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Journal articles on the topic 'APOBEC family'

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Published: 14 March 2023

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1

Dang, Ying, Xiaojun Wang, Walter J. Esselman, and Yong-Hui Zheng. "Identification of APOBEC3DE as Another Antiretroviral Factor from the Human APOBEC Family." Journal of Virology 80, no. 21 (2006): 10522–33. http://dx.doi.org/10.1128/jvi.01123-06.

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ABSTRACT A tandem arrayed gene cluster encoding seven cytidine deaminase genes is present on human chromosome 22. These are APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H. Three of them, APOBEC3G, APOBEC3F, and APOBEC3B, block replication of human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. In addition, APOBEC3A and APOBEC3C block intracellular retrotransposons and simian immunodeficiency virus (SIV), respectively. In opposition to APOBEC genes, HIV-1 and SIV contain a virion infectivity factor (Vif) that targets APOBEC3F and APOBEC3G for polyu
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2

Chu, Charles C., Stefano Vergani, Xiao-Jie Yan, et al. "APOBEC gene family expression and hallmarks in chronic lymphocytic leukemia." Journal of Immunology 198, no. 1_Supplement (2017): 76.16. http://dx.doi.org/10.4049/jimmunol.198.supp.76.16.

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Abstract The hallmark activity of APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family of cytidine deaminases, including activation-induced deaminase (AID) and APOBEC3 genes, has been detected in somatic mutation signatures by ultra-deep sequencing of the genomes of many cancers, including chronic lymphocytic leukemia (CLL). The acquisition of these mutations is hypothesized to lead to the progression towards aggressive disease in cancer. To examine this in CLL, we tested if increased APOBEC family member gene expression in CLL cells, as measured by microarray and quanti
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3

Caswell, Deborah, and Charles Swanton. "Distinct Mutagenic Activity of APOBEC3G Cytidine Deaminase Identified in Bladder Cancer." Cancer Research 83, no. 4 (2023): 487–88. http://dx.doi.org/10.1158/0008-5472.can-22-3598.

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Abstract The APOBEC cytidine deaminase enzyme family is linked to mutational signatures identified in cancer. While previous work has provided insights into the role of APOBEC3A and APOBEC3B in mutational processes in cancer, understanding of the mutational signatures induced by other APOBEC family members is limited. In this issue of Cancer Research, Liu and colleagues investigated the role of APOBEC3G (A3G) in bladder cancer. The authors revealed that transgenic expression of A3G in a murine bladder cancer model promotes tumorigenesis and induces a unique mutational signature distinct from p
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4

Chu, Charles C., Xiao-Jie Yan, Arvind Dhayalan, et al. "The Correlation of APOBEC Gene Family Member Expression with Worse CLL Patient Outcome Suggests a Role in CLL Mutational Evolution." Blood 126, no. 23 (2015): 363. http://dx.doi.org/10.1182/blood.v126.23.363.363.

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Abstract A mutational signature consistent with APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) activity has been identified in somatic mutations found in large-scale surveys of ultra-deep sequencing data from many human cancers including chronic lymphocytic leukemia (CLL). APOBEC is a cytidine deaminase family made up of eleven genes, including AID (activation-induced cytidine deaminase) and APOBEC3B, both of which have been implicated in somatic mutation in various cancers, including CLL. These observations have led to the hypothesis that APOBEC cytidine deaminases may b
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5

Mikl, Marie C., Ian N. Watt, Mason Lu, et al. "Mice Deficient in APOBEC2 and APOBEC3." Molecular and Cellular Biology 25, no. 16 (2005): 7270–77. http://dx.doi.org/10.1128/mcb.25.16.7270-7277.2005.

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ABSTRACT The activation-induced deaminase/apolipoprotein B-editing catalytic subunit 1 (AID/APOBEC) family comprises four groups of proteins. Both AID, a lymphoid-specific DNA deaminase that triggers antibody diversification, and APOBEC2 (function unknown) are found in all vertebrates examined. In contrast, APOBEC1, an RNA-editing enzyme in gastrointestinal cells, and APOBEC3 are restricted to mammals. The function of most APOBEC3s, of which there are seven in human but one in mouse, is unknown, although several human APOBEC3s act as host restriction factors that deaminate human immunodeficien
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6

Harris, Reuben S., Matthew C. Jarvis, Michael A. Carpenter, et al. "Abstract P5-12-01: Apobec mutation signature in breast cancer explained by combinatorial action of apobec3a and apobec3b." Cancer Research 82, no. 4_Supplement (2022): P5–12–01—P5–12–01. http://dx.doi.org/10.1158/1538-7445.sabcs21-p5-12-01.

