APOBEC3A Expression Research Articles

Regulation, functional impact, and therapeutic targeting of APOBEC3A in cancer

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.

APOBEC3-related mutations in the spike protein-encoding region facilitate SARS-CoV-2 evolution

SARS-CoV-2 evolves gradually to cause COVID-19 epidemic. One of driving forces of SARS-CoV-2 evolution might be activation of apolipoprotein B mRNA editing catalytic subunit-like protein 3 (APOBEC3) by inflammatory factors. Here, we aimed to elucidate the effect of the APOBEC3-related viral mutations on the infectivity and immune evasion of SARS-CoV-2. The APOBEC3-related C > U mutations ranked as the second most common mutation types in the SARS-CoV-2 genome. mRNA expression of APOBEC3A (A3A), APOBEC3B (A3B), and APOBEC3G (A3G) in peripheral blood cells increased with disease severity. A3B, a critical member of the APOBEC3 family, was significantly upregulated in both severe and moderate COVID-19 patients and positively associated with neutrophil proportion and COVID-19 severity. We identified USP18 protein, a key molecule centralizing the protein-protein interaction network of key APOBEC3 proteins. Furthermore, mRNA expression of USP18 was significantly correlated to ACE2 and TMPRSS2 expression in the tissue of upper airways. Knockdown of USP18 mRNA significantly decreased A3B expression. Ectopic expression of A3B gene increased SARS-CoV-2 infectivity. C > U mutations at S371F, S373L, and S375F significantly conferred with the immune escape of SARS-CoV-2. Thus, APOBEC3, whose expression are upregulated by inflammatory factors, might promote SARS-CoV-2 evolution and spread via upregulating USP18 level and facilitating the immune escape. A3B and USP18 might be therapeutic targets for interfering with SARS-CoV-2 evolution.

Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells.

APOBEC-induced mutations occur in 50% of sequenced human tumors, with APOBEC3A (A3A) being a major contributor to mutagenesis in breast cancer cells. The mechanisms that cause A3A activation and mutagenesis in breast cancers are still unknown. Here, we describe factors that influence basal A3A mRNA transcript levels in breast cancer cells. We found that basal A3A mRNA correlates with A3A protein levels and predicts the amount of APOBEC signature mutations in a panel of breast cancer cell lines, indicating that increased basal transcription may be one mechanism leading to breast cancer mutagenesis. We also show that alteration of ERBB2 expression can drive A3A mRNA levels, suggesting the enrichment of the APOBEC mutation signature in Her2-enriched breast cancer could in part result from elevated A3A transcription. Hierarchical clustering of transcripts in primary breast cancers determined that A3A mRNA was co-expressed with other genes functioning in viral restriction and interferon responses. However, reduction of STAT signaling via inhibitors or shRNA in breast cancer cell lines had only minor impact on A3A abundance. Analysis of single cell RNA-seq from primary tumors indicated that A3A mRNA was highest in infiltrating immune cells within the tumor, indicating that correlations of A3A with STAT signaling in primary tumors may be result from higher immune infiltrates and are not reflective of STAT signaling controlling A3A expression in breast cancer cells. Analysis of ATAC-seq data in multiple breast cancer cell lines identified two transcription factor sites in the APOBEC3A promoter region that could promote A3A transcription. We determined that Rel-A, and Bach1, which have binding sites in these peaks, elevated basal A3A expression. Our findings highlight a complex and variable set of transcriptional activators for A3A in breast cancer cells.

