ABSTRACT
OBJECTIVES: The present study aimed to contribute to the catalog of genetic mutations involved in the carcinogenic processes of uterine sarcomas (USs) and carcinosarcomas (UCSs), which may assist in the accurate diagnosis of, and selection of treatment regimens for, these conditions. METHODS: We performed gene-targeted next-generation sequencing (NGS) of 409 cancer-related genes in 15 US (7 uterine leiomyosarcoma [ULMS], 7 endometrial stromal sarcoma [ESS], 1 adenosarcoma [ADS]), 5 UCS, and 3 uterine leiomyoma (ULM) samples. Quality, frequency, and functional filters were applied to select putative somatic variants. RESULTS: Among the 23 samples evaluated in this study, 42 loss-of-function (LOF) mutations and 111 missense mutations were detected, with a total of 153 mutations. Among them, 66 mutations were observed in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. TP53 (48%), ATM (22%), and PIK3CA (17%) were the most frequently mutated genes. With respect to specific tumor subtypes, ESS showed mutations in the PDE4DIP, IGTA10, and DST genes, UCS exhibited mutations in ERBB4, and ULMS showed exclusive alterations in NOTCH2 and HER2. Mutations in the KMT2A gene were observed exclusively in ULM and ULMS. In silico pathway analyses demonstrated that many genes mutated in ULMS and ESS have functions associated with the cellular response to hypoxia and cellular response to peptide hormone stimulus. In UCS and ADS, genes with most alterations have functions associated with phosphatidylinositol kinase activity and glycerophospholipid metabolic process. CONCLUSION: This preliminary study observed pathogenic mutations in US and UCS samples. Further studies with a larger cohort and functional analyses will foster the development of a precision medicine-based approach for the treatment of US and UCS.
Subject(s)
Carcinosarcoma , Sarcoma , Uterine Neoplasms , Brazil , Carcinosarcoma/genetics , Female , Humans , Mutation , Sarcoma/genetics , Uterine Neoplasms/geneticsABSTRACT
OBJECTIVES: The present study aimed to contribute to the catalog of genetic mutations involved in the carcinogenic processes of uterine sarcomas (USs) and carcinosarcomas (UCSs), which may assist in the accurate diagnosis of, and selection of treatment regimens for, these conditions. METHODS: We performed gene-targeted next-generation sequencing (NGS) of 409 cancer-related genes in 15 US (7 uterine leiomyosarcoma [ULMS], 7 endometrial stromal sarcoma [ESS], 1 adenosarcoma [ADS]), 5 UCS, and 3 uterine leiomyoma (ULM) samples. Quality, frequency, and functional filters were applied to select putative somatic variants. RESULTS: Among the 23 samples evaluated in this study, 42 loss-of-function (LOF) mutations and 111 missense mutations were detected, with a total of 153 mutations. Among them, 66 mutations were observed in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. TP53 (48%), ATM (22%), and PIK3CA (17%) were the most frequently mutated genes. With respect to specific tumor subtypes, ESS showed mutations in the PDE4DIP, IGTA10, and DST genes, UCS exhibited mutations in ERBB4, and ULMS showed exclusive alterations in NOTCH2 and HER2. Mutations in the KMT2A gene were observed exclusively in ULM and ULMS. In silico pathway analyses demonstrated that many genes mutated in ULMS and ESS have functions associated with the cellular response to hypoxia and cellular response to peptide hormone stimulus. In UCS and ADS, genes with most alterations have functions associated with phosphatidylinositol kinase activity and glycerophospholipid metabolic process. CONCLUSION: This preliminary study observed pathogenic mutations in US and UCS samples. Further studies with a larger cohort and functional analyses will foster the development of a precision medicine-based approach for the treatment of US and UCS.
Subject(s)
Humans , Female , Sarcoma/genetics , Uterine Neoplasms/genetics , Carcinosarcoma/genetics , Brazil , MutationABSTRACT
AIM: The aim of the study was to evaluate the use of global and gene-specific DNA methylation changes as potential biomarkers for gallbladder cancer (GBC) in a cohort from Chile. MATERIAL & METHODS: DNA methylation was analyzed through an ELISA-based technique and quantitative methylation-specific PCR. RESULTS: Global DNA Methylation Index (p = 0.02) and promoter methylation of SSBP2 (p = 0.01) and ESR1 (p = 0.05) were significantly different in GBC when compared with cholecystitis. Receiver curve operator analysis revealed promoter methylation of APC, CDKN2A, ESR1, PGP9.5 and SSBP2, together with the Global DNA Methylation Index, had 71% sensitivity, 95% specificity, a 0.97 area under the curve and a positive predictive value of 90%. CONCLUSION: Global and gene-specific DNA methylation may be useful biomarkers for GBC clinical assessment.