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Abstract Background: Mutations drive the initiation and progression of cancer. A leading druggable source of mutation in cancer is enzymatic deamination of single-stranded DNA cytosines by cellular APOBEC3 enzymes. Cytosine-to-uracil deamination can result in a variety of different mutational outcomes including DNA breakage and chromosomal aberrations as well as single base substitution mutations. The latter are comprised of C-to-T and C-to-G mutations in TCA or TCT trinucleotides and attributable to the intrinsic preference of several APOBEC3 family members for binding to these motifs. This m
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7

Talluri, Srikanth, Mehmet Kemal Samur, Jialan Shi, et al. "Critical Role for Apobec and Its Interacting Partners in Mediating Mutations and Cell Growth in Multiple Myeloma (MM)." Blood 132, Supplement 1 (2018): 4462. http://dx.doi.org/10.1182/blood-2018-99-118441.

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Abstract The APOBEC family of cytidine deaminases include AID (activity induced deaminase) and 10 related APOBEC enzymes (A1,A2,A3A,A3B,A3C,A3D,A3F,A3G,A3H and A4). AID is well studied for its role in somatic hyper mutation and class switch recombination of immunoglobulin genes. APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) have been shown to have roles in mRNA editing and in antiviral immunity. Recently, a causal role for the AID/APOBECs in inducing somatic mutations in myeloma has been proposed and we have previously published that APOBEC signature mutations as a
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8

Talluri, Srikanth, Mehmet Kemal Samur, Leutz Buon, et al. "Dysregulated Aid/Apobec Family Proteins Promote Genomic Instability in Multiple Myeloma." Blood 128, no. 22 (2016): 803. http://dx.doi.org/10.1182/blood.v128.22.803.803.

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Abstract The AID/APOBEC family of cytidine deaminase proteins includes AID (activity induced deaminase), and 10 related APOBEC enzymes (A1, A2, A3A, A3B, A3C, A3D, A3F, A3G, A3H and A4). AID has been well-studied for its role in somatic hyper mutation and class switch recombination of immunoglobulin genes whereas APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) have been shown to have roles in mRNA editing and in antiviral immunity. Dysregulated activity of APOBECs causes C >T transitions or C>G, C>A transversions in DNA. We have recently shown APOBEC signatu
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9

Köck, Josef, and Hubert E. Blum. "Hypermutation of hepatitis B virus genomes by APOBEC3G, APOBEC3C and APOBEC3H." Journal of General Virology 89, no. 5 (2008): 1184–91. http://dx.doi.org/10.1099/vir.0.83507-0.

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Hepatitis B virus (HBV) is a DNA virus that causes liver disease and replicates by reverse transcription of an RNA template. Previous studies have reported that HBV genomes bearing G→A hypermutation are present at low frequency in human serum. These mutations are most likely due to the activity of apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) cytosine deaminases, cellular proteins known to confer innate immunity against retroviruses by generating lethal hypermutations in viral genomes. This study assessed APOBEC3G, APOBEC3C and APOBEC3H, three members of this protein
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10

Granadillo Rodríguez, Milaid, Ben Flath, and Linda Chelico. "The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead." Open Biology 10, no. 12 (2020): 200188. http://dx.doi.org/10.1098/rsob.200188.

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Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse ‘off-target’ cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the
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11

Xu, Wendy Kaichun, Hyewon Byun, and Jaquelin P. Dudley. "The Role of APOBECs in Viral Replication." Microorganisms 8, no. 12 (2020): 1899. http://dx.doi.org/10.3390/microorganisms8121899.

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Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was disco
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Liu, Qin, Yue-wen Luo, Ruo-yan Cao, et al. "Association between APOBEC3H-Mediated Demethylation and Immune Landscape in Head and Neck Squamous Carcinoma." BioMed Research International 2020 (July 25, 2020): 1–17. http://dx.doi.org/10.1155/2020/4612375.

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Immunotherapy has been demonstrated as a promising strategy in controlling head and neck squamous cell carcinoma (HNSC). The AID/APOBEC family is well characterized as DNA mutator and considered to play critical roles in immune responses in HNSC. However, the expression pattern and deamination-dependent demethylation roles of AID/APOBECs in HNSC are unclear. In this study, the RNA-seq and DNA methylation profiles of HNSC from TCGA database and cell-based experiments were applied to analyze the relationships between AID/APOBEC expression levels, patients’ clinical outcomes, methylation alterati
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13

Cheng, Adam Z., Sofia N. Moraes, Nadine M. Shaban, et al. "APOBECs and Herpesviruses." Viruses 13, no. 3 (2021): 390. http://dx.doi.org/10.3390/v13030390.

