Desacetilases de histonas no câncer colorretal: expressão gênica, indicadores prognósticos e perspectivas para a terapia epigenética
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Data
2021-04-08
Autores
Callegari, Diogo Pessuto
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Editor
Universidade Estadual Paulista (Unesp)
Resumo
O termo câncer colorretal (CRC) inclui os tumores localizados no intestino grosso separado em cólon e reto. Globalmente, o CRC apresenta alta incidência e taxa de mortalidade. A doença é heterogênea, possui etiologia complexa, desenvolvendo-se em múltiplas etapas em decorrência do acúmulo de alterações genéticas e epigenéticas. Estudos recentes identificaram perfis moleculares específicos caracterizados por alterações genéticas e epigenéticas: i) instabilidade cromossômica (CIN), ii) instabilidade de microssatélites (MSI), iii) fenótipo metilador de ilha CpG (CIMP) e iv) hipometilação global do DNA. Alterações epigenéticas, incluindo mudanças no perfil de metilação do DNA e de modificações pós-traducionais das histonas, são detectadas em todas as etapas do processo de carcinogênese. Neste contexto, a perda da acetilação da cromatina mediada pelas enzimas denominadas desacetilases de histonas (HDACs) têm sido implicadas na progressão do CRC e na resistência à quimioterapia. Este estudo teve como objetivo principal avaliar o padrão de expressão de genes codificadores de desacetilases de histonas em CRC e sua correlação com parâmetros clínico-patológicos. O trabalho encontra-se apresentado em duas partes: o primeiro capítulo apresenta os principais fatores epidemiológicos do câncer colorretal, sua classificação, fatores epigenéticos que acompanham seu desenvolvimento e sua relação com as HDACs, assim como o efeito das modificações de histonas na resposta à terapia. O segundo capítulo apresenta a análise do padrão de expressão dos 18 genes codificadores de desacetilases de histonas em CRC comparado a amostras de intestino normal a partir de dados de RNA-Seq disponíveis nos bancos de dados públicos The Cancer Genome Atlas (TCGA) e Genotype-Tissue Expression (GTEx) bem como possíveis correlações entre os genes diferencialmente expressos com parâmetros prognósticos. Dentre os dados disponíveis, foram selecionados aqueles obtidos a partir de amostras de tumores com alto nível de pureza de acordo com o valor de CPE (Consensus Purity Estimate). As análises foram conduzidas com o pacote DESeq2 para linguagem R (R Bioconductor v 3.8). Foram detectados seis genes diferencialmente expressos (log2FoldChange >+1 ou < –1 e p-value <0,0001; student t-test): os genes HDAC1, 2 e 8 apresentaram altos níveis de expressão enquanto osgenes HDAC 4, 9 e 10 apresentaram níveis menores nos tumores quando comparados tecido normal. Em conjunto, os genes diferencialmente expressos mostraram padrão heterogêneo entre as amostras tumorais e foram associados com a ocorrência de mutações no oncogene BRAF (genes HDAC1 e HDAC10), instabilidade de microssatélites (gene HDAC2) e o fenótipo CIMP (gene HDAC10). Considerando-se as interações entre os diferentes membros da família das HDACs e a participação dessas proteínas em complexos repressores da transcrição, novos estudos são necessários para se investigar o impacto das alterações descritas na biologia tumoral e suas implicações para as estratégias de terapia epigenética.