Abstract PO5-27-03: Mutational impact of APOBEC3A and APOBEC3B in a human cell line

Abstract A major source of mutation in cancer is DNA cytosine deamination by APOBEC3 enzymes resulting in C-to-T and C-to-G mutations in TCA and TCT motifs. Here, we develop a selectable system to quantify genomic mutations and compare the mutagenic activities of three leading APOBEC3 candidates - APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and nearly indistinguishable TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from TK mutant clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs over 70% of the time and APOBEC3B just under 50% of the time (Y=C/T; W=A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes are contributing in a combinatorial manner to the overall mutation landscape. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both enzymes. Citation Format: Michael Carpenter, Nuri Temiz, Mahmoud Ibrahim, Matthew Jarvis, Margaret Brown, Prokopios Argyris, William Brown, Douglas Yee, Reuben Harris. Mutational impact of APOBEC3A and APOBEC3B in a human cell line [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-27-03.

Abstract 3289: APOBEC3A drives tumor evolution through activation of ERVs in non small cell lung cancer

Abstract Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We recently demonstrated that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Preventing therapy-induced A3A mutagenesis by gene deletion decreased the chromosomal aberration events and delayed the emergence of drug resistance. Thus, inhibition of A3A may represent a potential therapeutic strategy to prevent acquired resistance. Understanding the regulatory mechanisms of A3A may provide alternative approaches to inhibit A3A mutagenesis. Using a panel drug screen, we found that DNA methyltransferase (DNMT) inhibitor remarkably induces A3A in non-small cell lung cancer cells. RNA-seq profiling revealed that targeted therapy as well as DNMT inhibitor treatment activate expression of distinct classes non-coding repetitive RNA elements, including endogenous retrovirus (ERVs), in drug-tolerant persister cells. Activation of intracellular viral sensing pathways by introduction of exogenous nucleic acids mimicking viral elements induced A3A expression. While the transcription factor NFkB was acutely activated by targeted therapy, TBK1-IRF3 signaling was activated at later time points. These findings suggest that reactivation of ERVs may underlie A3A mutagenic activity and tumor evolution during targeted therapy. Citation Format: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Michael Lawrence, Aaron Hata. APOBEC3A drives tumor evolution through activation of ERVs in non small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3289.

Abstract 4347: Cell-type specific transcriptional regulation of APOBEC3A in cancers

Abstract APOBEC3s (A-H) are a family of seven cytosine deaminases that inactivate viruses as part of the innate immune response. However, APOBEC3A and APOBEC3B have been found to mediate mutagenesis in tumor genomes by deaminating ssDNA that transiently arise during transcription and DNA replication. The mechanisms that trigger these enzymes to generate high mutation burdens in some cancers and affect disease progression and clinical outcomes are largely unknown. Here, we explored cell-type-specific transcriptional regulation of APOBEC3s using single-nucleus/cell RNA-seq (sn/scRNA-seq) data (>100 samples and >300,000 cells) from four tumor types - bladder, lung, breast, and kidney - that display different levels of APOBEC-induced mutation burden. Our analyses revealed that among seven members of the APOBEC3 family, APOBEC3A is expressed in a cell-type-specific manner. The expression was predominant in KRT13 and CDH12 epithelial cell-types and inflamed macrophages. The APOBEC3A+ epithelial cell populations were abundant in the bladder, moderate in the lung and breast, and nearly absent in the kidney tumors. APOBEC3A expression correlated with interferon and pro-inflammatory signaling in KRT13+ cells. Transcription factors ELF3 and ATF3 were significantly upregulated in APOBEC3A+ KRT13 cells. Pseudotime analysis of sn/scRNA-seq data revealed that APOBEC3A cells are in epithelial-mesenchymal transition. Finally, several gene markers defining APOBEC3A+ KRT13 cell types were identified. Ongoing analyses include investigations into clinical correlates, cell-type-specific mutation burdens, and validation through in vitro functional approaches. Our results propose that APOBEC3A is turned on in specific epithelial cell types by multiple signaling pathways during tumorigenesis, thereby driving tumor heterogeneity, particularly in high mutation-burden cancers. Citation Format: Dhanusha Yesudhas, Bilal Lone, Kelly Butler, Arup Chakraborty, Abdul Rouf Banday. Cell-type specific transcriptional regulation of APOBEC3A in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4347.