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The apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of DNA cytosine deaminases provides a broad and overlapping defense against viral infections. Successful viral pathogens, by definition, have evolved strategies to escape restriction by the APOBEC enzymes of their hosts. HIV-1 and related retroviruses are thought to be the predominant natural substrates of APOBEC enzymes due to obligate single-stranded (ss)DNA replication intermediates, abundant evidence for cDNA strand C-to-U editing (genomic strand G-to-A hypermutation), and a potent APOBEC degradation mecha
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14

Guo, Honghong, Ling Zhu, Lu Huang, et al. "APOBEC Alteration Contributes to Tumor Growth and Immune Escape in Pan-Cancer." Cancers 14, no. 12 (2022): 2827. http://dx.doi.org/10.3390/cancers14122827.

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The accumulating evidence demonstrates that the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC), DNA-editing protein plays an important role in the molecular pathogenesis of cancer. In particular, the APOBEC3 family was shown to induce tumor mutations by an aberrant DNA editing mechanism. However, knowledge regarding the reconstitution of the APOBEC family genes across cancer types is still lacking. Here, we systematically analyzed the molecular alterations, immuno-oncological features, and clinical relevance of the APOBEC family in pan-cancer. We found that APOBEC gen
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15

Delebecque, Frédéric, Rodolphe Suspène, Sara Calattini, et al. "Restriction of Foamy Viruses by APOBEC Cytidine Deaminases." Journal of Virology 80, no. 2 (2006): 605–14. http://dx.doi.org/10.1128/jvi.80.2.605-614.2006.

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ABSTRACT Foamy viruses (FVs) are nonpathogenic retroviruses infecting many species of mammals, notably primates, cattle, and cats. We have examined whether members of the apolipoprotein B-editing catalytic polypeptide-like subunit (APOBEC) family of antiviral cytidine deaminases restrict replication of simian FV. We show that human APOBEC3G is a potent inhibitor of FV infectivity in cell culture experiments. This antiviral activity is associated with cytidine editing of the viral genome. Both molecular FV clones and primary uncloned viruses were susceptible to APOBEC3G, and viral infectivity w
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16

Wiegand, Heather L., and Bryan R. Cullen. "Inhibition of Alpharetrovirus Replication by a Range of Human APOBEC3 Proteins." Journal of Virology 81, no. 24 (2007): 13694–99. http://dx.doi.org/10.1128/jvi.01646-07.

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ABSTRACT The mammalian APOBEC3 family of cytidine deaminases includes members that can act as potent inhibitors of retroviral infectivity and retrotransposon mobility. Here, we have examined whether the alpharetrovirus Rous sarcoma virus (RSV) is susceptible to inhibition by a range of human APOBEC3 proteins. We report that RSV is highly susceptible to inhibition by human APOBEC3G, APOBEC3F, and APOBEC3B and moderately susceptible to inhibition by human APOBEC3C and APOBEC3A. For all five proteins, inhibition of RSV infectivity was associated with selective virion incorporation and with C-to-T
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17

Zheng, Yong-Hui, Dan Irwin, Takeshi Kurosu, Kenzo Tokunaga, Tetsutaro Sata, and B. Matija Peterlin. "Human APOBEC3F Is Another Host Factor That Blocks Human Immunodeficiency Virus Type 1 Replication." Journal of Virology 78, no. 11 (2004): 6073–76. http://dx.doi.org/10.1128/jvi.78.11.6073-6076.2004.

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ABSTRACT Recently, APOBEC3G has been identified as a host factor that blocks retroviral replication. It introduces G to A hypermutations in newly synthesized minus strand viral cDNA at the step of reverse transcription in target cells. Here, we identified the human APOBEC3F protein as another host factor that blocks human immunodeficiency virus type 1 (HIV-1) replication. Similar to APOBEC3G, APOBEC3F also induced G to A hypermutations in HIV genomic DNA, and the viral Vif protein counteracted its activity. Thus, APOBEC family members might have evolved as a general defense mechanism of the bo
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18

Walker, Brian A., Christopher P. Wardell, Alexander Murison, et al. "Apobec Family Mutational Signatures Are Associated with Poor Prognosis Translocations in Multiple Myeloma." Blood 124, no. 21 (2014): 723. http://dx.doi.org/10.1182/blood.v124.21.723.723.

