Somatic Copy Number Alterations and Associated Genes in Clear-Cell Renal-Cell Carcinoma in Brazilian Patients.

Somatic copy number aberrations (CNAs) have been associated with clear-cell renal carcinoma (ccRCC) pathogenesis and are a potential source of new diagnostic, prognostic and therapeutic biomarkers. Recurrent CNAs include loss of chromosome arms 3p, 14q, 9p, and gains of 5q and 8q. Some of these regional CNAs are suspected of altering gene expression and could influence clinical outcomes. Despite many studies of CNAs in RCC, there are currently no descriptions of genomic copy number alterations in a Brazilian ccRCC cohort. This study was designed to evaluate the chromosomal profile of CNAs in Brazilian ccRCC tumors and explore clinical associations. A total of 92 ccRCC Brazilian patients that underwent nephrectomy at Barretos Cancer Hospital were analyzed for CNAs by array comparative genomic hybridization. Most patients in the cohort had early-stage localized disease. The most significant alterations were loss of 3p (87.3%), 14q (35.8%), 6q (29.3%), 9p (28.6%) and 10q (25.0%), and gains of 5q (59.7%), 7p (29.3%) and 16q (20.6%). Bioinformatics analysis revealed 19 genes mapping to CNA significant regions, including SETD2, BAP1, FLT4, PTEN, FGFR4 and NSD1. Moreover, gain of 5q34-q35.3 (FLT4 and NSD1) and loss of 6q23.2-q23.3 (MYB) and 9p21.3 (MLLT3) had gene expression levels that correlated with TCGA data and was also associated with advanced disease features, such as larger tumors, Fuhrman 3, metastasis at diagnosis and death. The loss of region 14q22.1 which encompasses the NIN gene was associated with poor overall survival. Overall, this study provides the first CNA landscape of Brazilian patients and pinpoints genomic regions and specific genes worthy of more detailed investigations. Our results highlight important genes that are associated with copy number changes involving large chromosomal regions that are potentially related to ccRCC tumorigenesis and disease biology for future clinical investigations.

DNA methylation changes in promoter region of CDKN2A gene in workers exposed in construction environment.

PURPOSE: Construction workers are exposed to a mixture of substances in the workplace considered carcinogenic. This study aimed to characterise gene-specific changes in DNA methylation over the workweek in this population as this type of environmental exposure has not been studied extensively. MATERIALS AND METHODS: We evaluated their DNA methylation in 4 gene-promoter regions (CDKN2A, RASSF1A, MLH1 and APC) and 2 repeat elements (ALU and LINE-1) in blood samples obtained on the first and fifth day of the same workweek of a group of 39 male construction workers. DNA methylation was measured by bisulphite-PCR-Pyrosequencing. We also measured the levels of trace elements in the whole blood by ICP-MS. RESULTS: Only the CDKN2A gene had significant differences in the average methylation level between the first and fifth day of the workweek. We also observed that the levels of Cu, Pb, Se, Mn, and Ti decreased during the fifth day of exposure, and only lead, titanium and copper showed a low significant correlation with the methylation level mean for three specific CpG sites of the CDKN2A. CONCLUSIONS: In summary, the data suggest that altered levels of CDKN2A methylation in construction workers may be a potential biomarker of recent exposure in this environment.

Methylation of the hsa-miR-124, SOX1, TERT, and LMX1A genes as biomarkers for precursor lesions in cervical cancer.

OBJECTIVES: The methylation profile of genes in precursor lesions in cervical cancer was characterized to improve screening techniques for high-grade intraepithelial neoplasia. METHODS: A total of 447 cervical cytology samples obtained from women who underwent colposcopy were examined. The cases were distributed as follows: (1) cervices without cervical intraepithelial neoplasia (CIN; n = 152); (2) cervices with a CIN grade of 1 (CIN 1; n = 147); and (3) cervices with a CIN grade of 2 or 3 (CIN 2/3; n = 148). The methylation pattern for a panel of 15 genes was analysed by quantitative methylation-specific PCR (qMSP) and compared between the groups (≤CIN 1 vs. CIN 2+). RESULTS: In the validation set, seven genes presented significantly different methylation profiles according to diagnosis, namely, DAPK1 (p = 0.001), EPB41L3 (p = 0.001), HIC1 (p = 0.028), hsa-miR-124-2 (p = 0.001), LMX1A (p = 0.001), SOX1 (p = 0.001), and TERT (p = 0.001). Six genes showed a significant increase in the frequency of methylation in the presence of hr-HPV, namely, DAPK1 (p = 0.001), EPB41L3 (p = 0.001), hsa-miR-124-2 (p = 0.001), LMX1A (p = 0.001), SOX1 (p = 0.001), and TERT (p = 0.001). The methylation of the hsa-miR-124 gene showed sensitivity and specificity (86.7% and 61.3%, respectively) similar to that of the HPV test (91.3% and 50.0%, respectively). The independent factors associated with the diagnosis of CIN 2+ and the methylation of the hsa-miR-124-2 (OR = 5.1), SOX1 (OR = 2.8), TERT (OR = 2.2), and LMX1A (OR = 2.0) genes were a positive test for hr-HPV (odds ratio [OR] = 5.5). CONCLUSIONS: Hypermethylation of the hsa-miR-124-2, SOX1, TERT, and LMX1A genes may be a promising biomarker for precursor lesions in cervical cancer regardless of the hr-HPV status.

