, Brown DN, Zhu Y, Patel J, Blanco-Heredia J, Stefanovska B, Carpenter MA, Pei X, Frosina D, Jungbluth AA, Ladanyi M, Curigliano G, Weigelt B, Riaz N, Powell SN, Razavi P, Harris RS, Reis-Filho JS, Marra A, Chandarlapaty S. APOBEC3 mutagenesis drives therapy resistance in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591453. [PMID: 38746158 PMCID: PMC11092499 DOI: 10.1101/2024.04.29.591453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Acquired genetic alterations commonly drive resistance to endocrine and targeted therapies in metastatic breast cancer 1-7 , however the underlying processes engendering these diverse alterations are largely uncharacterized. To identify the mutational processes operant in breast cancer and their impact on clinical outcomes, we utilized a well-annotated cohort of 3,880 patient samples with paired tumor-normal sequencing data. The mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were highly prevalent and enriched in post-treatment compared to treatment-naïve hormone receptor-positive (HR+) cancers. APOBEC3 mutational signatures were independently associated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor combination therapy in patients with HR+ metastatic breast cancer. Whole genome sequencing (WGS) of breast cancer models and selected paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted resistance to both endocrine and targeted therapies through characteristic alterations such as RB1 loss-of-function mutations. Evidence of APOBEC3 activity in pre-treatment samples illustrated a pervasive role for this mutational process in breast cancer evolution. The study reveals APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlights its potential as a biomarker and target for overcoming resistance.
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7
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Costanzi JM, Stosic MS, Løvestad AH, Ambur OH, Rounge TB, Christiansen IK. Changes in intrahost genetic diversity according to lesion severity in longitudinal HPV16 samples. J Med Virol 2024; 96:e29641. [PMID: 38708811 DOI: 10.1002/jmv.29641] [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: 12/28/2023] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/07/2024]
Abstract
Human papillomavirus type 16 (HPV16) is the most common cause of cervical cancer, but most infections are transient with lesions not progressing to cancer. There is a lack of specific biomarkers for early cancer risk stratification. This study aimed to explore the intrahost HPV16 genomic variation in longitudinal samples from HPV16-infected women with different cervical lesion severity (normal, low-grade, and high-grade). The TaME-seq deep sequencing protocol was used to generate whole genome HPV16 sequences of 102 samples collected over time from 40 individuals. Single nucleotide variants (SNVs) and intrahost SNVs (iSNVs) were identified in the viral genomes. A majority of individuals had a unique set of SNVs and these SNVs were stable over time. Overall, the number of iSNVs and APOBEC3-induced iSNVs were significantly lower in high-grade relative to normal and low-grade samples. A significant increase in the number of APOBEC3-induced iSNVs over time was observed for normal samples when compared to high-grade. Our results indicates that the lower incidence of iSNVs and APOBEC3-induced iSNVs in high-grade lesions may have implications for novel biomarkers discoveries, potentially aiding early stratification of HPV-induced cervical precancerous lesions.
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Affiliation(s)
- Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Centre of Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Milan S Stosic
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Alexander H Løvestad
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
- Clinical Molecular Biology (EpiGen), Akershus University Hospital Lørenskog, Norway and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole H Ambur
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Trine B Rounge
- Centre of Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Irene K Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
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8
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Jones KFM, Demir Ö, Wyllie MK, Grillo MJ, Morris C, Hirakis SP, Kardile RD, Walters MA, Harris RS, Amaro RE, Harki DA. Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591187. [PMID: 38712210 PMCID: PMC11071470 DOI: 10.1101/2024.04.25.591187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
APOBEC3B cytosine deaminase contributes to the mutational burdens of tumors, resulting in tumor progression and therapy resistance. Small molecule APOBEC3B inhibitors have potential to slow or mitigate these detrimental outcomes. Through molecular dynamics (MD) simulations and computational solvent mapping analysis, we identified a novel putative allosteric pocket on the C-terminal domain of APOBEC3B (A3Bctd), and virtually screened the ChemBridge Diversity Set (N~110,000) against both the active and potential allosteric sites. Selected high-scoring compounds were subsequently purchased, characterized for purity and composition, and tested in biochemical assays, which yielded 13 hit compounds. Orthogonal NMR assays verified binding to the target protein. Initial selectivity studies suggest these compounds preferentially target A3Bctd over related deaminase APOBEC3A (A3A), and MD simulations indicate this selectivity may be due to the steric repulsion from H56 that is unique to A3A. Taken together, our studies represent the first virtual screening effort against A3Bctd that has yielded candidate inhibitors suitable for further development.
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Affiliation(s)
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California – San Diego, La Jolla, CA, USA
| | - Mackenzie K. Wyllie
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Michael J. Grillo
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Clare Morris
- Department of Chemistry and Biochemistry, University of California – San Diego, La Jolla, CA, USA
| | - Sophia P. Hirakis
- Department of Chemistry and Biochemistry, University of California – San Diego, La Jolla, CA, USA
| | | | - Michael A. Walters
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Reuben S. Harris
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California – San Diego, La Jolla, CA, USA
| | - Daniel A. Harki
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
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9
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Nakauma-González JA, Rijnders M, Noordsij MTW, Martens JWM, van der Veldt AAM, Lolkema MPJ, Boormans JL, van de Werken HJG. Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature. CELL GENOMICS 2024; 4:100528. [PMID: 38552621 PMCID: PMC11019362 DOI: 10.1016/j.xgen.2024.100528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes mutate specific DNA sequences and hairpin-loop structures, challenging the distinction between passenger and driver hotspot mutations. Here, we characterized 115 whole genomes of metastatic urothelial carcinoma (mUC) to identify APOBEC mutagenic hotspot drivers. APOBEC-associated mutations were detected in 92% of mUCs and were equally distributed across the genome, while APOBEC hotspot mutations (ApoHMs) were enriched in open chromatin. Hairpin loops were frequent targets of didymi (twins in Greek), two hotspot mutations characterized by the APOBEC SBS2 signature, in conjunction with an uncharacterized mutational context (Ap[C>T]). Next, we developed a statistical framework that identified ApoHMs as drivers in coding and non-coding genomic regions of mUCs. Our results and statistical framework were validated in independent cohorts of 23 non-metastatic UCs and 3,744 samples of 17 metastatic cancers, identifying cancer-type-specific drivers. Our study highlights the role of APOBEC in cancer development and may contribute to developing novel targeted therapy options for APOBEC-driven cancers.
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Affiliation(s)
- J Alberto Nakauma-González
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
| | - Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Minouk T W Noordsij
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Martijn P J Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
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10
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Hata AN, Larijani M. Targeting APOBECs in cancer: It's about timing. Cancer Cell 2024; 42:497-501. [PMID: 38593778 DOI: 10.1016/j.ccell.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
APOBEC3 cytidine deaminases have emerged as key drivers of mutagenesis in a wide spectrum of tumor types and are now appreciated to play a causal role in driving tumor evolution and drug resistance. As efforts to develop APOBEC3 inhibitors progress, understanding the timing and consequences of APOBEC3-mediated mutagenesis in distinct clinical contexts will be critical for guiding the development of anti-cancer therapeutic strategies.
