RESUMO
Aberrant alternative splicing and epigenetic changes are both associated with various cancers, but epigenetic regulation of alternative splicing in cancer is largely unknown. Here we report that the intragenic DNA methylation-mediated binding of Brother of Regulator of Imprinted Sites (BORIS) at the alternative exon of Pyruvate Kinase (PKM) is associated with cancer-specific splicing that promotes the Warburg effect and breast cancer progression. Interestingly, the inhibition of DNA methylation, BORIS depletion, or CRISPR/Cas9-mediated deletion of the BORIS binding site leads to a splicing switch from cancer-specific PKM2 to normal PKM1 isoform. This results in the reversal of the Warburg effect and the inhibition of breast cancer cell growth, which may serve as a useful approach to inhibit the growth of breast cancer cells. Importantly, our results show that in addition to PKM splicing, BORIS also regulates the alternative splicing of several genes in a DNA methylation-dependent manner. Our findings highlight the role of intragenic DNA methylation and DNA binding protein BORIS in cancer-specific splicing and its role in tumorigenesis.
Assuntos
Neoplasias da Mama/metabolismo , Metilação de DNA , Proteínas de Ligação a DNA/metabolismo , Caspases/genética , Caspases/metabolismo , Linhagem Celular Tumoral , Sobrevivência Celular , Imunoprecipitação da Cromatina , DNA/genética , Proteínas de Ligação a DNA/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Glucose/metabolismo , Humanos , Análise Serial de Proteínas , Interferência de RNA , RNA Interferente Pequeno , TranscriptomaRESUMO
The discovery of an increasing number of alternative splicing events in the human genome highlighted that â¼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by 'cis' RNA-binding sites and 'trans' RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing. The epigenetic modifications may regulate alternative splicing by either influencing the transcription elongation rate of RNA polymerase II or by recruiting a specific splicing regulator via different chromatin adaptors. The epigenetic alterations and aberrant alternative splicing are known to be associated with various diseases individually, but this review discusses/highlights the latest literature on the role of epigenetic alterations in the regulation of alternative splicing and thereby cancer progression. This review also points out the need for further studies to understand the interplay between epigenetic modifications and aberrant alternative splicing in cancer progression.
Assuntos
Processamento Alternativo , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Neoplasias/genética , Elongação da Transcrição Genética , Acetilação , Metilação de DNA , Progressão da Doença , Histonas/genética , Histonas/metabolismo , Humanos , Metilação , Neoplasias/metabolismo , Neoplasias/patologia , RNA Polimerase II/genética , RNA Polimerase II/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismoRESUMO
The tumor microenvironment is marked by gradients in the level of oxygen and nutrients, with oxygen levels reaching a minimum at the core of the tumor, a condition known as tumor hypoxia. Mediated by members of the HIF family of transcription factors, hypoxia leads to a more aggressive tumor phenotype by transactivation of several genes as well as reprogramming of pre-mRNA splicing. Intragenic DNA methylation, which is known to affect alternative splicing in cancer, could be one of several reasons behind the changes in splicing patterns under hypoxia. Here, we have tried to establish a correlation between intragenicDNA methylation and alternative usage of exons in tumor hypoxia. First, we have generated a customhypoxia signature consisting of 34 genes that are upregulated under hypoxia and are direct targets of HIF-1α. Using this gene expression signature, we have successfully stratified publicly available breast cancer patient samples into hypoxia positive and hypoxia negative groups followed by mining of differentially spliced isoforms between these groups. The Hypoxia Hallmark signature from MSigDB was also used independently to stratify the same tumor samples into hypoxic and normoxic.We found that 821 genes were showing differential splicing between samples stratified using a custom signature, whereas, 911 genes were showing differential splicing between samples stratified using the MSigDB signature. Finally, we performed multiple correlation tests between the methylation levels (ß) of microarray probes located within 1 kilo base pairs of isoform-specific exons using those exons' expression levels in the same patient samples in which the methylation level was recorded. We found that the expression level of one of the exons ofDHX32 and BICD2 significantly correlated with the methylation levels, and we were also able to predict patient survival (p-value: 0.02 for DHX32 and 0.0024 for BICD2). Our findings provide new insights into the potential functional role of intragenic DNA methylation in modulating alternative splicing during hypoxia.
Assuntos
Neoplasias da Mama/genética , RNA Helicases DEAD-box/genética , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Proteínas Associadas aos Microtúbulos/genética , Adulto , Idoso , Processamento Alternativo/genética , Neoplasias da Mama/patologia , Metilação de DNA/genética , Proteínas de Ligação a DNA/genética , Intervalo Livre de Doença , Feminino , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Células MCF-7 , Pessoa de Meia-Idade , Proteínas de Neoplasias/genética , Regiões Promotoras Genéticas , Ativação Transcricional , Transcriptoma/genética , Hipóxia Tumoral/genéticaRESUMO
AIM: LncRNAs may act as promising biomarkers in esophageal cancer (EC). Here, we illustrate the LncRNA profile and their clinical relevance in EC. PATIENTS & METHODS: In this study, we utilized the Cancer Genome Atlas RNA-sequencing and clinical data from 186 patients and 13 normal samples. Various statistical and gene set enrichment analysis (GSEA) were performed to identify the biomarkers. RESULTS: In a differential expression analysis, we identified a total of 127 LncRNAs with more differentially expressed in EC compared with normal and showed their function using guilt-by-association analysis. We generated a LncRNAs prognostic signature for EC. Using Cox regression analysis, we showed the prognostic ability of LncRNAs' prognostic signature in training and test-cohort (p-value < 0.01). CONCLUSION: In summary, we explored the LncRNA expression profile and their clinical utility in EC patients.
Assuntos
Biomarcadores Tumorais/genética , Neoplasias Esofágicas/diagnóstico , RNA Longo não Codificante/metabolismo , Área Sob a Curva , Biomarcadores Tumorais/metabolismo , Neoplasias Esofágicas/genética , Neoplasias Esofágicas/mortalidade , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Estimativa de Kaplan-Meier , Masculino , Pessoa de Meia-Idade , Prognóstico , Modelos de Riscos Proporcionais , RNA Longo não Codificante/genética , Curva ROC , Fatores de Risco , Transdução de Sinais/genéticaRESUMO
The histone demethylase KDM1A specifically demethylates lysine residues and its deregulation has been implicated in the initiation and progression of various cancers. However, KDM1A's molecular role and its pathological consequences, and prognostic significance in oral cancer remain less understood. In the present study, we sought to investigate the expression of KDM1A and its downstream role in oral cancer pathogenesis. By comparing mRNA expression profiles, we identified an elevated KDM1A expression in oral tumors when compared to normal oral tissues. In silico pathway prediction identified the association between KDM1A and E2F1 signaling in oral cancer. Pathway scanning, functional annotation analysis and In vitro assays showed the KDM1A's involvement in oral cancer cell proliferation and the cell cycle. Moreover, real time PCR and luciferase assays confirmed KDM1A's role in regulation of E2F1 signaling activity in oral cancer. Elevated KDM1A expression is associated with poor clinical outcome in oral cancer. Our data indicate that deregulated KDM1A expression is positively associated with proliferative phenotype of oral cancer and confers poor clinical outcome. These cumulative data suggest that KDM1A might be a potential diagnostic and therapeutic target for oral cancer.