m6A 基因型和预后特征评估急性髓系白血病患者的预后。

m6A genotypes and prognostic signature for assessing the prognosis of patients with acute myeloid leukemia.

机构信息

Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China.

出版信息

BMC Med Genomics. 2023 Aug 18;16(1):191. doi: 10.1186/s12920-023-01629-1.

DOI:10.1186/s12920-023-01629-1

PMID:37596597

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10436408/

Abstract

BACKGROUND

N6-methyladenosine (m6A) has been confirmed to function critically in acute myeloid leukemia (AML) progression. Hitherto, the subtyping and prognostic predictive significance of m6A-correlated genes in AML is unclear.

METHOD

From The Cancer Genome Atlas (TCGA-LAML), Therapeutically Applicable Research to Generate Effective Treatments (TARGET-AML) and Gene Expression Omnibus (GEO, GSE71014) databases, we collected the sequencing data of AML patients. The batch effect was removed via limma package for TCGA-LAML and TARGET-AML, and the aggregated samples were AML cohorts. Samples in the AML cohort identified m6A models in AML by consensus clustering based on 23-m6A-related modulators. M6A-related differentially expressed genes (m6ARDEGs) influencing the overall survival (OS) of AML were determined by performing differential expression analysis and univariate COX analysis, and consensus-based clustering was utilized to access AML molecular subtypes. LASSO and multivariate COX analyses were performed to obtain the optimized m6ARDEGs to construct the m6A Prognostic Risk Score (m6APR_Score). Whether the model was robust was evaluated according to Kaplan-Meier (K-M) and receiver operator characteristic (ROC) curves. Further, the abundance of immune cell infiltration was explored in different m6A modification patterns and molecular subtypes and m6APR_Score groupings. Finally, nomogram was constructed to predict OS in AML. Quantitative real-time polymerase chain reaction (RT-qPCR) and cell counting kit-8 (CCK-8) assay were used to validate the genes in m6APR_Score in AML cells.

RESULTS

The m6A models (m6AM1, m6AM2, m6AM3) and molecular subtypes (C1, C2, C3) were identified in the AML cohort, exhibiting different prognosis and immunoreactivity. We recognized novel prognostic biomarkers of AML such as CD83, NRIP1, ACSL1, METTL7B, OGT, and C4orf48. AML patients were grouped into high-m6APR_Score and low-m6APR_Score groups, with the later group showing a better prognosis than former one. Both the AML cohort and the validation cohort GSE71014 demonstrated excellent prediction. Finally, the nomogram accurately predicted the survival of patients suffering from AML. Further, the decision curves showed that both nomogram and m6APR_Score showed excellent prediction. It was confirmed in vitro experiments that mRNA expressions of NRIP1, ACSL1, METTL7B and OGT were elevated, while CD83 and C4orf48 mRNA expressions downregulated in AML cells. A significant increase in the viability of U937 and THP-1 cell lines after inhibition of CD83, while siMETTL7B had contrast results.

CONCLUSION

Our study demonstrated that m6APR_Score and CD83, NRIP1, ACSL1, METTL7B, OGT, and C4orf48 potentially provided novel and promising prognostic support for AML patients.

摘要

背景

N6-甲基腺苷（m6A）已被证实对急性髓系白血病（AML）的进展起着至关重要的作用。迄今为止，m6A 相关基因在 AML 中的亚分型和预后预测意义尚不清楚。

方法

从癌症基因组图谱（TCGA-LAML）、治疗性适用研究以产生有效治疗方法（TARGET-AML）和基因表达综合数据库（GEO，GSE71014）中，我们收集了 AML 患者的测序数据。通过 limma 包去除 TCGA-LAML 和 TARGET-AML 的批次效应，并将汇总样本定义为 AML 队列。在 AML 队列中，基于 23 个 m6A 相关调节剂，通过共识聚类确定 m6A 模型。通过差异表达分析和单变量 COX 分析确定影响 AML 总生存期（OS）的 m6A 差异表达基因（m6ARDEGs），并利用共识聚类确定 AML 分子亚型。通过 LASSO 和多变量 COX 分析获得优化的 m6ARDEGs 以构建 m6A 预后风险评分（m6APR_Score）。根据 Kaplan-Meier（K-M）和接收器操作特征（ROC）曲线评估模型的稳健性。进一步探索不同 m6A 修饰模式和分子亚型以及 m6APR_Score 分组中免疫细胞浸润的丰度。最后，构建列线图以预测 AML 的 OS。定量实时聚合酶链反应（RT-qPCR）和细胞计数试剂盒-8（CCK-8）测定用于验证 AML 细胞中 m6APR_Score 的基因。

结果

在 AML 队列中鉴定出 m6A 模型（m6AM1、m6AM2、m6AM3）和分子亚型（C1、C2、C3），它们表现出不同的预后和免疫活性。我们发现了 AML 的新的预后生物标志物，如 CD83、NRIP1、ACSL1、METTL7B、OGT 和 C4orf48。AML 患者被分为高 m6APR_Score 和低 m6APR_Score 组，后者的预后优于前者。AML 队列和验证队列 GSE71014 均表现出优异的预测能力。最后，列线图准确预测了 AML 患者的生存情况。进一步的决策曲线表明，列线图和 m6APR_Score 均具有出色的预测能力。体外实验证实，AML 细胞中 NRIP1、ACSL1、METTL7B 和 OGT 的 mRNA 表达上调，而 CD83 和 C4orf48 的 mRNA 表达下调。CD83 抑制后 U937 和 THP-1 细胞系的活力显著增加，而 siMETTL7B 则相反。