Passive Smoking–Induced Mutagenesis as a Promoter of Lung Carcinogenesis

IntroductionThe International Agency for Research on Cancer has classified passive smoking (PS) or secondhand smoke exposure as a group 1 carcinogen linked to lung cancer. However, in contrast to active smoking, the mutagenic properties of PS remain unclear. MethodsA consecutive cohort of 564 lung adenocarcinoma samples from female never-smokers, who provided detailed information about their exposure to PS during adolescence and in their thirties through a questionnaire, was prepared. Of these, all 291 cases for whom frozen tumor tissues were available were subjected to whole exome sequencing to estimate tumor mutational burden, and the top 84 cases who were exposed daily, or not, to PS during adolescence, in their thirties or in both periods, were further subjected to whole genome sequencing. ResultsA modest yet statistically significant increase in tumor mutational burden was observed in the group exposed to PS compared with the group not exposed to PS (median values = 1.44 versus 1.29 per megabase, respectively; p = 0.020). Instead of inducing driver oncogene mutations, PS-induced substantial subclonal mutations exhibiting APOBEC-type signatures, including SMAD4 and ADGRG6 hotspot mutations. A polymorphic APOBEC3A/3B allele-specific to the Asian population that leads to up-regulated expression of APOBEC3A accentuated the mutational load in individuals exposed daily to PS during adolescence. ConclusionsThis study reveals that PS–induced mutagenesis can promote lung carcinogenesis. The APOBEC3A/3B polymorphism may serve as a biomarker for identifying passive nonsmoking individuals at high risk of developing lung cancer.

APOBEC3A induces DNA gaps through PRIMPOL and confers gap-associated therapeutic vulnerability.

Mutation signatures associated with apolipoprotein B mRNA editing catalytic polypeptide-like 3A/B (APOBEC3A/B) cytidine deaminases are prevalent across cancers, implying their roles as mutagenic drivers during tumorigenesis and tumor evolution. APOBEC3A (A3A) expression induces DNA replication stress and increases the cellular dependency on the ataxia telangiectasia and Rad3-related (ATR) kinase for survival. Nonetheless, how A3A induces DNA replication stress remains unclear. We show that A3A induces replication stress without slowing replication forks. We find that A3A induces single-stranded DNA (ssDNA) gaps through PrimPol-mediated repriming. A3A-induced ssDNA gaps are repaired by multiple pathways involving ATR, RAD51, and translesion synthesis. Both ATR inhibition and trapping of poly(ADP-ribose) polymerase (PARP) on DNA by PARP inhibitor impair the repair of A3A-induced gaps, preferentially killing A3A-expressing cells. When used in combination, PARP and ATR inhibitors selectively kill A3A-expressing cells synergistically in a manner dependent on PrimPol-generated gaps. Thus, A3A-induced replication stress arises from PrimPol-generated ssDNA gaps, which confer a therapeutic vulnerability to gap-targeted DNA repair inhibitors.

Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.

A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.

Prognostic value of APOBEC3A in patients with cervical squamous cell carcinoma in a major urban center in China: a retrospective study.

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). 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. 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). 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.

Mitochondrial double-stranded RNA triggers induction of the antiviral DNA deaminase APOBEC3A and nuclear DNA damage

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.

Therapy-induced APOBEC3A drives evolution of persistent cancer cells.

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.

