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STK11/LKB1 功能丧失与人类肺腺癌中的全基因组 DNA 低甲基化和 - 腺苷甲硫氨酸耗竭相关。

STK11/LKB1 Loss of Function Is Associated with Global DNA Hypomethylation and -Adenosyl-Methionine Depletion in Human Lung Adenocarcinoma.

机构信息

Department of Internal Medicine, The Ohio State University, Columbus, Ohio.

Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.

出版信息

Cancer Res. 2021 Aug 15;81(16):4194-4204. doi: 10.1158/0008-5472.CAN-20-3199. Epub 2021 May 27.

Abstract

STK11 (liver kinase B1, LKB1) is the fourth most frequently mutated gene in lung adenocarcinoma, with loss of function observed in up to 30% of all cases. Our previous work identified a 16-gene signature for LKB1 loss of function through mutational and nonmutational mechanisms. In this study, we applied this genetic signature to The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples and discovered a novel association between LKB1 loss and widespread DNA demethylation. LKB1-deficient tumors showed depletion of -adenosyl-methionine (SAM-e), which is the primary substrate for DNMT1 activity. Lower methylation following LKB1 loss involved repetitive elements (RE) and altered RE transcription, as well as decreased sensitivity to azacytidine. Demethylated CpGs were enriched for FOXA family consensus binding sites, and nuclear expression, localization, and turnover of FOXA was dependent upon LKB1. Overall, these findings demonstrate that a large number of lung adenocarcinomas exhibit global hypomethylation driven by LKB1 loss, which has implications for both epigenetic therapy and immunotherapy in these cancers. SIGNIFICANCE: Lung adenocarcinomas with LKB1 loss demonstrate global genomic hypomethylation associated with depletion of SAM-e, reduced expression of DNMT1, and increased transcription of repetitive elements.

摘要

STK11(肝激酶 B1,LKB1)是肺腺癌中第四种最常发生突变的基因,在所有病例中约有 30%观察到功能丧失。我们之前的工作通过突变和非突变机制确定了 LKB1 功能丧失的 16 基因特征。在这项研究中,我们将该遗传特征应用于癌症基因组图谱(TCGA)肺腺癌样本中,发现了 LKB1 缺失与广泛的 DNA 去甲基化之间的新关联。LKB1 缺陷型肿瘤表现出 -腺苷甲硫氨酸(SAM-e)的耗竭,SAM-e 是 DNMT1 活性的主要底物。LKB1 缺失后,低甲基化涉及重复元件(RE)和改变的 RE 转录,以及对阿扎胞苷的敏感性降低。去甲基化的 CpG 富含 FOXA 家族的共识结合位点,FOXA 的核表达、定位和周转依赖于 LKB1。总的来说,这些发现表明大量肺腺癌表现出由 LKB1 缺失驱动的全基因组低甲基化,这对这些癌症的表观遗传治疗和免疫治疗都有影响。意义:LKB1 缺失的肺腺癌表现出与 SAM-e 耗竭、DNMT1 表达降低和重复元件转录增加相关的全基因组低甲基化。

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