多种癌症组织中蛋白磷酸酶表观遗传沉默对细胞和临床的影响。

IF 3.8 3区 医学 Q2 GENETICS & HEREDITY
Edward Wiltshire, Manuel Castro de Moura, David Piñeyro, Ricky S Joshi
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引用次数: 0

摘要

背景:蛋白磷酸酶(PPE)和蛋白激酶同时控制着磷酸化机制,而磷酸化机制可严格调节细胞内信号通路并刺激细胞反应。在人类恶性肿瘤中,蛋白磷酸酶和蛋白激酶经常发生突变,导致激酶活性失控和蛋白磷酸酶抑制,从而导致细胞增殖、迁移和对抗癌疗法产生抗药性。与癌症相关的 PPE 启动子 DNA 高甲基化会导致转录沉默(表突变),这是癌症的一大特征。尽管最近在测序技术、数据可用性和计算能力方面取得了进展,但只有一小部分 PPE 因表型突变而转录失活:在这项研究中,我们通过三种细胞模型(原发性肿瘤、癌细胞系和三维嵌入式癌细胞培养物)检测了705名癌症患者的五种组织(大肠、食道、肺、胰腺和胃)中蛋白磷酸酶酶及其相互作用蛋白(PPEIP)的启动子相关DNA甲基化图谱。由于 PPEIP 的一部分是已知的肿瘤抑制基因,我们分析了 PPEIP 启动子高甲基化标记对基因表达、细胞网络和临床环境的影响:结果:在此,我们报告了 PPEIP 的表突变在癌症基因组中的频繁发生,其表现与转录活性无关。我们观察到不同肿瘤对表观突变的易感性不同,并确定了主要受表观突变影响的特定细胞信号网络。此外,RNA-seq分析显示表观突变对大多数(而非全部)蛋白酪氨酸磷酸酶转录有负面影响。最后,我们发现了一些新的临床生物标志物,这些标志物可为患者死亡率和抗癌治疗敏感性提供信息:我们认为,PPEIP 上的 DNA 高甲基化标记经常导致恶性肿瘤的发病机制,在精准医疗领域,它有望作为生物标志物,为患者生存和治疗反应等临床特征提供信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Cellular and clinical impact of protein phosphatase enzyme epigenetic silencing in multiple cancer tissues.

Background: Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signalling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases are frequently mutated resulting in uncontrolled kinase activity and PPE suppression, leading to cell proliferation, migration and resistance to anti-cancer therapies. Cancer associated DNA hypermethylation at PPE promoters gives rise to transcriptional silencing (epimutations) and is a hallmark of cancer. Despite recent advances in sequencing technologies, data availability and computational capabilities, only a fraction of PPE have been reported as transcriptionally inactive as a consequence of epimutations.

Methods: In this study, we examined promoter-associated DNA methylation profiles in Protein Phosphatase Enzymes and their Interacting Proteins (PPEIP) in a cohort of 705 cancer patients in five tissues (Large intestine, Oesophagus, Lung, Pancreas and Stomach) in three cell models (primary tumours, cancer cell lines and 3D embedded cancer cell cultures). As a subset of PPEIP are known tumour suppressor genes, we analysed the impact of PPEIP promoter hypermethylation marks on gene expression, cellular networks and in a clinical setting.

Results: Here, we report epimutations in PPEIP are a frequent occurrence in the cancer genome and manifest independent of transcriptional activity. We observed that different tumours have varying susceptibility to epimutations and identify specific cellular signalling networks that are primarily affected by epimutations. Additionally, RNA-seq analysis showed the negative impact of epimutations on most (not all) Protein Tyrosine Phosphatase transcription. Finally, we detected novel clinical biomarkers that inform on patient mortality and anti-cancer treatment sensitivity.

Conclusions: We propose that DNA hypermethylation marks at PPEIP frequently contribute to the pathogenesis of malignancies and within the precision medicine space, hold promise as biomarkers to inform on clinical features such as patient survival and therapeutic response.

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来源期刊
Human Genomics
Human Genomics GENETICS & HEREDITY-
CiteScore
6.00
自引率
2.20%
发文量
55
审稿时长
11 weeks
期刊介绍: Human Genomics is a peer-reviewed, open access, online journal that focuses on the application of genomic analysis in all aspects of human health and disease, as well as genomic analysis of drug efficacy and safety, and comparative genomics. Topics covered by the journal include, but are not limited to: pharmacogenomics, genome-wide association studies, genome-wide sequencing, exome sequencing, next-generation deep-sequencing, functional genomics, epigenomics, translational genomics, expression profiling, proteomics, bioinformatics, animal models, statistical genetics, genetic epidemiology, human population genetics and comparative genomics.
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