Abstract 137: Epigenetic regulation of APOBEC3A mutagenesis and tumor evolution during targeted therapy in non-small cell lung cancer

Abstract Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We recently demonstrated that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug tolerant cancer cells persisting during therapy. Preventing therapy-induced A3A mutagenesis by gene deletion decreased the accumulation of chromosomal aberrations and delayed the emergence of drug resistance. Thus, we hypothesize that inhibition of A3A may represent a potential therapeutic strategy to halt the evolution of resistant clones and prevent acquired resistance to lung cancer targeted therapies. Understanding the molecular mechanism of A3A induction during targeted therapy is a crucial step to develop targeting A3A therapies.Using a targeted drug combination screen, we found that DNA methyltransferase (DNMT) inhibitors induce expression of APOBEC3A in non-small cell lung cancer cells, phenocopying the effects of targeted therapies. RNA-seq profiling revealed that both targeted therapies and DNMT inhibitors increase expression of non-coding repeat RNAs. Repeatome analysis identified distinct classes of non-codding RNAs including endogenous retrovirus elements (ERV) in drug tolerant persister cells. Activation of endogenous intracellular viral sensing pathways by exogenous nucleic acids mimicking viral infection induced APOBEC3A, and genetic perturbation of RIG-I or MAVS reduced APOBEC3A induced by targeted therapy. These findings suggest that epigenetic derepression of retroviral repeat elements may underly APOBEC3A mutagenic activity and tumor evolution during lung cancer targeted therapy. Citation Format: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Jessica Lin, Lecia Sequist, Zofia Piotrowska, Justin Gainor, Rémi Buisson, Michael Lawrence, Aaron Hata. Epigenetic regulation of APOBEC3A mutagenesis and tumor evolution during targeted therapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 137.

Abstract 636: Role of Apobec3a in pancreatitis and inflammation triggered carcinogenesis

Abstract Background: Despite great efforts over the last decades, the complex pathogenesis of acute (AP) and chronic pancreatitis (CP), involving the interplay of environmental, metabolic, and genetic factors and how CP eventually progresses to pancreatic cancer, remains incompletely understood. While mutated Kras, an important oncogenic driver in PDAC, has been found mutated in about 40% of CP patients, other mutations or mutagenic drivers potentially arising during the course of this chronic inflammatory disease are not well established. Recently, inflammation-triggered APOBEC single-strand DNA-specific cytidine deaminases were identified as important mutagenic drivers in PDAC. In addition, we unraveled a so far unrecognized role for A3A in driving chromosomal instability (CIN) independent of its deaminase function. Importantly, we found APOBEC3A (A3A), a member of the APOBEC family, to be associated with an IFNg immune response, activated during CP, and in a mouse model of AP, A3A significantly aggravated the course of the disease. These findings led us to conclude that A3A may be an important player in the inflammatory disease of the pancreas, AP and CP, and could act as a mutagenic driver fueling cancer evolution. Methods: Utilizing our novel genetically engineered mouse models (GEMMs) of conditional humanized wildtype and E72A mutant A3A expression, cerulein-induced AP and CP models, and human CP specimens, as well as a variety of molecular biology assays and sequencing approaches, we aim to elucidate the role of deaminase-competent and deaminase-deficient (mutant) A3A during AP and CP and early carcinogenesis and its implications on inflammation-triggered mutagenesis. Results: Interestingly, we found that deaminase-competent but not mutant A3A aggravates the severity (edema, necrosis, apoptosis, serum lipase) and inflammatory response during AP and CP. We found an increased inflammatory response in the pancreas as well as in the lungs by performing RNAseq, qPCR, MPO assays, and multiplex immunostainings. In addition, by analyzing human CP specimens, we were able to show that expression of A3A correlates with fibrosis, formation of pre-cancerous lesions, and the severity of the disease. Targeted DNA sequencing revealed a higher rate of mutations in important tumor suppressor/oncogenes when A3A was highly expressed, suggesting that A3A may facilitate inflammation-triggered mutagenesis in a pre-oncogenic setting. Conclusions: A3A significantly impacts the severity and inflammatory response of AP and CP and may facilitate inflammation-triggered carcinogenesis. Citation Format: Sonja Maria Woermann, Fredrik Thege, Laura Valenciana, Robert Cowan, Anirban Maitra. Role of Apobec3a in pancreatitis and inflammation triggered carcinogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 636.