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Abstract Aberrant chromosomal translocations are seen in ~40% of presenting patients and predominantly involve the IGH locus at 14q32. The five main translocations involving the IGH locus are t(4;14), t(6;14), t(11;14), t(14;16) and t(14;20), which result in over-expression of MMSET/FGFR3, CCND3, CCND1, MAF and MAFB, respectively. In previous clinical trials we have shown that the t(4;14), t(14;16) and t(14;20) are associated with a poor prognosis. In initial sequencing studies of myeloma it has been noted that the spectrum of mutations fall into two groups, one of which is characterised by an
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19

Malim, Michael H. "APOBEC proteins and intrinsic resistance to HIV-1 infection." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1517 (2008): 675–87. http://dx.doi.org/10.1098/rstb.2008.0185.

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Members of the APOBEC family of cellular polynucleotide cytidine deaminases, most notably APOBEC3G and APOBEC3F, are potent inhibitors of HIV-1 infection. Wild type HIV-1 infections are largely spared from APOBEC3G/F function through the action of the essential viral protein, Vif. In the absence of Vif, APOBEC3G/F are encapsidated by budding virus particles leading to excessive cytidine (C) to uridine (U) editing of negative sense reverse transcripts in newly infected cells. This registers as guanosine (G) to adenosine (A) hypermutations in plus-stranded cDNA. In addition to this profoundly de
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Wurtzer, Sebastien, Armelle Goubard, Fabrizio Mammano, et al. "Functional Central Polypurine Tract Provides Downstream Protection of the Human Immunodeficiency Virus Type 1 Genome from Editing by APOBEC3G and APOBEC3B." Journal of Virology 80, no. 7 (2006): 3679–83. http://dx.doi.org/10.1128/jvi.80.7.3679-3683.2006.

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ABSTRACT Lentiviruses utilize two polypurine tracts for initiation of plus-strand viral DNA synthesis. We have examined to what extent human immunodeficiency virus type 1 plus-strand initiation at the central polypurine tract (cPPT) could protect the viral genome from DNA editing by APOBEC3G and APOBEC3B. The presence of a functional cPPT, but not of a mutated cPPT, extensively reduced editing by both APOBEC3G and APOBEC3B of sequences downstream, but not upstream, of the cPPT, with significant protection observed as far as 400 bp downstream. Thus, in addition to other potential functions, the
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Vieira, Valdimara C., and Marcelo A. Soares. "The Role of Cytidine Deaminases on Innate Immune Responses against Human Viral Infections." BioMed Research International 2013 (2013): 1–18. http://dx.doi.org/10.1155/2013/683095.

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The APOBEC family of proteins comprises deaminase enzymes that edit DNA and/or RNA sequences. The APOBEC3 subgroup plays an important role on the innate immune system, acting on host defense against exogenous viruses and endogenous retroelements. The role of APOBEC3 proteins in the inhibition of viral infection was firstly described for HIV-1. However, in the past few years many studies have also shown evidence of APOBEC3 action on other viruses associated with human diseases, including HTLV, HCV, HBV, HPV, HSV-1, and EBV. APOBEC3 inhibits these viruses through a series of editing-dependent an
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Holland, Stephen J., Lesley M. Berghuis, Justin J. King, et al. "Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys." Proceedings of the National Academy of Sciences 115, no. 14 (2018): E3211—E3220. http://dx.doi.org/10.1073/pnas.1720871115.

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Cytidine deaminases of the AID/APOBEC family catalyze C-to-U nucleotide transitions in mRNA or DNA. Members of the APOBEC3 branch are involved in antiviral defense, whereas AID contributes to diversification of antibody repertoires in jawed vertebrates via somatic hypermutation, gene conversion, and class switch recombination. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the generation of somatic diversity of the variable lymphocyte receptors (VLRs). Expression studies linked CDA1 and CDA2 genes to the assembly of VLRA/C genes in T-like
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Chen, Xiaojiang S. "Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions." Viruses 13, no. 3 (2021): 497. http://dx.doi.org/10.3390/v13030497.

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Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) proteins belong to a family of deaminase proteins that can catalyze the deamination of cytosine to uracil on single-stranded DNA or/and RNA. APOBEC proteins are involved in diverse biological functions, including adaptive and innate immunity, which are critical for restricting viral infection and endogenous retroelements. Dysregulation of their functions can cause undesired genomic mutations and RNA modification, leading to various associated diseases, such as hyper-IgM syndrome and cancer. This review focuses on the structural
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Ghorbani, Atefeh, Justin J. King, and Mani Larijani. "The optimal pH of AID is skewed from that of its catalytic pocket by DNA-binding residues and surface charge." Biochemical Journal 479, no. 1 (2022): 39–55. http://dx.doi.org/10.1042/bcj20210529.

