RESUMO
Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence that is not fully explained by known lifestyle and environmental risk factors. It has been speculated that an unknown exogenous exposure(s) could be responsible. Here we combine the fields of mutational signature analysis with cancer epidemiology to study 552 ESCC genomes from eight countries with varying incidence rates. Mutational profiles were similar across all countries studied. Associations between specific mutational signatures and ESCC risk factors were identified for tobacco, alcohol, opium and germline variants, with modest impacts on mutation burden. We find no evidence of a mutational signature indicative of an exogenous exposure capable of explaining differences in ESCC incidence. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC)-associated mutational signatures single-base substitution (SBS)2 and SBS13 were present in 88% and 91% of cases, respectively, and accounted for 25% of the mutation burden on average, indicating that APOBEC activation is a crucial step in ESCC tumor development.
Assuntos
Neoplasias Esofágicas/epidemiologia , Neoplasias Esofágicas/genética , Carcinoma de Células Escamosas do Esôfago/epidemiologia , Carcinoma de Células Escamosas do Esôfago/genética , Mutação , Desaminases APOBEC/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Aldeído-Desidrogenase Mitocondrial/genética , Brasil/epidemiologia , China/epidemiologia , Feminino , Humanos , Incidência , Irã (Geográfico)/epidemiologia , Masculino , Pessoa de Meia-Idade , Proteína Supressora de Tumor p53/genética , Reino Unido/epidemiologia , Sequenciamento Completo do GenomaRESUMO
Mechanisms of viral oncogenesis are diverse and include the off-target activity of enzymes expressed by the infected cells, which evolved to target viral genomes for controlling their infection. Among these enzymes, the single-strand DNA editing capability of APOBECs represent a well-conserved viral infection response that can also cause untoward mutations in the host DNA. Here we show, after evaluating somatic single-nucleotide variations and transcriptome data in 240 gastric cancer samples, a positive correlation between APOBEC3s mRNA-expression and the APOBEC-mutation signature, both increased in EBV+ tumors. The correlation was reinforced by the observation of APOBEC mutations preferentially occurring in the genomic loci of the most active transcripts. This EBV infection and APOBEC3 mutation-signature axis were confirmed in a validation cohort of 112 gastric cancer patients. Our findings suggest that APOBEC3 upregulation in EBV+ cancer may boost the mutation load, providing further clues to the mechanisms of EBV-induced gastric carcinogenesis. After further validation, this EBV-APOBEC axis may prove to be a secondary driving force in the mutational evolution of EBV+ gastric tumors, whose consequences in terms of prognosis and treatment implications should be vetted.
Assuntos
Citidina Desaminase/genética , DNA de Neoplasias/genética , Herpesvirus Humano 4/patogenicidade , Neoplasias Gástricas/virologia , Desaminases APOBEC , Carcinogênese , Genes Virais , Herpesvirus Humano 4/genética , Humanos , Mutação , Neoplasias Gástricas/patologiaRESUMO
Adenocarcinoma gástrico (AdG) possui uma alta incidência na população mundial e brasileira. É um tipo tumoral cujos sintomas são bastante inespecíficos no seu início, resultando no diagnóstico já em estadios avançados. Recentemente, foi proposta uma nova classificação, estratificando o AdG em quatro subtipos, sendo um deles caracterizado pela infecção pelo Epstein Barr vírus (EBV). Neste subtipo, por sua vez, não são totalmente conhecidos os mecanismos subjacentes à infecção, os quais podem estar relacionados à instabilidade genômica e mecanismos adicionais de tumorigênese. Deste modo, o presente estudo fez uso de abordagens de Bioinformática para análise de dados públicos (TCGA) e sua validação no painel gênico de pacientes com AdG do A.C.Camargo Cancer Center, buscando assinaturas mutacionais relacionadas à instabilidade genômica na presença de EBV. A partir dos dados obtidos do consórcio TCGA, observamos expressão aumentada de APOBEC3s no subtipo molecular de AdG EBV positivo. Também foi possível ver maior taxa mutacional, no contexto TCW, nesse subtipo molecular, condizente com a ação de APOBECs. Na coorte do A.C.Camargo Cancer Center, foram obtidas amostras de tecido e de suco gástrico de 240 pacientes com AdG (caso) e 137 controles saudáveis. Nos pacientes caso, foi possível observar 6% de amplificação de fragmento de EBV na biópsia e 11,1% no Suco Gástrico. Os achados do TCGA foram validados na coorte do hospital, utilizando painel gênico. Foi possível cofirmar que a ação da família APOBEC3 está mais presente em amostras EBV positivas, indicando a ação viral na instabilidade gênica em AdG, através da família APOBEC