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Affiliation(s)
- Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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11
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O'Leary DR, Hansen AR, Fingerman DF, Tran T, Harris BR, Hayer KE, Fan J, Chen E, Tennakoon M, DeWeerd RA, Meroni A, Szeto JH, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.568952. [PMID: 38077016 PMCID: PMC10705431 DOI: 10.1101/2023.11.28.568952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
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12
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes. Nat Commun 2024; 15:2370. [PMID: 38499542 PMCID: PMC10948877 DOI: 10.1038/s41467-024-45909-5] [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: 07/31/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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Affiliation(s)
- Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexandrea Becker
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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13
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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- 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
| | - Reuben S. Harris
- 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
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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14
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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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15
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Alonso de la Vega A, Temiz NA, Tasakis R, Somogyi K, Salgueiro L, Zimmer E, Ramos M, Diaz-Jimenez A, Chocarro S, Fernández-Vaquero M, Stefanovska B, Reuveni E, Ben-David U, Stenzinger A, Poth T, Heikenwälder M, Papavasiliou N, Harris RS, Sotillo R. Acute expression of human APOBEC3B in mice results in RNA editing and lethality. Genome Biol 2023; 24:267. [PMID: 38001542 PMCID: PMC10668425 DOI: 10.1186/s13059-023-03115-4] [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: 02/20/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through DNA mutation, but whether it also functions as an RNA editing enzyme has not been studied. RESULTS Here, we engineer a novel doxycycline-inducible mouse model of human APOBEC3B-overexpression to understand the impact of this enzyme in tissue homeostasis and address a potential role in C-to-U RNA editing. Elevated and sustained levels of APOBEC3B lead to rapid alteration of cellular fitness, major organ dysfunction, and ultimately lethality in mice. Importantly, RNA-sequencing of mouse tissues expressing high levels of APOBEC3B identifies frequent UCC-to-UUC RNA editing events that are not evident in the corresponding genomic DNA. CONCLUSIONS This work identifies, for the first time, a new deaminase-dependent function for APOBEC3B in RNA editing and presents a preclinical tool to help understand the emerging role of APOBEC3B as a driver of carcinogenesis.
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Affiliation(s)
- Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Nuri Alpay Temiz
- Health Informatics Institute, University of Minnesota, Minneapolis, 55455, USA
| | - Rafail Tasakis
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Kalman Somogyi
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Lorena Salgueiro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Eleni Zimmer
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Maria Ramos
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Alberto Diaz-Jimenez
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Mirian Fernández-Vaquero
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bojana Stefanovska
- 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
| | - Eli Reuveni
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Tanja Poth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Reuben S Harris
- 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
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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16
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He H, Lu S, Lu N, Huang N, Xu M. Prognostic value of APOBEC3A in patients with cervical squamous cell carcinoma in a major urban center in China: a retrospective study. Transl Cancer Res 2023; 12:2673-2681. [PMID: 37969401 PMCID: PMC10643969 DOI: 10.21037/tcr-23-383] [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: 03/09/2023] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Background APOBEC3A (A3A) has been implicated to have vital prognostic value in several common cancers. This study aimed to investigate the prognostic value of A3A expression in cervical squamous cell carcinoma (CESC). Methods This retrospective study enrolled 59 patients with CESC or cervical squamous intraepithelial neoplasia from January 2014 to January 2017 in Changhai Hospital, Naval Medical University. Then, A3A histoscores (H-scores) using immunohistochemistry (IHC) were analyzed in formalin-fixed paraffin-embedded archival tissue blocks. Moreover, overall survival was analyzed by the Kaplan-Meier method. Results The H-score of A3A protein expression was relatively higher in CESC than in squamous intraepithelial neoplasia, and the relative expression level of normal cervical tissues was lower than that of cervical squamous intraepithelial neoplasia (P<0.001). Moreover, the H-score of poorly differentiated cases was 6, which was higher than that of moderately differentiated cases (H-score =3), while the H-score of well-differentiated cases was 2, which was lower than that of moderately differentiated cases. Moreover, patients in the A3A low expression group had higher overall survival rates by prognostic analysis (P=0.027). Conclusions A3A protein expression was increased during CESC progression. Moreover, A3A expression was tightly related to poor prognosis in CESC. Thus, these results showed that A3A overexpression may provide a marker for poor prognosis in CESC.
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Affiliation(s)
- Haiwei He
- Department of Obstetrics and Gynecology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shenglian Lu
- Department of Obstetrics and Gynecology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Nan Lu
- Department of Obstetrics and Gynecology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Nian Huang
- Department of Integrative Medicine, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Mingjuan Xu
- Department of Obstetrics and Gynecology, Changhai Hospital, Naval Medical University, Shanghai, China
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17
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Secrier M, McGrath L, Ng F, Gulati S, Raymond A, Nuttall BRB, Berthe J, Jones EV, Sidders BS, Galon J, Barrett JC, Angell HK. Immune Cell Abundance and T-cell Receptor Landscapes Suggest New Patient Stratification Strategies in Head and Neck Squamous Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2133-2145. [PMID: 37819239 PMCID: PMC10588680 DOI: 10.1158/2767-9764.crc-23-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/04/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a molecularly and spatially heterogeneous disease frequently characterized by impairment of immunosurveillance mechanisms. Despite recent success with immunotherapy treatment, disease progression still occurs quickly after treatment in the majority of cases, suggesting the need to improve patient selection strategies. In the quest for biomarkers that may help inform response to checkpoint blockade, we characterized the tumor microenvironment (TME) of 162 HNSCC primary tumors of diverse etiologic and spatial origin, through gene expression and IHC profiling of relevant immune proteins, T-cell receptor (TCR) repertoire analysis, and whole-exome sequencing. We identified five HNSCC TME categories based on immune/stromal composition: (i) cytotoxic, (ii) plasma cell rich, (iii) dendritic cell rich, (iv) macrophage rich, and (v) immune-excluded. Remarkably, the cytotoxic and plasma cell rich subgroups exhibited a phenotype similar to tertiary lymphoid structures (TLS), which have been previously linked to immunotherapy response. We also found an increased richness of the TCR repertoire in these two subgroups and in never smokers. Mutational patterns evidencing APOBEC activity were enriched in the plasma cell high subgroup. Furthermore, specific signal propagation patterns within the Ras/ERK and PI3K/AKT pathways associated with distinct immune phenotypes. While traditionally CD8/CD3 T-cell infiltration and immune checkpoint expression (e.g., PD-L1) have been used in the patient selection process for checkpoint blockade treatment, we suggest that additional biomarkers, such as TCR productive clonality, smoking history, and TLS index, may have the ability to pull out potential responders to benefit from immunotherapeutic agents. SIGNIFICANCE Here we present our findings on the genomic and immune landscape of primary disease in a cohort of 162 patients with HNSCC, benefitting from detailed molecular and clinical characterization. By employing whole-exome sequencing and gene expression analysis of relevant immune markers, TCR profiling, and staining of relevant proteins involved in immune response, we highlight how distinct etiologies, cell intrinsic, and environmental factors combine to shape the landscape of HNSCC primary disease.