Abstract 104: The role of APOBEC3A in ovarian cancer progression

Abstract Cancer progression is enabled by the accumulation of somatic mutations and genomic aberrations, leading to metastasis, treatment resistance, and poor clinical outcomes. The analysis of cancer genomes has identified APOBEC3A (A3A) cytidine deaminase activity as a cause of somatic mutagenesis in over 20 tumor types. In particular, A3A mutational signatures are found in a large proportion of ovarian tumors, ranging from 2-26% depending on subtype. Furthermore, genomic analyses of ovarian tumors suggest that A3A mutagenesis occurred during early metastatic progression, indicating the potential for A3A activity to promote clonal evolution. In non-ovarian tumors, A3A activity is associated with metastatic progression through the identification of A3A mutational patterns enriched in or unique to metastatic sites. Therefore, we hypothesized that aberrant A3A activity on OC genomes would increase mutagenesis, promote clonal diversity, and enable tumor progression. To examine the impact of aberrant A3A activity during OC progression, we developed a model system of inducible A3A expression in OC cell lines. We treated cells for 45 days with doxycycline to induce A3A expression (long-term, LT-A3A) and generated three biological replicates by treating individual wells of the parental lines independently. A3A is known to mutate the genome stochastically. Despite this, all versions of LT-A3A cells exhibited similar phenotypes compared to non-treated isogenic controls (NT). LT-A3A cells demonstrated increased colony formation relative to NT cells, indicating improved cell survival. We assessed cellular migration by scratch-wound assays and found that LT-A3A cells exhibited accelerated wound closure rates compared to NT controls, despite similar proliferation rates. In addition, cellular invasion was assessed by spheroid Matrigel invasion assays in which the invasive distance was significantly greater in LT-A3A cells relative to NT controls. By generating cell lines with a catalytically inactive doxycycline-inducible A3A transgene, we determined that the observed A3A-mediated cellular phenotypes were deaminase-dependent. To assess the molecular alterations driving these phenotypic differences, we performed RNA-seq on LT-A3A and NT cell lines. Gene set enrichment analysis of differentially expressed genes identified significant overlap between the Epithelial-Mesenchymal Transition (EMT) and WNT/Beta Catenin, Hedgehog, and TGFβ signaling gene sets. These related signaling pathways converge on the promotion of metastasis and cancer progression. These data suggest that aberrant A3A activity promotes the survival, migration, and invasion of OC cells by altering intracellular signaling pathways that promote EMT. Our ongoing experimental investigation will assess how long-term A3A mutagenesis impacts genomic heterogeneity and how A3A affects tumor behavior in animal models. Citation Format: Jessica Merritt Devenport, Mary Mullen, Katherine Fuh, Abby Green. The role of APOBEC3A in ovarian cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 104.

APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization.

APOBEC3A (A3A)-catalyzed DNA cytosine deamination is implicated in virus and cancer mutagenesis, and A3A is a target for small molecule drug discovery. The catalytic glutamic acid (E72) is frequently mutated in biochemical studies to characterize deamination-dependent versus deamination-independent A3A functions. Additionally, catalytically active A3A is toxic in bacterial expression systems, which adversely affects yield during recombinant A3A expression. Here, we demonstrate that mutating the catalytic glutamic acid to an isosteric glutamine (E72Q) significantly decreases the thermal stability of the protein, compared to the alanine-inactivating mutation (E72A). Differential scanning fluorimetry and mass spectrometry reveal that A3A E72Q is less thermally stable than A3A E72A or wild-type A3A. Strikingly, A3A E72Q is partially denatured at 37 °C and binds single-stranded DNA with significantly poorer affinity compared to A3A E72A. This study constitutes an important cautionary note on A3A protein design and informs that A3A E72A is the preferred catalytic inactivation mutation for most applications.

Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome.

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.

APOBEC3A suppresses cervical cancer via apoptosis.