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Activation-induced cytidine deaminase (AID) is a member of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases. AID mutates immunoglobulin loci to initiate secondary antibody diversification. The APOBEC3 (A3) sub-branch mutates viral pathogens in the cytosol and acidic endosomal compartments. Accordingly, AID functions optimally near-neutral pH, while most A3s are acid-adapted (optimal pH 5.5–6.5). To gain a structural understanding for this pH disparity, we constructed high-resolution maps of AID catalytic activity vs pH. We found AID's
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Blanc, Valerie, Jeffrey O. Henderson, Elizabeth P. Newberry, Susan Kennedy, Jianyang Luo, and Nicholas O. Davidson. "Targeted Deletion of the Murine apobec-1 Complementation Factor (acf) Gene Results in Embryonic Lethality." Molecular and Cellular Biology 25, no. 16 (2005): 7260–69. http://dx.doi.org/10.1128/mcb.25.16.7260-7269.2005.

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ABSTRACT apobec-1 complementation factor (ACF) is an hnRNP family member which functions as the obligate RNA binding subunit of the core enzyme mediating C-to-U editing of the nuclear apolipoprotein B (apoB) transcript. ACF binds to both apoB RNA and apobec-1, the catalytic cytidine deaminase, which then results in site-specific posttranscriptional editing of apoB mRNA. Targeted deletion of apobec1 eliminates C-to-U editing of apoB mRNA but is otherwise well tolerated. However, the functions and potential targets of ACF beyond apoB mRNA editing are unknown. Here we report the results of genera
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Stewart, Jessica A., Grant Schauer, and Ashok S. Bhagwat. "Visualization of uracils created by APOBEC3A using UdgX shows colocalization with RPA at stalled replication forks." Nucleic Acids Research 48, no. 20 (2020): e118-e118. http://dx.doi.org/10.1093/nar/gkaa845.

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Abstract The AID/APOBEC enzymes deaminate cytosines in single-stranded DNA (ssDNA) and play key roles in innate and adaptive immunity. The resulting uracils cause mutations and strand breaks that inactivate viruses and diversify antibody repertoire. Mutational evidence suggests that two members of this family, APOBEC3A (A3A) and APOBEC3B, deaminate cytosines in the lagging-strand template during replication. To obtain direct evidence for the presence of these uracils, we engineered a protein that covalently links to DNA at uracils, UdgX, for mammalian expression and immunohistochemistry. We sh
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Mayekar, Manasi, Deborah Caswell, Natalie Vokes, et al. "Abstract 2197: Targeted cancer therapy induces APOBEC fueling the evolution of drug resistance." Cancer Research 82, no. 12_Supplement (2022): 2197. http://dx.doi.org/10.1158/1538-7445.am2022-2197.

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Abstract Introduction: Increasing our understanding of drivers of mutagenesis in lung cancer is critical in our efforts to prevent tumor reoccurrence and resistance. Results: Using the multi-region TRACERx lung cancer study, we uncovered that APOBEC3B is significantly upregulated when compared with other APOBEC family members in EGFR driven lung cancer and identified subclonal enrichment of APOBEC mutational signatures. To model APOBEC mutagenesis in lung cancer, several novel EGFR mutant mouse models containing a human APOBEC3B transgene were generated. Using these models, it was uncovered th
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Siu, Karen, Azmiri Sultana, Farshad Azimi, and Jeffrey Lee. "Structural determinants of ssDNA- and HIV-1 Vif-binding in APOBEC3F." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C118. http://dx.doi.org/10.1107/s2053273314098817.

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The human APOBEC3 family of DNA cytosine deaminases serves as a front-line intrinsic immune response to inhibit the replication of diverse retroviruses. APOBEC3F and APOBEC3G are the most potent factors against HIV-1. As a countermeasure, HIV-1 viral infectivity factor (Vif) targets APOBEC3s for proteasomal degradation. Here, we report the crystal structure of the Vif-binding domain in APOBEC3F and a novel assay to assess Vif-APOBEC3 binding. Our results reveal a conserved, amphipathic surface in APOBEC3s that is critical for Vif binding. APOBEC3F-Vif interaction is likely mediated via electro
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Takaori-Kondo, Akifumi. "APOBEC Family Proteins: Novel Antiviral Innate Immunity." International Journal of Hematology 83, no. 3 (2006): 213–16. http://dx.doi.org/10.1532/ijh97.05187.

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Riva, Giuseppe, Camilla Albano, Francesca Gugliesi, et al. "HPV Meets APOBEC: New Players in Head and Neck Cancer." International Journal of Molecular Sciences 22, no. 3 (2021): 1402. http://dx.doi.org/10.3390/ijms22031402.

