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Cancer Cell Apr 2024APOBEC3 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...
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.
Topics: Humans; Neoplasms; Mutagenesis; Cytidine Deaminase; APOBEC Deaminases
PubMed: 38593778
DOI: 10.1016/j.ccell.2024.03.010 -
Science (New York, N.Y.) Nov 2023Historically, mpox has been characterized as an endemic zoonotic disease that transmits through contact with the reservoir rodent host in West and Central Africa....
Historically, mpox has been characterized as an endemic zoonotic disease that transmits through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were detected spreading internationally beyond countries with known endemic reservoirs. When the first cases from 2022 were sequenced, they shared 42 nucleotide differences from the closest mpox virus (MPXV) previously sampled. Nearly all these mutations are characteristic of the action of APOBEC3 deaminases, host enzymes with antiviral function. Assuming APOBEC3 editing is characteristic of human MPXV infection, we developed a dual-process phylogenetic molecular clock that-inferring a rate of ~6 APOBEC3 mutations per year-estimates that MPXV has been circulating in humans since 2016. These observations of sustained MPXV transmission present a fundamental shift to the perceived paradigm of MPXV epidemiology as a zoonosis and highlight the need for revising public health messaging around MPXV as well as outbreak management and control.
Topics: Animals; Humans; Africa, Central; Africa, Western; APOBEC Deaminases; Disease Outbreaks; Mpox (monkeypox); Monkeypox virus; Mutation; Phylogeny; Viral Zoonoses; RNA Editing
PubMed: 37917680
DOI: 10.1126/science.adg8116 -
Molecular & Cellular Proteomics : MCP May 2024Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements....
Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination-independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence are not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and mapped a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein-folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology. Data are available via ProteomeXchange with the identifier PXD044275.
Topics: Humans; Cytidine Deaminase; Protein Interaction Maps; Deamination; APOBEC Deaminases; Aminohydrolases; HEK293 Cells; Cytosine Deaminase; APOBEC-3G Deaminase; Spliceosomes; Protein Binding; Mass Spectrometry; RNA; Minor Histocompatibility Antigens
PubMed: 38548018
DOI: 10.1016/j.mcpro.2024.100755 -
Nature Communications Jul 2023The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health....
The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C > T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil.
Topics: Animals; Humans; Chikungunya virus; Brazil; Chikungunya Fever; Yellow Fever; Zika Virus; Nucleotides; Zika Virus Infection
PubMed: 37479700
DOI: 10.1038/s41467-023-40099-y -
Science Advances Sep 2023CRISPR nucleases generate a broad spectrum of mutations that includes undesired editing outcomes. Here, we develop optimized C-to-T base editing systems for the...
CRISPR nucleases generate a broad spectrum of mutations that includes undesired editing outcomes. Here, we develop optimized C-to-T base editing systems for the generation of precise loss- or gain-of-function alleles in and identify temperature as a crucial parameter for efficiency. We find that a variant of the widely used APOBEC1 deaminase has attenuated activity at 18° to 29°C and shows considerable dose-dependent toxicity. In contrast, the temperature-tolerant evoCDA1 domain mediates editing of typically more than 90% of alleles and is substantially better tolerated. Furthermore, formation of undesired mutations is exceptionally rare in compared to other species. The predictable editing outcome, high efficiency, and product purity enables near homogeneous induction of STOP codons or alleles encoding protein variants in vivo. Last, we demonstrate how optimized expression enables conditional base editing in marked cell populations. This work substantially facilitates creation of precise alleles in and provides key design parameters for developing efficient base editing systems in other ectothermic species.
Topics: Drosophila; Gene Editing; Animals; APOBEC-1 Deaminase; Cytidine Deaminase; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Silencing
PubMed: 37647411
DOI: 10.1126/sciadv.adj1568 -
Nature Cancer Jun 2024
Topics: Gemcitabine; Deoxycytidine; Humans; Drug Resistance, Neoplasm; Cytidine Deaminase; Up-Regulation; Antimetabolites, Antineoplastic; APOBEC Deaminases; Gene Expression Regulation, Neoplastic; Cell Line, Tumor
PubMed: 38778178
DOI: 10.1038/s43018-024-00755-8 -
Proceedings of the National Academy of... Mar 2024Human retroviruses are derived from simian ones through cross-species transmission. These retroviruses are associated with little pathogenicity in their natural hosts,...