Background: Family members of Apolipoprotein B mRNA-editing enzyme catalytic 3 (APOBEC3) play critical roles in cancer evolution and development. However, the role of APOBEC3A in cervical cancer remains to be clarified. Methods: We used bioinformatics to investigate APOBEC3A expression and outcomes using The Cancer Genome Atlas (TCGA)-cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) dataset, GTEx, and GSE7803. Immunohistochemistry was then used to identify APOBEC3A's expression pattern. We performed Cell Counting Kit-8, wound-healing, Transwell, and flow cytometry assays to measure proliferation, migration, invasion, and apoptosis, respectively, using the SiHa and HeLa cell lines transfected with APOBEC3A. BALB/c nude mice were used to investigate the effects of APOBEC3A in vivo. The phosphorylated gamma-H2AX staining assay was applied to measure DNA damage. RNA sequencing (RNA-Seq) was applied to explore APOBEC3A-related signaling pathways. Results: APOBEC3A was more significantly expressed in cancer tissues than in adjacent normal tissues. Higher expression of APOBEC3A was associated with better outcomes in TCGA-CESC and GTEx. Immunohistochemistry showed that the expression of APOBEC3A was significantly higher in cancer tissues than in normal tissues. Transfection experiments showed that APOBEC3A inhibited proliferation, upregulated S-phase cells, inhibited migration and invasion, induced DNA damage, and promoted apoptosis. Overexpression of APOBEC3A inhibited tumor formation in the mouse model. RNA-seq analysis showed that ectopic expression of APOBEC3A inhibited several cancer-associated signaling pathways. Conclusions: APOBEC3A is significantly upregulated in cervical cancer, and higher expression of APOBEC3A is associated with better outcomes. APOBEC3A is a tumor suppressor whose overexpression induces apoptosis in cervical cancer.

Exploring APOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

SummaryAPOBEC3 family members are cytidine deaminases catalyzing conversion of cytidine to uracil. Many studies have established a link between APOBEC3 expression and cancer development and progression, especially APOBEC3A (A3A) and APOBEC3B (A3B). Preclinical studies with human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) and clinical trial specimens revealed induction of A3B, but not A3A expression after demethylation. We examined the kinetic features of the cytidine deaminase activity for full length A3B and found that longer substrates and a purine at −2 position favored by A3B, whereas A3A prefers shorter substrates and an adenine or thymine at −2 position. The importance and biological significance of A3B catalytic activity rather than A3A and a preference for purine at the −2 position was also established in HPV+ HNSCCs. Our study explored factors influencing formation of A3A and A3B-related cancer mutations that are essential for understanding APOBEC3-related carcinogenesis and facilitating drug discovery.

Evaluation of APOBEC3 expression as prognostic marker in squamous cell carcinoma of the penis

Squamous cell carcinoma of the penis (PSC) is a rare disease with limited information on the molecular events leading to malignant transformation. In a third of PSC cases, presence of human papilloma virus (HPV) is found. The APOBEC3 family of proteins is known to play a significant role in defense against HPV infection, but their role in PSC is largely unknown. In this study, we aim to assess mRNA expression levels of APOBEC3 family members in HPV+ and HPV− PSC to get insight into their association with clinicopathological features and to evaluate their prognostic impact. Expression levels of six APOBEC3 family members in tissue from 50 patients with PSC were determined by RT-PCR and correlated with clinical and histopathological features. Lower expression of APOBEC3A, APOBEC3B, and APOBEC3C was observed in advanced PSC stages. Except for APOBEC3D, HPV+ samples showed higher expression of APOBEC3s compared to HPV− samples. In univariate analyses, APOBEC3A and APOBEC3C expression tended to be associated with disease-free survival and APOBEC3A expression with overall survival; however, multivariable analyses failed to confirm these associations with outcome. More extensive external validation and functional laboratory studies are needed to evaluate further their role in PSC development and progression.