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Besides smoking and alcohol, human papillomavirus (HPV) is a factor promoting head and neck squamous cell carcinoma (HNSCC). In some human tumors, including HNSCC, a number of mutations are caused by aberrantly activated DNA-modifying enzymes, such as the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) family of cytidine deaminases. As the enzymatic activity of APOBEC proteins contributes to the innate immune response to viruses, including HPV, the role of APOBEC proteins in HPV-driven head and neck carcinogenesis has recently gained increasing attention. Ongoing resea
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Doehle, Brian P., Alexandra Schäfer, Heather L. Wiegand, Hal P. Bogerd, and Bryan R. Cullen. "Differential Sensitivity of Murine Leukemia Virus to APOBEC3-Mediated Inhibition Is Governed by Virion Exclusion." Journal of Virology 79, no. 13 (2005): 8201–7. http://dx.doi.org/10.1128/jvi.79.13.8201-8207.2005.

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ABSTRACT While members of the APOBEC3 family of human intrinsic resistance factors are able to restrict the replication of Vif-deficient forms of human immunodeficiency virus type 1 (HIV-1), they are unable to block replication of wild-type HIV-1 due to the action of Vif, which induces their degradation. In contrast, HIV-1 Vif is unable to block inhibition mediated by APOBEC3 proteins expressed by several heterologous species, including mice. Here, we have asked whether the simple retrovirus murine leukemia virus (MLV) is sensitive to restriction by the cognate murine or heterologous, human AP
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Lerner, Taga, F. Papavasiliou, and Riccardo Pecori. "RNA Editors, Cofactors, and mRNA Targets: An Overview of the C-to-U RNA Editing Machinery and Its Implication in Human Disease." Genes 10, no. 1 (2018): 13. http://dx.doi.org/10.3390/genes10010013.

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One of the most prevalent epitranscriptomic modifications is RNA editing. In higher eukaryotes, RNA editing is catalyzed by one of two classes of deaminases: ADAR family enzymes that catalyze A-to-I (read as G) editing, and AID/APOBEC family enzymes that catalyze C-to-U. ADAR-catalyzed deamination has been studied extensively. Here we focus on AID/APOBEC-catalyzed editing, and review the emergent knowledge regarding C-to-U editing consequences in the context of human disease.
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Anant, Shrikant, Debnath Mukhopadhyay, Vakadappu Sankaranand, Susan Kennedy, Jeffrey O. Henderson, and Nicholas O. Davidson. "ARCD-1, an apobec-1-related cytidine deaminase, exerts a dominant negative effect on C to U RNA editing." American Journal of Physiology-Cell Physiology 281, no. 6 (2001): C1904—C1916. http://dx.doi.org/10.1152/ajpcell.2001.281.6.c1904.

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Mammalian apolipoprotein B (apoB) C to U RNA editing is catalyzed by a multicomponent holoenzyme containing a single catalytic subunit, apobec-1. We have characterized an apobec-1 homologue, ARCD-1, located on chromosome 6p21.1, and determined its role in apoB mRNA editing. ARCD-1 mRNA is ubiquitously expressed; phylogenetic analysis reveals it to be a distant member of the RNA editing family. Recombinant ARCD-1 demonstrates cytidine deaminase and apoB RNA binding activity but does not catalyze C to U RNA editing, either in vitro or in vivo. Although not competent itself to mediate deamination
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34

Shapiro, Kate, Maxwell Shapiro, and Thomas MacCarthy. "#84: Evolutionary Pressure from APOBEC Causes an Underrepresentation of TC Motifs in Human Polyomavirus." Journal of the Pediatric Infectious Diseases Society 10, Supplement_1 (2021): S14—S15. http://dx.doi.org/10.1093/jpids/piaa170.043.

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Abstract Background Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) is a family of enzymes found in mammals that deaminate cytidine to uridine on ssDNA, facilitating a C-to-T mutation. Less commonly, APOBEC effectively mutates C-to-G as well. APOBEC has the potential to mutate the viral genome, rendering the virus nonproductive. The enzyme targets certain mutational motifs, also known as hotspots: most APOBECs deaminate at TC motifs. We hypothesize that human polyomaviruses (hPyV) have an under-representation of TC hotspots in their genomes to avoid APOBEC targeting.
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Pilzecker, Bas, Olimpia Alessandra Buoninfante, Colin Pritchard, et al. "PrimPol prevents APOBEC/AID family mediated DNA mutagenesis." Nucleic Acids Research 44, no. 10 (2016): 4734–44. http://dx.doi.org/10.1093/nar/gkw123.

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36

Conticello, Silvestro G. "The AID/APOBEC family of nucleic acid mutators." Genome Biology 9, no. 6 (2008): 229. http://dx.doi.org/10.1186/gb-2008-9-6-229.