Micronucleus evaluation of exfoliated buccal epithelial cells using liquid-based cytology preparation.

OBJECTIVE: Micronuclei (MN) are biomarkers that can be applied to buccal epithelial cells to assess populations occupationally exposed to potentially carcinogenic agents. Liquid-based cytology (LBC) is a way to improve and refine the results obtained by this test. STUDY DESIGN: Exfoliated buccal cells were collected from 40 subjects (20 construction workers from the Barretos Cancer Hospital and 20 administrative staff from the same institution). LBC and three stains (Feulgen/fast green, Papanicolaou and Giemsa) were used to prepare the slides. Student's t test was applied for statistical comparisons of the data. A p value of <0.05 was considered statistically significant. RESULTS: Regardless of the stain employed, the frequency of MN was greater in the case group (Feulgen/fast green: 5.15; Papanicolaou: 29; Giemsa: 26) than in the control group (Feulgen/fast green: 2.30; Papanicolaou: 17; Giemsa: 15). CONCLUSIONS: Using LBC to prepare slides and evaluate the frequency of MN potentially serves as a screening option for more comprehensive studies of cancer risk among populations occupationally exposed to potentially carcinogenic agents. In addition, the residual fluid enables the preparation of slides for DNA-specific stains that can be compared to those with Papanicolaou stain.

Emissions generated by sugarcane burning promote genotoxicity in rural workers: a case study in Barretos, Brazil.

BACKGROUND: To determine the possible genotoxic effect of exposure to the smoke generated by biomass burning on workers involved in manual sugar cane harvesting. METHODS: The frequency of micronuclei in exfoliated buccal cells and peripheral blood lymphocytes was determined in sugarcane workers in the Barretos region of Brazil, during the harvest season and compared to a control population, comprised of administrative employees of Barretos Cancer Hospital. RESULTS: The frequency of micronuclei was higher in the sugar cane workers. The mean frequency in blood lymphocytes (micronuclei/1000 cells) in the test group was 8.22 versus 1.27 in the control group. The same effect was observed when exfoliated buccal cells were considered (22.75 and 9.70 micronuclei/1000 cells for sugar cane workers and controls, respectively). CONCLUSION: Exposure to emissions produced by the burning of sugar cane during harvesting induces genomic instability in workers, indicating the necessity of adopting more advanced techniques of harvesting sugar cane to preserve human health.

Burden of occupational cancer in Brazil and federative units, 1990-2019.

OBJECTIVE: To analyze the spatiotemporal distribution of the burden of occupational cancer in Brazil and federative units between 1990 and 2019. METHODS: Data were extracted from the Global Burden of Disease (GBD) study. Deaths from cancer whose attributable risk factor was occupational carcinogens were considered. Spatial analysis was performed with the first and last years of the series (1990 and 2019). Age-adjusted mortality rates were used to estimate the global Moran's Index (Moran's I), and the local indicator of spatial association (LISA) to identify clusters in the country with the respective statistical significance. The occupational cancer mortality rate, adjusted for age, was analyzed based on its trend for Brazil and federative units, in the period between 1990 and 2019. RESULTS: Between 1990 and 2019, occupational cancer mortality rate showed a decreasing trend (R2=0.62; p<0.001) as well as the burden of disease indicator - DALY (R2=0.84; p<0.001). However, mortality is increasing in most states, suggesting that a minority of federative units induce the country's global trend. There is also the development of a spatial pattern of autocorrelation, indicating clusters of states with low mortality and DALY rates in the Northeast and high values in the South of the country. CONCLUSION: The overall decreasing trend in the trend of occupational cancer masks the heterogeneity across states. This scenario may be associated with the diversity of economic activities, and suggests a decentralized and equitable plan for occupational cancer surveillance.

Gene expression alterations predict the pathological complete response in triple-negative breast cancer exploratory analysis of the NACATRINE trial.

This exploratory analysis of the Neoadjuvant Carboplatin in Triple Negative Breast Cancer (NACATRINE) study aimed to identify the biomarkers of pathological complete response (pCR) in patients with triple-negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NAC) within the context of a clinical trial. The NACATRINE trial is a phase II, single-center, randomized, open-label clinical trial that investigated the addition of carboplatin to sequential anthracycline- and taxane-based NAC for TNBC. We evaluated the gene expression in untreated samples to investigate its association with pCR, overall survival (OS), and disease-free survival (DFS). RNA was extracted from the tissue biopsy, and the nCounter Breast Cancer panel was used to analyze gene expression. Of the 66 patients included in the gene expression profiling analysis, 24 (36.4%) achieved pCR and 42 (63.6%) had residual disease. In unsupervised hierarchical clustering analyses, differentially expressed genes between patients with and without pCR were identified irrespective of the treatment (24 genes), carboplatin (37 genes), and non-carboplatin (27 genes) arms. In receiver operating characteristic (ROC) curve analysis, 10 genes in the carboplatin arm (area under the ROC curve [AUC], 0.936) and three genes in the non-carboplatin arm (AUC, 0.939) were considered to be potential pCR-associated biomarkers. We identified genes that were associated with improvements in OS and DFS in addition to being related to pCR. We successfully identified gene expression signatures associated with pCR in pretreatment samples of patients with TNBC treated with NAC. Further investigation of these biomarkers is warranted.