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Affiliation(s)
- Maria Secrier
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lara McGrath
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | - Felicia Ng
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sakshi Gulati
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Amelia Raymond
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | | | - Julie Berthe
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Emma V. Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Ben S. Sidders
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Sorbonne Université, Université Paris Cité, Centre de Recherche des Cordeliers, Paris, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - J. Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | - Helen K. Angell
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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18
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, Alonso de la Vega A, Proehl J, Holzhauer AM, Seeman ZJ, Liu X, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases. Cell Rep Med 2023; 4:101211. [PMID: 37797615 PMCID: PMC10591044 DOI: 10.1016/j.xcrm.2023.101211] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many cancers. However, despite years of work, a causal relationship has yet to be established in vivo. Here, we report a murine model that expresses tumor-like levels of human APOBEC3B. Animals expressing full-body APOBEC3B appear to develop normally. However, adult males manifest infertility, and older animals of both sexes show accelerated rates of carcinogenesis, visual and molecular tumor heterogeneity, and metastasis. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Enrichment for APOBEC3B-attributable single base substitution mutations also associates with elevated levels of insertion-deletion mutations and structural variations. APOBEC3B catalytic activity is required for all of these phenotypes. Together, these studies provide a cause-and-effect demonstration that human APOBEC3B is capable of driving both tumor initiation and evolution in vivo.
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Lene Alsøe
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xingyu Liu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Hilde Nilsen
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Reuben S Harris
- 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.
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19
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Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB. Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A. Nat Commun 2023; 14:6382. [PMID: 37821454 PMCID: PMC10567711 DOI: 10.1038/s41467-023-42174-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: 03/07/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
The normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations. APOBEC3A inhibitors may therefore comprise a unique class of anti-cancer agents that work by blocking mutagenesis, slowing tumor evolvability, and preventing detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC substrate motif that is part of a 3-nucleotide loop. In addition, the structural basis of APOBEC3A's preference for YTCD motifs (Y = T, C; D = A, G, T) is explained. The nuclease-resistant phosphorothioated derivatives of these inhibitors have nanomolar potency in vitro and block APOBEC3A activity in human cells. These inhibitors may be useful probes for studying APOBEC3A activity in cellular systems and leading toward, potentially as conjuvants, next-generation, combinatorial anti-mutator and anti-cancer therapies.
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Affiliation(s)
- Stefan Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Amanda E Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maitsetseg Bayarjargal
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jana Filitcheva
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yongdong Su
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Department of Pediatrics, Emory University School of Medicine, and the Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tracy K Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Elena Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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20
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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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21
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Wick C, Moghadasi SA, Becker JT, Fanunza E, Oh S, Bournique E, Buisson R, Harris RS. Mitochondrial double-stranded RNA triggers induction of the antiviral DNA deaminase APOBEC3A and nuclear DNA damage. J Biol Chem 2023; 299:105073. [PMID: 37474103 PMCID: PMC10457583 DOI: 10.1016/j.jbc.2023.105073] [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: 05/08/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
APOBEC3A is an antiviral DNA deaminase often induced by virus infection. APOBEC3A is also a source of cancer mutation in viral and nonviral tumor types. It is therefore critical to identify factors responsible for APOBEC3A upregulation. Here, we test the hypothesis that leaked mitochondrial (mt) double-stranded (ds)RNA is recognized as foreign nucleic acid, which triggers innate immune signaling, APOBEC3A upregulation, and DNA damage. Knockdown of an enzyme responsible for degrading mtdsRNA, the exoribonuclease polynucleotide phosphorylase, results in mtdsRNA leakage into the cytosol and induction of APOBEC3A expression. APOBEC3A upregulation by cytoplasmic mtdsRNA requires RIG-I, MAVS, and STAT2 and is likely part of a broader type I interferon response. Importantly, although mtdsRNA-induced APOBEC3A appears cytoplasmic by subcellular fractionation experiments, its induction triggers an overt DNA damage response characterized by elevated nuclear γ-H2AX staining. Thus, mtdsRNA dysregulation may induce APOBEC3A and contribute to observed genomic instability and mutation signatures in cancer.
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Affiliation(s)
- Chloe Wick
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jordan T Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA; Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA; Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA; Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA.
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22
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA Features Impact APOBEC3A and APOBEC3B Deaminase Activity and Shape Tumor Mutational Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551499. [PMID: 37577509 PMCID: PMC10418229 DOI: 10.1101/2023.08.02.551499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets singlestranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have been fully established, and the specific influence of the DNA sequence on APOBEC3A APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B selectively targets DNA stem-loop structures, and they are distinct from those subjected deamination by APOBEC3A. We develop Oligo-seq, a novel in vitro sequencing-based to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A an APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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23
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Butt Y, Sakhtemani R, Mohamad-Ramshan R, Lawrence MS, Bhagwat AS. Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551518. [PMID: 37577595 PMCID: PMC10418155 DOI: 10.1101/2023.08.01.551518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The APOBEC3 family of enzymes convert cytosines in single-stranded DNA to uracils thereby causing mutations. These enzymes protect human cells against viruses and retrotransposons, but in many cancers they contribute to mutations that diversify the tumors and help them escape anticancer drug treatments. To understand the mechanism of mutagenesis by APOBEC3B, we expressed the complete enzyme or its catalytic carboxy-terminal domain (CTD) in repair-deficient Eschericia coli and mapped the resulting uracils using uracil pull-down and sequencing technology. The uracilomes of A3B-full and A3B-CTD showed peaks in many of the same regions where APOBEC3A also created uracilation peaks. Like A3A, the two A3B enzymes also preferred to deaminate cytosines near transcription start sites and in the lagging-strand template at replication forks. In contrast to an earlier report that A3B does not favor hairpin loops over linear DNA, we found that both A3B-full and A3B-CTD showed a strong preference for cytosines in hairpin loops. The major difference between A3A and A3B was that while the former enzyme prefers 3 nt loops the best, A3B prefers loops of 4 nt over those of other lengths. Furthermore, within 5 nt loops, A3A prefers cytosine to be in the penultimate position, while A3B prefers it to be at the 3' end of the loop. We confirmed these loop size and sequence preferences experimentally using purified A3A and A3B-CTD proteins. Reanalysis of hairpin loop mutations in human tumors using the size, sequence and position preferences of the two enzymes found that the tumors displayed mutations with intrinsic characteristics of both the enzymes with a stronger contribution from A3A.