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37

Kazuma, Yasuhiro, Kotaro Shirakawa, Anamaria Daniela Sarca, et al. "Interactome Analysis of APOBEC3B in Multiple Myeloma." Blood 134, Supplement_1 (2019): 1259. http://dx.doi.org/10.1182/blood-2019-126856.

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Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) family proteins restrict retroviruses and retrotransposons by inducing hypermutation or degradation of the replication intermediates through their DNA cytidine deaminase activity. APOBECs can also act as endogenous sources of DNA damage that mutate many human cancers. Accumulation of APOBEC signature mutations is associated with disease progression and poor overall survival in multiple myeloma (Walker et al. Nat Commun, 2015). Among APOBEC3 enzymes, APOBEC3B (A3B) is the only family member that is predominantly located in
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Chu, Charles C., Piers E. M. Patten, Thomas MacCarthy, et al. "IGHV-D-J Ultra-Deep Sequencing Reveals APOBEC and AID Targeted Mutations during Clonal Evolution of CLL in a Xenograft Mouse Model." Blood 124, no. 21 (2014): 300. http://dx.doi.org/10.1182/blood.v124.21.300.300.

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Abstract Targeted ultra-deep sequencing of chronic lymphocytic leukemia (CLL) cells has enabled the assessment of subclone development based on mutations in the IGHV-D-J signature sequence in the dominant CLL clone. We have utilized the Roche 454 FLX pyrosequencing system, which can generate long sequencing reads containing both the immunoglobulin variable region (IGHV-D-J) and part of the immunoglobulin μ constant region (IGHM) in a single sequence, to analyze the mutational characteristics of newly evolved subclones to determine if they derive from AID/APOBEC activity. APOBEC (apolipoprotein
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39

Browne, Edward P., and Dan R. Littman. "Species-Specific Restriction of Apobec3-Mediated Hypermutation." Journal of Virology 82, no. 3 (2007): 1305–13. http://dx.doi.org/10.1128/jvi.01371-07.

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ABSTRACT Apobec proteins are a family of cellular cytidine deaminases, among which several members have been shown to have potent antiviral properties. This antiviral activity is associated with the ability to cause hypermutation of retroviral cDNA. However, recent research has indicated that Apobec proteins are also able to inhibit retroviruses by other mechanisms that are independent of their deaminase activity. We have compared the antiviral activities of human and murine Apobec3 (A3) proteins, and we have found that, consistent with previous reports, human immunodeficiency virus (HIV) is a
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Smith, Harold C., Ryan P. Bennett, Ayse Kizilyer, William M. McDougall, and Kimberly M. Prohaska. "Functions and regulation of the APOBEC family of proteins." Seminars in Cell & Developmental Biology 23, no. 3 (2012): 258–68. http://dx.doi.org/10.1016/j.semcdb.2011.10.004.

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41

Verhalen, Brandy, Gabriel J. Starrett, Reuben S. Harris, and Mengxi Jiang. "Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses." Journal of Virology 90, no. 14 (2016): 6379–86. http://dx.doi.org/10.1128/jvi.00771-16.

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ABSTRACTThe APOBEC3 family of DNA cytosine deaminases has important roles in innate immunity and cancer. It is unclear how DNA tumor viruses regulate these enzymes and how these interactions, in turn, impact the integrity of both the viral and cellular genomes. Polyomavirus (PyVs) are small DNA pathogens that contain oncogenic potentials. In this study, we examined the effects of PyV infection on APOBEC3 expression and activity. We demonstrate that APOBEC3B is specifically upregulated by BK polyomavirus (BKPyV) infection in primary kidney cells and that the upregulated enzyme is active. We fur
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42

Chelico, Linda. "Special Issue “APOBECs and Virus Restriction”." Viruses 13, no. 8 (2021): 1613. http://dx.doi.org/10.3390/v13081613.

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43

Stefanovska, Bojana, Kevin Lin, Benjamin Troness, Chad Myers, and Reuben Harris. "Abstract P2-17-01: Targeted CRISPR screen to identify synthetic lethal combinations between APOBEC3B and DNA repair." Cancer Research 83, no. 5_Supplement (2023): P2–17–01—P2–17–01. http://dx.doi.org/10.1158/1538-7445.sabcs22-p2-17-01.