Subject(s)
Cholecystitis/diagnosis , DNA Methylation , Gallbladder Neoplasms/diagnosis , Adult , Aged , Aged, 80 and over , Cell Line, Tumor , Chile , Cholecystitis/genetics , Female , Gallbladder Neoplasms/genetics , Humans , Male , Middle Aged , Molecular Diagnostic Techniques , Promoter Regions, Genetic , ROC Curve , Sequence Analysis, DNAABSTRACT
BACKGROUND: To identify new epigenetic markers and further characterize Urothelial Cell Carcinoma (UCC), we tested the promoter methylation (PM) status of 19 genes previously identified as cancer specific methylated genes in other solid tumors. METHODS: We used bisulfite sequencing, methylation specific PCR and quantitative methylation specific PCR (QMSP) to test the PM status of 19 genes in urothelial cancer cell lines. RESULTS: Among the 19 genes tested, VGF was found to be completely methylated in several UCC cell lines. VGF QMSP analysis showed that methylation values of almost all the primary 19 UCC tissues were higher than the paired normal tissues (P=0.009). In another cohort, 12/35 (34.3%) of low grade UCC cases displayed VGF methylation. As a biomarker for non-invasive detection of UCC, VGF showed a significantly higher frequency of methylation in urine from UCC cases (8/20) compared to controls (1/20) (P=0.020). After treatment of cell lines with 5-Aza-2'-deoxycytidine, VGF was robustly re-expressed. Forced expression of VGF in bladder cancer cell lines inhibited cell growth. CONCLUSION: Selection of candidates from genome-wide screening approach in other solid tumors successfully identified UCC specific methylated genes.
Subject(s)
Biomarkers, Tumor/genetics , Biomarkers, Tumor/urine , Carcinoma, Transitional Cell/genetics , Epigenesis, Genetic , Nerve Growth Factors/genetics , Urinary Bladder Neoplasms/genetics , Carcinoma, Transitional Cell/urine , Cell Line, Tumor , DNA Methylation , Gene Expression Regulation, Neoplastic , Gene Silencing , Humans , Nerve Growth Factors/urine , Promoter Regions, Genetic/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Urinary Bladder Neoplasms/urineABSTRACT
O carcinoma de pênis é um tumor pouco frequente. No entanto, em países em desenvolvimento o trata-se uma doença comum e em algumas regiões é o câncer mais frequente em homens. O principal fator clínico para determinação do prognóstico é a presença de metástases linfonodais, que está associada a redução significativa da sobrevida dos pacientes com câncer de pênis. Porém, até o presente momento não foi possível estabelecer marcadores clínicos ou moleculares de prognóstico. No presente estudo, foi avaliada a presença de hipermetilação nos genes CDKN2A e MGMT em amostras de carcinoma epidermóide (CE) de pênis. Além disso, os níveis de expressão das proteínas codificadas por esses genes (p16 e MGMT, respectivamente) foram quantificados e sua associação com o status de metilação do gene avaliada. A frequência de hipermetilação, o padrão de expressão e os dados clínicos e anatomopatológicos foram analisados na tentativa de identificar possíveis marcadores de prognóstico para os pacientes com CE de pênis. A frequência de hipermetilação dos genes CDKN2A e MGMT foi avaliada em 128 amostras incluídas em parafina. Nenhum dos casos apresentou metilação do gene CDKN2A e o gene MGMT apresentou-se metilado em 57,4% dos casos. A análise dos níveis de expressão das proteínas p16 e MGMT, em 351 casos, indicou que em 33,2% e 12,6%, respectivamente, ocorreu redução na expressão proteica. Não houve associação entre a presença de hipermetilação do gene MGMT e a expressão da proteína. Níveis reduzidos de expressão de MGMT foram mais frequentes em pacientes com tumores com espessura maior do que 5 milímetros e em pacientes com linfonodos positivos ao exame clínico. Dentre os fatores clínicos e anatomopatológicos, o estadiamento N clínico, o grau de diferenciação do tumor e a invasão perineural se mostraram variáveis independentes de risco para a ocorrência de metástases linfonodais e para redução da sobrevida. ...