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24
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Isozaki H, Sakhtemani R, Abbasi A, Nikpour N, Stanzione M, Oh S, Langenbucher A, Monroe S, Su W, Cabanos HF, Siddiqui FM, Phan N, Jalili P, Timonina D, Bilton S, Gomez-Caraballo M, Archibald HL, Nangia V, Dionne K, Riley A, Lawlor M, Banwait MK, Cobb RG, Zou L, Dyson NJ, Ott CJ, Benes C, Getz G, Chan CS, Shaw AT, Gainor JF, Lin JJ, Sequist LV, Piotrowska Z, Yeap BY, Engelman JA, Lee JJK, Maruvka YE, Buisson R, Lawrence MS, Hata AN. Therapy-induced APOBEC3A drives evolution of persistent cancer cells. Nature 2023; 620:393-401. [PMID: 37407818 PMCID: PMC10804446 DOI: 10.1038/s41586-023-06303-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
Acquired drug resistance to anticancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1-4, the underlying molecular mechanisms shaping tumour evolution during treatment are incompletely understood. Genomic profiling of patient tumours has implicated apolipoprotein B messenger RNA editing catalytic polypeptide-like (APOBEC) cytidine deaminases in tumour evolution; however, their role during therapy and the development of acquired drug resistance is undefined. Here we report that lung cancer targeted therapies commonly used in the clinic can induce cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Therapy-induced A3A promotes the formation of double-strand DNA breaks, increasing genomic instability in drug-tolerant persisters. Deletion of A3A reduces APOBEC mutations and structural variations in persister cells and delays the development of drug resistance. APOBEC mutational signatures are enriched in tumours from patients with lung cancer who progressed after extended responses to targeted therapies. This study shows that induction of A3A in response to targeted therapies drives evolution of drug-tolerant persister cells, suggesting that suppression of A3A expression or activity may represent a potential therapeutic strategy in the prevention or delay of acquired resistance to lung cancer targeted therapy.
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Affiliation(s)
- Hideko Isozaki
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ammal Abbasi
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Naveed Nikpour
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Sunwoo Oh
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Susanna Monroe
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Wenjia Su
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Heidie Frisco Cabanos
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Nicole Phan
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Pégah Jalili
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Daria Timonina
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Samantha Bilton
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | | | - Varuna Nangia
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Kristin Dionne
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Amanda Riley
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Matthew Lawlor
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Rosemary G Cobb
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cyril Benes
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Chang S Chan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School and Center for Systems and Computational Biology, Rutgers Cancer Institute, New Brunswick, NJ, USA
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Beow Y Yeap
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jake June-Koo Lee
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yosef E Maruvka
- Faculty of Biotechnology and Food Engineering, Lorey Loki Center for Life Science and Engineering, Technion, Haifa, Israel
| | - Rémi Buisson
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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25
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Garcia NMG, Becerra JN, McKinney BJ, DiMarco AV, Wu F, Fitzgibbon M, Alvarez JV. APOBEC3 activity promotes the survival and evolution of drug-tolerant persister cells during acquired resistance to EGFR inhibitors in lung cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547443. [PMID: 37461590 PMCID: PMC10350004 DOI: 10.1101/2023.07.02.547443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
APOBEC mutagenesis is one of the most common endogenous sources of mutations in human cancer and is a major source of genetic intratumor heterogeneity. High levels of APOBEC mutagenesis are associated with poor prognosis and aggressive disease across diverse cancers, but the mechanistic and functional impacts of APOBEC mutagenesis on tumor evolution and therapy resistance remain relatively unexplored. To address this, we investigated the contribution of APOBEC mutagenesis to acquired therapy resistance in a model of EGFR-mutant non-small cell lung cancer. We find that inhibition of EGFR in lung cancer cells leads to a rapid and pronounced induction of APOBEC3 expression and activity. Functionally, APOBEC expression promotes the survival of drug-tolerant persister cells (DTPs) following EGFR inhibition. Constitutive expression of APOBEC3B alters the evolutionary trajectory of acquired resistance to the EGFR inhibitor gefitinib, making it more likely that resistance arises through de novo acquisition of the T790M gatekeeper mutation and squamous transdifferentiation during the DTP state. APOBEC3B expression is associated with increased expression of the squamous cell transcription factor ΔNp63 and squamous cell transdifferentiation in gefitinib-resistant cells. Knockout of ΔNp63 in gefitinibresistant cells reduces the expression of the p63 target genes IL1a/b and sensitizes these cells to the thirdgeneration EGFR inhibitor osimertinib. These results suggest that APOBEC activity promotes acquired resistance by facilitating evolution and transdifferentiation in DTPs, and suggest that approaches to target ΔNp63 in gefitinib-resistant lung cancers may have therapeutic benefit.
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Affiliation(s)
- Nina Marie G Garcia
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine
| | - Jessica N Becerra
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Brock J McKinney
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Ashley V DiMarco
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine
| | - Feinan Wu
- Genomics and Bioinformatics, Fred Hutchinson Cancer Center
| | | | - James V Alvarez
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
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26
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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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Mendez Ruiz S, Chalk AM, Goradia A, Heraud-Farlow J, Walkley C. Over-expression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo. NAR Cancer 2023; 5:zcad023. [PMID: 37275274 PMCID: PMC10233902 DOI: 10.1093/narcan/zcad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023] Open
Abstract
Adenosine to inosine editing (A-to-I) in regions of double stranded RNA (dsRNA) is mediated by adenosine deaminase acting on RNA 1 (ADAR1) or ADAR2. ADAR1 and A-to-I editing levels are increased in many human cancers. Inhibition of ADAR1 has emerged as a high priority oncology target, however, whether ADAR1 overexpression enables cancer initiation or progression has not been directly tested. We established a series of in vivo models to allow overexpression of full-length ADAR1, or its individual isoforms, to test if increased ADAR1 expression was oncogenic. Widespread over-expression of ADAR1 or the p110 or p150 isoforms individually as sole lesions was well tolerated and did not result in cancer initiation. Therefore, ADAR1 overexpression alone is not sufficient to initiate cancer. We demonstrate that endogenous ADAR1 and A-to-I editing increased upon immortalization in murine cells, consistent with the observations from human cancers. We tested if ADAR1 over-expression could co-operate with cancer initiated by loss of tumour suppressors using a model of osteosarcoma. We did not see a disease potentiating or modifying effect of overexpressing ADAR1 or its isoforms in the models assessed. We conclude that increased ADAR1 expression and A-to-I editing in cancers is most likely a consequence of tumor formation.