Human retroviruses are derived from simian ones through cross-species transmission. These retroviruses are associated with little pathogenicity in their natural hosts, but in humans, HIV causes AIDS, and human T-cell leukemia virus type 1 (HTLV-1) induces adult T-cell leukemia-lymphoma (ATL). We analyzed the proviral sequences of HTLV-1, HTLV-2, and simian T-cell leukemia virus type 1 (STLV-1) from Japanese macaques () and found that APOBEC3G (A3G) frequently generates G-to-A mutations in the HTLV-1 provirus, whereas such mutations are rare in the HTLV-2 and STLV-1 proviruses. Therefore, we investigated the mechanism of how HTLV-2 is resistant to human A3G (hA3G). HTLV-1, HTLV-2, and STLV-1 encode the so-called antisense proteins, HTLV-1 bZIP factor (HBZ), Antisense protein of HTLV-2 (APH-2), and STLV-1 bZIP factor (SBZ), respectively. APH-2 efficiently inhibits the deaminase activity of both hA3G and simian A3G (sA3G). HBZ and SBZ strongly suppress sA3G activity but only weakly inhibit hA3G, suggesting that HTLV-1 is incompletely adapted to humans. Unexpectedly, hA3G augments the activation of the transforming growth factor (TGF)-β/Smad pathway by HBZ, and this activation is associated with ATL cell proliferation by up-regulating and . In contrast, the combination of APH-2 and hA3G, or the combination of SBZ and sA3G, does not enhance the TGF-β/Smad pathway. Thus, HTLV-1 is vulnerable to hA3G but utilizes it to promote the proliferation of infected cells via the activation of the TGF-β/Smad pathway. Antisense factors in each virus, differently adapted to control host cellular functions through A3G, seem to dictate the pathogenesis.
Topics: Humans; Cell Line; Virulence; Human T-lymphotropic virus 1; Leukemia-Lymphoma, Adult T-Cell; Proviruses; Transforming Growth Factor beta; Basic-Leucine Zipper Transcription Factors; APOBEC-3G Deaminase
PubMed: 38502701
DOI: 10.1073/pnas.2309925121 -
Journal of Molecular Biology Sep 2023The APOBEC3 family of human cytidine deaminases is involved in various cellular processes, including the innate and acquired immune system, mostly through inducing...
The APOBEC3 family of human cytidine deaminases is involved in various cellular processes, including the innate and acquired immune system, mostly through inducing C-to-U in single-stranded DNA and/or RNA mutations. Although recent studies have examined RNA editing by APOBEC3A (A3A), its intracellular target specificity are not fully characterized. To address this gap, we performed in-depth analysis of cellular RNA editing using our recently developed sensitive cell-based fluorescence assay. Our findings demonstrate that A3A and an A3A-loop1-containing APOBEC3B (A3B) chimera are capable of RNA editing. We observed that A3A prefers to edit specific RNA substrates which are not efficiently deaminated by other APOBEC members. The editing efficiency of A3A is influenced by the RNA sequence contexts and distinct stem-loop secondary structures. Based on the identified RNA specificity features, we predicted potential A3A-editing targets in the encoding region of cellular mRNAs and discovered novel RNA transcripts that are extensively edited by A3A. Furthermore, we found a trend of increased synonymous mutations at the sites for more efficient A3A-editing, indicating evolutionary adaptation to the higher editing rate by A3A. Our results shed light on the intracellular RNA editing properties of A3A and provide insights into new RNA targets and potential impact of A3A-mediated RNA editing.
Topics: Humans; Base Sequence; Cytidine Deaminase; HEK293 Cells; Nucleic Acid Conformation; Proteins; RNA; RNA Editing; Substrate Specificity
PubMed: 37442413
DOI: 10.1016/j.jmb.2023.168198 -
Pathogens (Basel, Switzerland) Feb 2024APOBEC3 proteins are cytidine deaminases that play a crucial role in the innate immune response against viruses, including DNA viruses. Their main mechanism for... (Review)
Review
APOBEC3 proteins are cytidine deaminases that play a crucial role in the innate immune response against viruses, including DNA viruses. Their main mechanism for restricting viral replication is the deamination of cytosine to uracil in viral DNA during replication. This process leads to hypermutation of the viral genome, resulting in loss of viral fitness and, in many cases, inactivation of the virus. APOBEC3 proteins inhibit the replication of a number of DNA tumour viruses, including herpesviruses, papillomaviruses and hepadnaviruses. Different APOBEC3s restrict the replication of different virus families in different ways and this restriction is not limited to one APOBEC3. Infection with DNA viruses often leads to the development and progression of cancer. APOBEC3 mutational signatures have been detected in various cancers, indicating the importance of APOBEC3s in carcinogenesis. Inhibition of DNA viruses by APOBEC3 proteins appears to play a dual role in this process. On the one hand, it is an essential component of the innate immune response to viral infections, and, on the other hand, it contributes to the pathogenesis of persistent viral infections and the progression of cancer. The current review examines the complex interplay between APOBEC3 proteins and DNA viruses and sheds light on the mechanisms of action, viral countermeasures and the impact on carcinogenesis. Deciphering the current issues in the interaction of APOBEC/DNA viruses should enable the development of new targeted cancer therapies.
PubMed: 38535531
DOI: 10.3390/pathogens13030187 -
BioRxiv : the Preprint Server For... May 2024Over the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a...
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.
PubMed: 38766133
DOI: 10.1101/2024.05.11.593688