APOBEC-mediated DNA alterations: A possible new mechanism of carcinogenesis in EBV-positive gastric cancer.

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.

Análise de assinaturas mutacionais no prognóstico de pacientes com adenocarcinoma gástrico e infecção por EBV / Mutational signature analysis in gastric cancer patients' prognosis and EBV infection

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

Genomics and epidemiology for gastric adenocarcinomas (GE4GAC): a Brazilian initiative to study gastric cancer

Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epidemiological factors and the rich ancestral admixture found in Brazil, stimulated the implementation of the GE4GAC project. GE4GAC aims to embrace epidemiological, clinical, molecular and microbiological data from Brazilian controls and patients with malignant and pre-malignant gastric disease. In this letter, we summarize the main goals of the project, including subject and sample accrual and current findings

PIK3CA exon 20 mutations are associated with poor prognosis in breast cancer patients.

OBJECTIVES: The phosphatidylinositol 3-kinase/AKT axis is an important cell-signaling pathway that mediates cell proliferation and survival, two biological processes that regulate malignant cell growth. The phosphatidylinositol 3-kinase CA gene encodes the p110α subunit of the phosphatidylinositol 3-kinase protein. There are phosphatidylinositol 3-kinase CA mutations in several types of human tumors, and they are frequently observed in breast cancer. However, these mutations have not been investigated in Brazilian breast cancer patients. METHODS: PCR-SSCP and direct DNA sequencing were performed to identify phosphatidylinositol 3-kinaseCA exon 9 and exon 20 mutations in 86 patients with sporadic breast cancer. The relationships between PIK3CA mutations and patient clinicopathological characteristics and survival were analyzed. The presence of the TP53 mutation was also examined. RESULTS: Twenty-three (27%) of the 86 primary breast tumors contained PIK3CA mutations. In exons 9 and 20, we identified the hotspot mutations E542K, E545K, and H1047R, and we identified two new missense mutations (I1022V and L1028S) and one nonsense (R992X) mutation. Phosphatidylinositol 3-kinase CA exon 20 mutations were associated with poor overall survival and TP53 gene mutations. CONCLUSIONS: Phosphatidylinositol 3-kinase CA mutations are common in tumors in Brazilian breast cancer patients, and phosphatidylinositol 3-kinase CA and TP53 mutations are not mutually exclusive. Phosphatidylinositol 3-kinase CA exon 20 mutations are associated with poor survival, and they may be useful biomarkers for identifying breast cancer patients with aggressive tumors and for predicting the response to treatment with PI3K pathway inhibitors.

PIK3CA exon 20 mutations are associated with poor prognosis in breast cancer patients

OBJECTIVES: The phosphatidylinositol 3-kinase/AKT axis is an important cell-signaling pathway that mediates cell proliferation and survival, two biological processes that regulate malignant cell growth. The phosphatidylinositol 3-kinase CA gene encodes the p110α subunit of the phosphatidylinositol 3-kinase protein. There are phosphatidylinositol 3-kinase CA mutations in several types of human tumors, and they are frequently observed in breast cancer. However, these mutations have not been investigated in Brazilian breast cancer patients. METHODS: PCR-SSCP and direct DNA sequencing were performed to identify phosphatidylinositol 3-kinaseCA exon 9 and exon 20 mutations in 86 patients with sporadic breast cancer. The relationships between PIK3CA mutations and patient clinicopathological characteristics and survival were analyzed. The presence of the TP53 mutation was also examined. RESULTS: Twenty-three (27%) of the 86 primary breast tumors contained PIK3CA mutations. In exons 9 and 20, we identified the hotspot mutations E542K, E545K, and H1047R, and we identified two new missense mutations (I1022V and L1028S) and one nonsense (R992X) mutation. Phosphatidylinositol 3-kinase CA exon 20 mutations were associated with poor overall survival and TP53 gene mutations. CONCLUSIONS: Phosphatidylinositol 3-kinase CA mutations are common in tumors in Brazilian breast cancer patients, and phosphatidylinositol 3-kinase CA and TP53 mutations are not mutually exclusive. Phosphatidylinositol 3-kinase CA exon 20 mutations are associated with poor survival, and they may be useful biomarkers for identifying breast cancer patients with aggressive tumors and for predicting the response to treatment with PI3K pathway inhibitors.

Portuguese c.156_157insAlu BRCA2 founder mutation: gastrointestinal and tongue neoplasias may be part of the phenotype.

We have screened BRCA2 c.156_157insAlu founder mutation in a cohort of 168 women with diagnosis of breast cancer referred for genetic counseling because of risk of being carriers of hereditary breast and ovarian cancer syndrome. Portuguese founder mutation BRCA2 c.156_157insAlu was identified in three unrelated breast cancer probands. Genotyping identified a common haplotype between markers D13S260 and D13S171, and allele sizes were compatible to those described in the Portuguese families. Allele sizes of marker D13S1246, however, were concordant in two families, suggesting that the haplotype may be larger in a subset of families. Tumor phenotypes in Brazilian families seem to reinforce the high prevalence of breast cancer among affected males. However, an apparent excess of gastrointestinal and tongue neoplasias were also observed in these families. Although these tumors are not part of the phenotypic spectrum of hereditary breast and ovarian cancer syndrome, they might be accounted for by other risk alleles contained in the founder haplotype region.