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Affiliation(s)
- Shannon Mendez Ruiz
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Alistair M Chalk
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Ankita Goradia
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | | | - Carl R Walkley
- To whom correspondence should be addressed. Tel: +61 3 9231 2480;
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28
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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: 0] [Impact Index Per Article: 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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Naumann JA, Argyris PP, Carpenter MA, Gupta HB, Chen Y, Temiz NA, Zhou Y, Durfee C, Proehl J, Koniar BL, Conticello SG, Largaespada DA, Brown WL, Aihara H, Vogel RI, Harris RS. DNA Deamination Is Required for Human APOBEC3A-Driven Hepatocellular Carcinoma In Vivo. Int J Mol Sci 2023; 24:9305. [PMID: 37298259 PMCID: PMC10253583 DOI: 10.3390/ijms24119305] [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: 04/28/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Although the APOBEC3 family of single-stranded DNA cytosine deaminases is well-known for its antiviral factors, these enzymes are rapidly gaining attention as prominent sources of mutation in cancer. APOBEC3's signature single-base substitutions, C-to-T and C-to-G in TCA and TCT motifs, are evident in over 70% of human malignancies and dominate the mutational landscape of numerous individual tumors. Recent murine studies have established cause-and-effect relationships, with both human APOBEC3A and APOBEC3B proving capable of promoting tumor formation in vivo. Here, we investigate the molecular mechanism of APOBEC3A-driven tumor development using the murine Fah liver complementation and regeneration system. First, we show that APOBEC3A alone is capable of driving tumor development (without Tp53 knockdown as utilized in prior studies). Second, we show that the catalytic glutamic acid residue of APOBEC3A (E72) is required for tumor formation. Third, we show that an APOBEC3A separation-of-function mutant with compromised DNA deamination activity and wildtype RNA-editing activity is defective in promoting tumor formation. Collectively, these results demonstrate that APOBEC3A is a "master driver" that fuels tumor formation through a DNA deamination-dependent mechanism.
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Affiliation(s)
- Jordan A. Naumann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Harshita B. Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yufan Zhou
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Brenda L. Koniar
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, 50139 Florence, Italy;
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - David A. Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Rachel I. Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Department of Obstetrics, Gynecology, and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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30
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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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31
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Li M, Mei YX, Wen JH, Jiao YR, Pan QR, Kong XX, Li J. Hepatoid adenocarcinoma-Clinicopathological features and molecular characteristics. Cancer Lett 2023; 559:216104. [PMID: 36863507 DOI: 10.1016/j.canlet.2023.216104] [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: 12/01/2022] [Revised: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
Hepatoid adenocarcinoma (HAC) is a rare, malignant, extrahepatic tumor with histologic features similar to those of hepatocellular carcinoma. HAC is most often associated with elevated alpha-fetoprotein (AFP). HAC can occur in multiple organs, including the stomach, esophagus, colon, pancreas, lungs, and ovaries. HAC differs greatly from typical adenocarcinoma in terms of its biological aggression, poor prognosis, and clinicopathological characteristics. However, the mechanisms underlying its development and invasive metastasis remain unclear. The purpose of this review was to summarize the clinicopathological features, molecular traits, and molecular mechanisms driving the malignant phenotype of HAC, in order to support the clinical diagnosis and treatment of HAC.
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Affiliation(s)
- Ming Li
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China
| | - Yan-Xia Mei
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China
| | - Ji-Hang Wen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China
| | - Yu-Rong Jiao
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China
| | - Qiang-Rong Pan
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China
| | - Xiang-Xing Kong
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China.
| | - Jun Li
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Clinical Research Center for Cancer, China; Cancer Center of Zhejiang University, China.
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Britan-Rosich Y, Ma J, Kotler E, Hassan F, Botvinnik A, Smith Y, Moshel O, Nasereddin A, Sharma G, Pikarsky E, Ross S, Kotler M. APOBEC3G protects the genome of human cultured cells and mice from radiation-induced damage. FEBS J 2023; 290:1822-1839. [PMID: 36325681 PMCID: PMC10079569 DOI: 10.1111/febs.16673] [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: 03/24/2022] [Revised: 09/14/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Cytosine deaminases AID/APOBEC proteins act as potent nucleic acid editors, playing important roles in innate and adaptive immunity. However, the mutagenic effects of some of these proteins compromise genomic integrity and may promote tumorigenesis. Here, we demonstrate that human APOBEC3G (A3G), in addition to its role in innate immunity, promotes repair of double-strand breaks (DSBs) in vitro and in vivo. Transgenic mice expressing A3G successfully survived lethal irradiation, whereas wild-type controls quickly succumbed to radiation syndrome. Mass spectrometric analyses identified the differential upregulation of a plethora of proteins involved in DSB repair pathways in A3G-expressing cells early following irradiation to facilitate repair. Importantly, we find that A3G not only accelerates DSB repair but also promotes deamination-dependent error-free rejoining. These findings have two implications: (a) strategies aimed at inhibiting A3G may improve the efficacy of genotoxic therapies used to cure malignant tumours; and (b) enhancing A3G activity may reduce acute radiation syndrome in individuals exposed to ionizing radiation.
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Affiliation(s)
- Yelena Britan-Rosich
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Jing Ma
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, USA
| | - Eran Kotler
- Department of Genetics, Stanford University School of Medicine, Ca, USA
| | - Faizan Hassan
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Alexander Botvinnik
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Yoav Smith
- Genomic Data Analysis, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Ofra Moshel
- Core Research Facility, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Abed Nasereddin
- Core Research Facility of the Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gunjan Sharma
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Susan Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, USA
| | - Moshe Kotler
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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Argyris PP, Naumann J, Jarvis MC, Wilkinson PE, Ho DP, Islam MN, Bhattacharyya I, Gopalakrishnan R, Li F, Koutlas IG, Giubellino A, Harris RS. Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B. Histopathology 2023; 82:608-621. [PMID: 36416305 PMCID: PMC10107945 DOI: 10.1111/his.14843] [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: 05/05/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022]
Abstract
AIMS Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs. METHODS AND RESULTS A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2). CONCLUSION The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.
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Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Jordan Naumann
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter E Wilkinson
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Dan P Ho
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Mohammed N Islam
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Indraneel Bhattacharyya
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Rajaram Gopalakrishnan
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Faqian Li
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Ioannis G Koutlas
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Alessio Giubellino
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, de la Vega AA, Proehl J, Holzhauer AM, Seeman ZJ, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529970. [PMID: 36865194 PMCID: PMC9980288 DOI: 10.1101/2023.02.24.529970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many different cancers. Despite over 10 years of work, a causal relationship has yet to be established between APOBEC3B and any stage of carcinogenesis. Here we report a murine model that expresses tumor-like levels of human APOBEC3B after Cre-mediated recombination. Animals appear to develop normally with full-body expression of APOBEC3B. However, adult males manifest infertility and older animals of both sexes show accelerated rates of tumorigenesis (mostly lymphomas or hepatocellular carcinomas). Interestingly, primary tumors also show overt heterogeneity, and a subset spreads to secondary sites. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Elevated levels of structural variation and insertion-deletion mutations also accumulate in these tumors. Together, these studies provide the first cause-and-effect demonstration that human APOBEC3B is an oncoprotein capable of causing a wide range of genetic changes and driving tumor formation in vivo .