Genomic instability evaluation by BMCyt and telomere length in Brazilian family farmers exposed to pesticides.

Brazil is one of the largest consumers of pesticides in the world. This high consumption has resulted in higher potential health risk to agricultural farm workers due to occupational exposure. Hence, the aim of this study is to evaluate genomic instability, using Buccal Micronucleus Cytome (BMCyt) and telomere length (TL) measurement as biomarkers of occupational exposure to pesticides in rural workers living in the State of São Paulo, Brazil. Genomic instability was evaluated in 81 pesticide-exposed farm workers (69 males and 12 females) with a mean age of 49.16 ± 10.06 years and a mean time job of 30.00 ± 14.00 years,81 non-exposed individuals (62 males and 15 females) with a mean age of 47.87 ± 10.66 years. BMCyt results showed significantly higher levels of cell damage (micronuclei and binucleated cells) and cell death (karyorrhectic and condensed chromatin cells) in subjects exposed to pesticide when compared to those non-exposed (p < 0.05). Although our results did not show significant differences in TL among exposed and non-exposed groups, effects in TL due to pesticide exposure was found in a multivariable linear regression model when we stratified the groups by age (≤ 49 years and ≥ 50 years old; ß = 11.21, p = 0.006). In addition, TL reduction on was identified in relation to an increase in cigarette pack consumption (ß = -0.633, p = 0.045). Furthermore, exposure to specific pesticides presented different effects in TL. Cypermethrin exposure resulted in a reduction in TL (ß = -18.039, p = 0.018), while abamectin exposure led to an increase in TL (ß = 23.990, p = 0.007). Thus, our findings substantiate genomic instability due to pesticides exposure.

Burden of occupational cancer in Brazil and federative units, 1990-2019 / Carga de câncer relacionado ao trabalho no Brasil e unidades da federação, 1990-2019

ABSTRACT: Objective: To analyze the spatiotemporal distribution of the burden of occupational cancer in Brazil and federative units between 1990 and 2019. Methods: Data were extracted from the Global Burden of Disease (GBD) study. Deaths from cancer whose attributable risk factor was occupational carcinogens were considered. Spatial analysis was performed with the first and last years of the series (1990 and 2019). Age-adjusted mortality rates were used to estimate the global Moran's Index (Moran's I), and the local indicator of spatial association (LISA) to identify clusters in the country with the respective statistical significance. The occupational cancer mortality rate, adjusted for age, was analyzed based on its trend for Brazil and federative units, in the period between 1990 and 2019. Results: Between 1990 and 2019, occupational cancer mortality rate showed a decreasing trend (R2=0.62; p<0.001) as well as the burden of disease indicator — DALY (R2=0.84; p<0.001). However, mortality is increasing in most states, suggesting that a minority of federative units induce the country's global trend. There is also the development of a spatial pattern of autocorrelation, indicating clusters of states with low mortality and DALY rates in the Northeast and high values in the South of the country. Conclusion: The overall decreasing trend in the trend of occupational cancer masks the heterogeneity across states. This scenario may be associated with the diversity of economic activities, and suggests a decentralized and equitable plan for occupational cancer surveillance.

RESUMO: Objetivo: Analisar a carga de câncer relacionado ao trabalho no Brasil e unidades da federação, entre 1990 e 2019. Métodos: Extraímos os dados do estudo Carga Global de Doenças (GBD). Consideramos as mortes por câncer cujo fator de risco atribuível fossem agentes ocupacionais carcinogênicos. A análise espacial foi realizada com o primeiro e último anos da série (1990 e 2019). As taxas de mortalidade ajustadas por idade foram utilizadas para calcular o índice de Moran global (I de Moran) e o indicador local de associação espacial (LISA). A taxa de mortalidade por câncer relacionado ao trabalho, ajustada por idade, foi analisada com base em sua tendência, para Brasil e unidades da federação, no período entre 1990 e 2019. Resultados: No período citado, a taxa de mortalidade por câncer relacionado ao trabalho exibiu tendência de decréscimo (R2=0,62; p<0,001), assim como o indicador de carga de doença — DALY (R2=0,84; p<0,001). Contudo, a mortalidade é crescente na maioria dos estados, o que sugere que uma minoria de unidades induz a tendência global do país. Há ainda formação de um padrão espacial de autocorrelação, indicando agrupamentos de estados com baixas taxas de mortalidade e DALY no Nordeste e valores altos no Sul do país. Conclusão: A tendência global de decréscimo na tendência do câncer relacionado ao trabalho mascara a heterogeneidade entre estados. Esse cenário pode estar associado à diversidade de atividades econômicas e sugere um plano descentralizado e equitativo da vigilância do câncer relacionado ao trabalho.