Gastric adenocarcinoma (GA) is highly frequent in the world and in Brazilian population. It's symptoms are rather nonspecific in the beginning, being diagnosed in advanced stages. Recently, a new classification was proposed, stratifying GA in four subtypes, one characterized by Epstein Barr Virus (EBV) infection. Yet, in this subtype, the underlying mechanisms of infection are not fully understood, which may be related to genomic instability and additional mechanisms of tumorigenesis. Thus, the present study made use of Bioinformatics approaches for public data analysis (TCGA) and its validation in the gene panel of A.C.Camargo Cancer Center patients with GA, searching for mutational signatures related to genomic instability in the presence of EBV. Analysing data from TCGA consortium, we observed increased expression of APOBEC3s in the EBV positive GA molecular subtype. It was also possible to observe a higher mutational rate, in TCW context, in GA with EBV infection, consistent with APOBECs action. In A.C.Camargo Cancer Center cohort, tissue samples and gastric juice were collected from 240 GA patients (case) and 137 healthy controls. It was possible to observe 6% EBV fragment amplification in biopsy and 11.1% in Gastric Juice. TCGA findings were validated in the hospital cohort, by gene panel. It was possible to confirm that APOBEC3 family members are more abundant in EBV positive samples, indicating a viral action in GA genomic instability through APOBEC3 members
Assuntos
Humanos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Prognóstico , Neoplasias Gástricas , Adenocarcinoma , Infecções por Vírus Epstein-Barr , Taxa de Mutação , Desaminases APOBEC , Estudos Retrospectivos , Bases de Dados de Compostos QuímicosRESUMO
DNA vaccines have failed to induce satisfactory immune responses in humans. Several mechanisms of double-stranded DNA (dsDNA) sensing have been described, and modulate DNA vaccine immunogenicity at many levels. We hypothesized that the immunogenicity of DNA vaccines in humans is suppressed by APOBEC (apolipoprotein B (APOB) mRNA-editing, catalytic polypeptide)-mediated plasmid degradation. We showed that plasmid sensing via STING (stimulator of interferon (IFN) genes) and TBK-1 (TANK-binding kinase 1) leads to IFN-ß induction, which results in APOBEC3A mRNA upregulation through a mechanism involving protein kinase C signaling. We also showed that murine APOBEC2 expression in HEK293T cells led to a 10-fold reduction in intracellular plasmid levels and plasmid-encoded mRNA, and a 2.6-fold reduction in GFP-expressing cells. A bicistronic DNA vaccine expressing an immunogen and an APOBEC2-specific shRNA efficiently silenced APOBEC2 both in vitro and in vivo, increasing the frequency of induced IFN-γ-secreting T cells. Our study brings new insights into the intracellular machinery involved in dsDNA sensing and how to modulate it to improve DNA vaccine immunogenicity in humans.
Assuntos
Apolipoproteínas B/metabolismo , Citidina Desaminase/metabolismo , HIV-1/fisiologia , Proteínas Musculares/metabolismo , Proteínas/metabolismo , Linfócitos T/imunologia , Vacinas de DNA/imunologia , Desaminases APOBEC , Animais , Antígenos Virais/genética , Apolipoproteínas B/genética , Citidina Desaminase/genética , Células HEK293 , Antígenos HLA-DR/genética , Humanos , Imunomodulação , Interferon beta/metabolismo , Proteínas de Membrana/metabolismo , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Knockout , Camundongos Transgênicos , Proteínas Musculares/genética , Fragmentos de Peptídeos/genética , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas/genética , Edição de RNA , RNA Interferente Pequeno/genética , Transdução de Sinais/genética , Transgenes/genética , Vacinas de DNA/genéticaRESUMO
BACKGROUND: The virion infectivity factor (Vif) is an accessory protein, which is essential for HIV replication in host cells. Vif neutralizes the antiviral host protein APOBEC3 through recruitment of the E3 ubiquitin ligase complex. METHODOLOGY: Fifty thousand Vif models were generated using the ab initio relax protocol of the Rosetta algorithm from sets of three- and nine-residue fragments using the fragment Monte Carlo insertion-simulated annealing strategy, which favors protein-like features, followed by an all-atom refinement. In the protocol, a constraints archive was used to define the spatial relationship between the side chains from Cys/His residues and zinc ions that formed the zinc-finger motif that is essential for Vif function. We also performed centroids analysis and structural analysis with respect to the formation of the zinc-finger, and the residue disposal in the protein binding domains. Additionally, molecular docking was used to explore details of Vif-A3G and Vif-EloBC interactions. Furthermore, molecular dynamics simulation was used to evaluate the stability of the complexes Vif-EloBC-A3G and Vif-EloC. PRINCIPAL FINDINGS: The zinc in the HCCH domain significantly alters the folding of Vif and changes the structural dynamics of the HCCH region. Ab initio modeling indicated that the Vif zinc-finger possibly displays tetrahedral geometry as suggested by Mehle et al. (2006). Our model also showed that the residues L146 and L149 of the BC-box motif bind to EloC by hydrophobic interactions, and the residue P162 of the PPLP motif is important to EloB binding. CONCLUSIONS/SIGNIFICANCE: The model presented here is the first complete three-dimensional structure of the Vif. The interaction of Vif with the A3G protein and the EloBC complex is in agreement with empirical data that is currently available in the literature and could therefore provide valuable structural information for advances in rational drug design.