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, Ohio, USA, 43210
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
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Harjes S, Kurup HM, Rieffer AE, Bayaijargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB. Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528918. [PMID: 36824964 PMCID: PMC9949147 DOI: 10.1101/2023.02.17.528918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The normally antiviral enzyme APOBEC3A1-4 is an endogenous mutagen in many different human cancers5-7, where it becomes hijacked to fuel tumor evolvability. APOBEC3A's single-stranded DNA C-to-U editing activity1,8 results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations5-7. Transgenic expression in mice demonstrates its tumorigenic potential9. APOBEC3A inhibitors may therefore comprise a novel class of anti-cancer agents that work by blocking mutagenesis, preventing tumor evolvability, and lessening detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC recognition motif that is part of a three-nucleotide loop. The nuclease-resistant phosphorothioated derivatives of these inhibitors maintain nanomolar in vitro potency against APOBEC3A, localize to the cell nucleus, and block APOBEC3A activity in human cells. These results combine to suggest roles for these inhibitors to study A3A activity in living cells, potentially as conjuvants, leading toward next-generation, combinatorial anti-mutator and anti-cancer therapies.
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Affiliation(s)
- Stefan Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Amanda E. Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota–Twin Cities, Minneapolis, MN, USA
| | - Maitsetseg Bayaijargal
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current address: Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jana Filitcheva
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yongdong Su
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current address: Department of Pediatrics, Emory University School of Medicine, and the Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Tracy K. Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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36
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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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Serrano JC, von Trentini D, Berríos KN, Barka A, Dmochowski IJ, Kohli RM. Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. ACS Chem Biol 2022; 17:3379-3388. [PMID: 36475588 PMCID: PMC9990883 DOI: 10.1021/acschembio.2c00796] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid structure plays a critical role in governing the selectivity of DNA- and RNA-modifying enzymes. In the case of the APOBEC3 family of cytidine deaminases, these enzymes catalyze the conversion of cytosine (C) to uracil (U) in single-stranded DNA, primarily in the context of innate immunity. DNA deamination can also have pathological consequences, accelerating the evolution of viral genomes or, when the host genome is targeted by either APOBEC3A (A3A) or APOBEC3B (A3B), promoting tumor evolution leading to worse patient prognosis and chemotherapeutic resistance. For A3A, nucleic acid secondary structure has emerged as a critical determinant of substrate targeting, with a predilection for DNA that can form stem loop hairpins. Here, we report the development of a specific nanomolar-level, nucleic acid-based inhibitor of A3A. Our strategy relies on embedding the nucleobase 5-methylzebularine, a mechanism-based inhibitor, into a DNA dumbbell structure, which mimics the ideal substrate secondary structure for A3A. Structure-activity relationship studies using a panel of diverse inhibitors reveal a critical role for the stem and position of the inhibitor moiety in achieving potent inhibition. Moreover, we demonstrate that DNA dumbbell inhibitors, but not nonstructured inhibitors, show specificity against A3A relative to the closely related catalytic domain of A3B. Overall, our work demonstrates the feasibility of leveraging secondary structural preferences in inhibitor design, offering a blueprint for further development of modulators of DNA-modifying enzymes and potential therapeutics to circumvent APOBEC-driven viral and tumor evolution.
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Affiliation(s)
- Juan C. Serrano
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Dora von Trentini
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Kiara N. Berríos
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Aleksia Barka
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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38
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Wong L, Sami A, Chelico L. Competition for DNA binding between the genome protector replication protein A and the genome modifying APOBEC3 single-stranded DNA deaminases. Nucleic Acids Res 2022; 50:12039-12057. [PMID: 36444883 PMCID: PMC9757055 DOI: 10.1093/nar/gkac1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/30/2022] Open
Abstract
The human APOBEC family of eleven cytosine deaminases use RNA and single-stranded DNA (ssDNA) as substrates to deaminate cytosine to uracil. This deamination event has roles in lipid metabolism by altering mRNA coding, adaptive immunity by causing evolution of antibody genes, and innate immunity through inactivation of viral genomes. These benefits come at a cost where some family members, primarily from the APOBEC3 subfamily (APOBEC3A-H, excluding E), can cause off-target deaminations of cytosine to form uracil on transiently single-stranded genomic DNA, which induces mutations that are associated with cancer evolution. Since uracil is only promutagenic, the mutations observed in cancer genomes originate only when uracil is not removed by uracil DNA glycosylase (UNG) or when the UNG-induced abasic site is erroneously repaired. However, when ssDNA is present, replication protein A (RPA) binds and protects the DNA from nucleases or recruits DNA repair proteins, such as UNG. Thus, APOBEC enzymes must compete with RPA to access their substrate. Certain APOBEC enzymes can displace RPA, bind and scan ssDNA efficiently to search for cytosines, and can become highly overexpressed in tumor cells. Depending on the DNA replication conditions and DNA structure, RPA can either be in excess or deficient. Here we discuss the interplay between these factors and how despite RPA, multiple cancer genomes have a mutation bias at cytosines indicative of APOBEC activity.
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Affiliation(s)
- Lai Wong
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Alina Sami
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Linda Chelico
- To whom correspondence should be addressed. Tel: +1 306 966 4318; Fax: +1 306 966 4298;
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39
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Dananberg A, Maciejowski J. Monitoring APOBEC3A protein levels in human cancer cells. Methods Cell Biol 2022; 182:313-327. [PMID: 38359985 PMCID: PMC10869936 DOI: 10.1016/bs.mcb.2022.10.008] [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] [Indexed: 11/19/2022]
Abstract
The APOBEC3 family of cytosine deaminases, which target single-stranded DNA and RNA of viruses and retroelements as part of the innate immune defense, generate mutations in many human cancers. Although the APOBEC3A paralog is a major endogenous source of these mutations, low APOBEC3A mRNA levels and protein abundance have hampered functional characterization. Extensive homology across APOBEC3 paralogs have further challenged the development of specific detection reagents. Here, we describe the isolation and use of monoclonal antibodies with specificity for APOBEC3A and the APOBEC3A/APOBEC3B/APOBEC3G proteins. We provide protocols and technical advice for detection and measurement of APOBEC3A protein across human cancer cell lines using standard immunoblotting and immunofluorescence protocols.