The term colorectal cancer (CRC) includes tumors located in the large intestine composed by colon and rectum. Globally, CRC has high incidence and mortality rates. This disease is heterogeneous, presents a complex etiology and develops in a multistep process, due to the accumulation of genetic and epigenetic changes. Recent advances have identified specific molecular profiles characterized by genetic and epigenetic alterations: i) chromosomal instability (CIN), ii) microsatellite instability (MSI), iii) CpG island-methylating phenotype (CIMP), and iv) global DNA hypomethylation. Epigenetic alterations can be detected during all stages of carcinogenesis, including DNA methylation and post-translational modifications of histones. In this context, the loss of chromatin acetylation mediated by histone deacetylases (HDACs) has been implicated in the progression and resistance to chemotherapy of CRC. This study evaluated the expression pattern of the encoding genes of histone deacetylases in CRC and its correlation with clinical-pathological parameters. Here, this work is presented in two parts: the first chapter summarizes the main epidemiological features of CRC, its classification, epigenetic factors that contribute to its development, and its relationship with HDACs, as well as the effect of histone modifications on the response to therapy. The second chapter presents the analysis of the expression pattern of the 18 histone deacetylase genes of CRC, compared to normal intestine samples using RNA-Seq data available in the public databases The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx), respectively. We also investigate the possible correlations between differentially expressed genes with prognostic parameters. Among the available data, those samples obtained from tumors with a high level of purity were selected, according to the CPE value (Consensus Purity Estimate). The analysis was conducted with the DESeq2 package for R language (R Bioconductor v 3.8). Six differentially expressed genes were detected (log2FoldChange >+1 or <–1 and p-value <0.0001; student t-test). The HDAC1, 2, and 8 genes showed high levels of expression while HDAC4, 9, and 10 presented lower levels in the tumors compared to normaltissue. The differentially expressed genes showed a heterogeneous pattern among tumor samples and were associated with the occurrence of mutations in the BRAF oncogene (HDAC1 and HDAC10), microsatellite instability (HDAC2), and the CIMP phenotype (HDAC10). Based on the potein-protein interactions of members of the HDAC family and their participation in repressor complexes of transcription, further studies are needed to investigate the impact of these changes in tumor biology features, and their implications for epigenetic therapy strategies.
The term colorectal cancer (CRC) includes tumors located in the large intestine composed by colon and rectum. Globally, CRC has high incidence and mortality rates. This disease is heterogeneous, presents a complex etiology and develops in a multistep process, due to the accumulation of genetic and epigenetic changes. Recent advances have identified specific molecular profiles characterized by genetic and epigenetic alterations: i) chromosomal instability (CIN), ii) microsatellite instability (MSI), iii) CpG island-methylating phenotype (CIMP), and iv) global DNA hypomethylation. Epigenetic alterations can be detected during all stages of carcinogenesis, including DNA methylation and post-translational modifications of histones. In this context, the loss of chromatin acetylation mediated by histone deacetylases (HDACs) has been implicated in the progression and resistance to chemotherapy of CRC. This study evaluated the expression pattern of the encoding genes of histone deacetylases in CRC and its correlation with clinical-pathological parameters. Here, this work is presented in two parts: the first chapter summarizes the main epidemiological features of CRC, its classification, epigenetic factors that contribute to its development, and its relationship with HDACs, as well as the effect of histone modifications on the response to therapy. The second chapter presents the analysis of the expression pattern of the 18 histone deacetylase genes of CRC, compared to normal intestine samples using RNA-Seq data available in the public databases The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx), respectively. We also investigate the possible correlations between differentially expressed genes with prognostic parameters. Among the available data, those samples obtained from tumors with a high level of purity were selected, according to the CPE value (Consensus Purity Estimate). The analysis was conducted with the DESeq2 package for R language (R Bioconductor v 3.8). Six differentially expressed genes were detected (log2FoldChange >+1 or <–1 and p-value <0.0001; student t-test). The HDAC1, 2, and 8 genes showed high levels of expression while HDAC4, 9, and 10 presented lower levels in the tumors compared to normaltissue. The differentially expressed genes showed a heterogeneous pattern among tumor samples and were associated with the occurrence of mutations in the BRAF oncogene (HDAC1 and HDAC10), microsatellite instability (HDAC2), and the CIMP phenotype (HDAC10). Based on the potein-protein interactions of members of the HDAC family and their participation in repressor complexes of transcription, further studies are needed to investigate the impact of these changes in tumor biology features, and their implications for epigenetic therapy strategies.
Descrição
Palavras-chave
Alvos terapeuticos, HDACs clássicas, Marcas epigenéticas, Modificadores de histonas, Sirtuínas, Therapeutic targets, Classic HDACs, Epigenetic marks