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Abstract APOBEC-catalyzed deamination of cytosine bases is the largest enzymatic and second largest overall source of mutation in cancer. One member from the APOBEC family of enzymes, APOBEC3B (A3B) is overexpressed and dysregulated in many different cancer types. In addition to hallmark C-to-T transitions and C-to-G transversions, APOBEC-catalyzed uracil lesions can be processed into single- and double-strand DNA breaks. Therefore, A3B-positive tumors are under continual stress to repair DNA breaks and may be vulnerable to DNA repair inhibition. Previous results from the Harris lab have ident
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Vázquez, Nancy, Hana Schmeisser, Michael A. Dolan, Joseph Bekisz, Kathryn C. Zoon та Sharon M. Wahl. "Structural variants of IFNα preferentially promote antiviral functions". Blood 118, № 9 (2011): 2567–77. http://dx.doi.org/10.1182/blood-2010-12-325027.

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AbstractIFNα, a cytokine with multiple functions in innate and adaptive immunity and a potent inhibitor of HIV, exerts antiviral activity, in part, by enhancing apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (APOBEC3) family members. Although IFNα therapy is associated with reduced viral burden, this cytokine also mediates immune dysfunction and toxicities. Through detailed mapping of IFNα receptor binding sites, we generated IFNα hybrids and mutants and determined that structural changes in the C-helix alter the ability of IFN to limit retroviral activity. Selective IFNα co
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Kanabe, Belan O., Mehmet Ozaslan, Sherwan Ahmed Aziz, Mustafa S. Al-Attar, İbrahim Halil Kılıç, and Rozhgar A. Khailany. "Expression patterns of LncRNA-GAS5 and its target APOBEC3C gene through miR-103 in breast cancer patients." Cellular and Molecular Biology 67, no. 3 (2021): 5–10. http://dx.doi.org/10.14715/cmb/2021.67.3.2.

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Early diagnosis of breast cancer can increase the survivability of the patients and the patient’s quality of life. There is growing evidence demonstrating the active role of LncRNA-GAS5 and miR-103 in cancer biology. APOBEC enzymes are important players in immunity and may contribute to carcinogenesis. Mutation and expression alteration in the APOBEC gene family was found to have a strong correlation with breast cancer risk. This study aimed to evaluate the expression level of lncRNA-GAS5 and its target APOBEC3C in women with breast cancer through expression evaluation of miR-103. Moreover, th
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Zotova, Irina, Elena Stepchenkova, and Youri Pavlov. "Contribution of cytosine desaminases of AID/APOBEC family to carcinogenesis." Biological Communications 64, no. 2 (2019): 110–23. http://dx.doi.org/10.21638/spbu03.2019.203.

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47

Salter, Jason D., Ryan P. Bennett, and Harold C. Smith. "The APOBEC Protein Family: United by Structure, Divergent in Function." Trends in Biochemical Sciences 41, no. 7 (2016): 578–94. http://dx.doi.org/10.1016/j.tibs.2016.05.001.

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48

Turelli, Priscilla, Alexandra Liagre-Quazzola, Bastien Mangeat, Sonia Verp, Stephanie Jost, and Didier Trono. "APOBEC3-Independent Interferon-Induced Viral Clearance in Hepatitis B Virus Transgenic Mice." Journal of Virology 82, no. 13 (2008): 6585–90. http://dx.doi.org/10.1128/jvi.00216-08.

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ABSTRACT Interferon (IFN) has been part of the standard treatment of chronic hepatitis B infection for more than 2 decades, yet the mechanism of action of this antiviral remains poorly understood. It was recently observed that members of the human APOBEC family of cytidine deaminases endowed with anti-hepatitis B virus (HBV) activity are upregulated by type I and II IFNs. However, we demonstrated that, in tissue culture, these cellular enzymes are not essential effectors of the anti-HBV action of these cytokines. Here, we show that murine APOBEC3 (muA3) can also block HBV replication. While ex
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Rogozin, Igor B., Malay K. Basu, I. King Jordan, Youri I. Pavlov, and Eugene V. Koonin. "APOBEC4, a New Member of the AID/APOBEC Family of Polynucleotide (Deoxy)Cytidine Deaminases Predicted by Computational Analysis." Cell Cycle 4, no. 9 (2005): 1281–85. http://dx.doi.org/10.4161/cc.4.9.1994.

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50

Anderson, Brett D., та Reuben S. Harris. "Transcriptional regulation of APOBEC3 antiviral immunity through the CBF-β/RUNX axis". Science Advances 1, № 8 (2015): e1500296. http://dx.doi.org/10.1126/sciadv.1500296.

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A diverse set of innate immune mechanisms protects cells from viral infections. The APOBEC3 family of DNA cytosine deaminases is an integral part of these defenses. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H would have the potential to destroy HIV-1 complementary DNA replication intermediates if not for neutralization by a proteasomal degradation mechanism directed by the viral protein Vif. At the core of this complex, Vif heterodimerizes with the transcription cofactor CBF-β, which results in fewer transcription complexes between CBF-β and its normal RUNX partners. Recent studie
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