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Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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40
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Li P, Meng Q, Xue Y, Teng Z, Chen H, Zhang J, Xu Y, Wang S, Yu R, Ou Q, Wu X, Jia B. Comprehensive genomic profiling of colorectal cancer patients reveals differences in mutational landscapes among clinical and pathological subgroups. Front Oncol 2022; 12:1000146. [DOI: 10.3389/fonc.2022.1000146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
With the widespread of colonoscopy, colorectal cancer remains to be one of the most detrimental types of cancer. Though there were multiple studies investigating the genomic landscape of colorectal cancer, a comprehensive analysis uncovering the differences between various types of colorectal cancer is still lacking. In our study, we performed genomic analysis on 133 patients with colorectal cancer. Mutated FAT1 and PKHD1 and altered Hippo pathway genes were found to be enriched in early-onset colorectal cancer. APOBEC signature was prevalent in microsatellite stable (MSS) patients and was related to lymph node metastasis. ZNF217 mutations were significantly associated with early-stage colorectal cancer. In all, this study represents a comprehensive genomic analysis uncovering potential molecular mechanisms underneath different subgroups of colorectal cancer thus providing new targets for precision treatment development.
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41
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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: 17] [Impact Index Per Article: 8.5] [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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42
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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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43
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Warren CJ, Santiago ML, Pyeon D. APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis? Annu Rev Virol 2022; 9:375-395. [PMID: 35671565 PMCID: PMC9637027 DOI: 10.1146/annurev-virology-092920-030354] [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] [Indexed: 11/09/2022]
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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44
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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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45
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Jafarpour S, Yazdi M, Nedaeinia R, Ghobakhloo S, Salehi R. Unfavorable prognosis and clinical consequences of APOBEC3B expression in breast and other cancers: A systematic review and meta-analysis. Tumour Biol 2022; 44:153-169. [DOI: 10.3233/tub-211577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION: Controversy exists regarding the association of apolipoprotein B mRNA editing enzyme catalytic subunit 3B APOBEC3B, (A3B) overexpression and poor prognosis, metastasis, and chemotherapy drug resistance in cancers. Here we conducted a systematic review and meta-analysis to determine its prognostic value and clinicopathological features in breast cancer and some other malignancies. MATERIALS AND METHODS: PubMed, Scopus, Cochrane Library, Web of Science, and EMBASE were searched up to Feb 2022 for the association of A3B with breast, ovarian, gastrointestinal and lung cancers. The pooled hazard ratios with 95% confidence interval (CI) were evaluated to assess disease-free survival (DFS), overall survival (OS), and recurrence-free survival (RFS) in cancers under study. RESULTS: Over 3700 patients were included in this meta-survey. Elevated levels of A3B were significantly related to low OS (pooled HR = 1.30; 95% CI:1.09–1.55, P < 0.01), poor DFS (pooled HR = 1.66; 95% CI:1.17–2.35, P < 0.01) and poor RFS (HR = 1.51, 95% CI:1.11–2.04, P = 0.01). Subgroup analysis revealed that high A3B expression was associated with poor OS in lung (HR = 1.85, 95% CI: 1.40–2.45), and breast cancers (HR = 1.38, 95% CI: 1.00–1.89). High expression of A3B did not display any significant association with clinicopathologic features. CONCLUSION: APOBEC3B overexpression is related to poor OS, DFS and RFS only in some cancer types and no generalized role could be predicted for all cancers.
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Affiliation(s)
- Sima Jafarpour
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Yazdi
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sepideh Ghobakhloo
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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Zhao R, Li H, Ge W, Zhu X, Zhu L, Wan X, Wang G, Pan H, Lu J, Han W. Comprehensive Analysis of Genomic Alterations in Hepatoid Adenocarcinoma of the Stomach and Identification of Clinically Actionable Alterations. Cancers (Basel) 2022; 14:cancers14163849. [PMID: 36010842 PMCID: PMC9405706 DOI: 10.3390/cancers14163849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Hepatoid adenocarcinoma of the stomach (HAS) is a subset of gastric cancer (GC) histologically characterized by hepatocellular carcinoma-like foci with or without alpha-fetoprotein secretion, which is easily misdiagnosed. Genomic alterations and potential targets for this population are still largely unknown. Additionally, treatment regimens of HAS are mainly based on GC guidelines, which is not reasonable for diseases with great heterogeneity. The present study comprehensively depicts the genomic features of HAS, and they are significantly different from GC, AFP-producing GC (AFPGC), and liver hepatocellular carcinoma (LIHC). Multiple aggressive behavior-related amplificated or deleted regions in HAS are firstly reported. Moreover, reliable and practicable clinically actionable alterations for HAS are identified, providing evidence for making personalized therapy based on the genomic characteristics of HAS instead of GC. Abstract Hepatoid adenocarcinoma of the stomach (HAS) is a rare malignancy with aggressive biological behavior. This study aimed to compare the genetic landscape of HAS with liver hepatocellular carcinoma (LIHC), gastric cancer (GC), and AFP-producing GC (AFPGC) and identify clinically actionable alterations. Thirty-eight cases of HAS were collected for whole-exome sequencing. Significantly mutated genes were identified. TP53 was the most frequently mutated gene (66%). Hypoxia, TNF-α/NFκB, mitotic spindle assembly, DNA repair, and p53 signaling pathways mutated frequently. Mutagenesis mechanisms in HAS were associated with spontaneous or enzymatic deamination of 5-methylcytosine to thymine and defective homologous recombination-related DNA damage repair. However, LIHC was characteristic of exposure to aflatoxin and aristolochic acid. The copy number variants (CNVs) in HAS was significantly different compared to LIHC, GC, and AFPGC. Aggressive behavior-related CNVs were identified, including local vascular invasion, advanced stages, and adverse prognosis. In 55.26% of HAS patients there existed at least one clinically actionable alteration, including ERBB2, FGFR1, CDK4, EGFR, MET, and MDM2 amplifications and BRCA1/2 mutations. MDM2 amplification with functional TP53 was detected in 5% of HAS patients, which was proved sensitive to MDM2 inhibitors. A total of 10.53% of HAS patients harbored TMB > 10 muts/Mb. These findings improve our understanding of the genomic features of HAS and provide potential therapeutic targets.
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Affiliation(s)
- Rongjie Zhao
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Hongshen Li
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Weiting Ge
- Cancer Institute, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310005, China
| | - Xiuming Zhu
- Department of Medical Oncology, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou 314408, China
| | - Liang Zhu
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310005, China
| | - Xiangbo Wan
- Department of Radical Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 518052, China
| | - Guanglan Wang
- Department of Pathology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Jie Lu
- Department of Gastroenterology, Gongli Hospital of Shanghai Pudong New Area, Shanghai University, Shanghai 200135, China
- Department of Gastroenterology, The Tenth People’s Hospital of Tongji University, Shanghai 311202, China
- Correspondence: (J.L.); (W.H.)
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
- Correspondence: (J.L.); (W.H.)
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Zhang H, Yao Y, Wu J, Zhou J, Zhao C, He J, Xu B. Comprehensive Analysis Identifies and Validates the Tumor Microenvironment Subtypes to Predict Anti-Tumor Therapy Efficacy in Hepatocellular Carcinoma. Front Immunol 2022; 13:838374. [PMID: 35924239 PMCID: PMC9339643 DOI: 10.3389/fimmu.2022.838374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveThe objective of this study was to explore and verify the subtypes in hepatocellular carcinoma based on the immune (lymphocyte and myeloid cells), stem, and stromal cells in the tumor microenvironment and analyze the biological characteristics and potential relevance of each cluster.MethodsWe used the xCell algorithm to calculate cell scores and got subtypes by k-means clustering. In the external validation sets, we verified the conclusion stability by a neural network model. Simultaneously, we speculated the inner connection between clusters by pseudotime trajectory analysis and confirmed it by pathway enrichment, TMB, CNV, etc., analysis.ResultAccording to the results of the consensus cluster, we chose k = 4 as the optimal value and got four different subtypes (C1, C2, C3, and C4) with different biological characteristics based on infiltrating levels of 48 cells in TME. In univariable Cox regression, the hazard ratio (HR) value of C3 versus C1 was 2.881 (95% CI: 1.572–5.279); in multivariable Cox regression, we corrected the age and TNM stage, and the HR value of C3 versus C1 was 2.510 (95% CI: 1.339–4.706). C1 and C2 belonged to the immune-active type, C3 and C4 related to the immune-insensitive type and the potential conversion relationships between clusters. We established a neural network model, and the area under the curves of the neural network model was 0.949 in the testing cohort; the same survival results were also observed in the external validation set. We compared the differences in cell infiltration, immune function, pathway enrichment, TMB, and CNV of four clusters and speculated that C1 and C2 were more likely to benefit from immunotherapy and C3 may benefit from FGF inhibitors.DiscussionOur analysis provides a new approach for the identification of four tumor microenvironment clusters in patients with liver cancer and identifies the biological differences and predicts the immunotherapy efficacy between the four subtypes.
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Affiliation(s)
- Haohan Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Provincial Research Center for Precision Medicine of Cancer, Wuhan, China
| | - Jie Wu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jin Zhou
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chen Zhao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Junju He
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Bin Xu,
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Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J, von Morgen P, Chen Y, Shah H, Sale JE, Alexandrov LB, Stratton MR, Maciejowski J. Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature 2022; 607:799-807. [PMID: 35859169 PMCID: PMC9329121 DOI: 10.1038/s41586-022-04972-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/13/2022] [Indexed: 02/07/2023]
Abstract
The APOBEC3 family of cytosine deaminases has been implicated in some of the most prevalent mutational signatures in cancer1-3. However, a causal link between endogenous APOBEC3 enzymes and mutational signatures in human cancer genomes has not been established, leaving the mechanisms of APOBEC3 mutagenesis poorly understood. Here, to investigate the mechanisms of APOBEC3 mutagenesis, we deleted implicated genes from human cancer cell lines that naturally generate APOBEC3-associated mutational signatures over time4. Analysis of non-clustered and clustered signatures across whole-genome sequences from 251 breast, bladder and lymphoma cancer cell line clones revealed that APOBEC3A deletion diminished APOBEC3-associated mutational signatures. Deletion of both APOBEC3A and APOBEC3B further decreased APOBEC3 mutation burdens, without eliminating them. Deletion of APOBEC3B increased APOBEC3A protein levels, activity and APOBEC3A-mediated mutagenesis in some cell lines. The uracil glycosylase UNG was required for APOBEC3-mediated transversions, whereas the loss of the translesion polymerase REV1 decreased overall mutation burdens. Together, these data represent direct evidence that endogenous APOBEC3 deaminases generate prevalent mutational signatures in human cancer cells. Our results identify APOBEC3A as the main driver of these mutations, indicate that APOBEC3B can restrain APOBEC3A-dependent mutagenesis while contributing its own smaller mutation burdens and dissect mechanisms that translate APOBEC3 activities into distinct mutational signatures.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevan Chu
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 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
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Patrick von Morgen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyang Chen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hina Shah
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, 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
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Abstract
The evolutionary history of hepatobiliary cancers is embedded in their genomes. By analysing their catalogue of somatic mutations and the DNA sequence context in which they occur, it is possible to infer the mechanisms underpinning tumorigenesis. These mutational signatures reflect the exogenous and endogenous origins of genetic damage as well as the capacity of hepatobiliary cells to repair and replicate DNA. Genomic analysis of thousands of patients with hepatobiliary cancers has highlighted the diversity of mutagenic processes active in these malignancies, highlighting a prominent source of the inter-cancer-type, inter-patient, intertumour and intratumoural heterogeneity that is observed clinically. However, a substantial proportion of mutational signatures detected in hepatocellular carcinoma and biliary tract cancer remain of unknown cause, emphasizing the important contribution of processes yet to be identified. Exploiting mutational signatures to retrospectively understand hepatobiliary carcinogenesis could advance preventative management of these aggressive tumours as well as potentially predict treatment response and guide the development of therapies targeting tumour evolution.
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Taura M, Frank JA, Takahashi T, Kong Y, Kudo E, Song E, Tokuyama M, Iwasaki A. APOBEC3A regulates transcription from interferon-stimulated response elements. Proc Natl Acad Sci U S A 2022; 119:e2011665119. [PMID: 35549556 PMCID: PMC9171812 DOI: 10.1073/pnas.2011665119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 04/11/2022] [Indexed: 01/04/2023] Open
Abstract
APOBEC3A (A3A) is a cytidine deaminase that inactivates a variety of viruses through introduction of lethal mutations to the viral genome. Additionally, A3A can suppress HIV-1 transcription in a deaminase-independent manner by binding to the long terminal repeat of proviral HIV-1. However, it is unknown whether A3A targets additional host genomic loci for repression. In this study, we found that A3A suppresses gene expression by binding TTTC doublets that are in close proximity to each other. However, one TTTC motif is sufficient for A3A binding. Because TTTC doublets are present in interferon (IFN)-stimulated response elements (ISRE), we hypothesized that A3A may impact IFN-stimulated gene (ISG) expression. After scanning the human genome for TTTC doublet occurrences, we discovered that these motifs are enriched in the proximal promoters of genes associated with antiviral responses and type I IFN (IFN-I) signaling. As a proof of principle, we examined whether A3A can impact ISG15 expression. We found that A3A binding to the ISRE inhibits phosphorylated STAT-1 binding and suppresses ISG15 induction in response to IFN-I treatment. Consistent with these data, our RNA-sequencing analyses indicate that A3A loss results in increased IFN-I–dependent induction of several ISGs. This study revealed that A3A plays an unexpected role in ISG regulation and suggests that A3A contributes to a negative feedback loop during IFN signaling.
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Affiliation(s)
- Manabu Taura
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- Laboratory of Bioresponse Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 565-0871 Suita, Japan
| | - John A. Frank
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Takehiro Takahashi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06520
| | - Eriko Kudo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- HHMI, Chevy Chase, MD 20815
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