Ge Fangfang, Wang Yulu, Chen Peng, Sharma Amit, Huang Xiaoli, Dakal Tikam Chand, Wang Zifeng, Jaehde Ulrich, Essler Markus, Schmid Matthias, Schmidt-Wolf Ingo G H
Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital of Bonn, Bonn, Germany.
Department of Neurosurgery, University Hospital of Bonn, Bonn, Germany.
Curr Med Chem. 2024 Oct 11. doi: 10.2174/0109298673311108240926062214.
We focused on the FOXN3 gene and selected its antisense transcripts (FOXN3-AS1) to investigate its potential involvement in acute myeloid leukemia (AML).
Several integrated multi-omics datasets have expanded the horizons of the cancer landscape. With the emergence of new high-throughput technologies, a large number of non-coding RNAs have been confirmed to be involved in the pathogenesis of different types of hematological malignancies.
We conducted experimental validation using quantitative polymerase chain reaction (qPCR) with bone marrow specimens from AML patients. Then, Kaplan-Meier (KM) and Receiver Operating Characteristic (ROC) curves were used to substantiate the prognostic association between FOXN3-AS1 and AML patients within the TCGA database. Correlation between FOXN3-AS1 expression and gene mutation, immune, and immune function using Spearman correlation analysis. To explore the physical and functional interaction between FOXN3-AS1 and the DNMT1 protein, we utilized the RPISeq web tool from Iowa State University. Subsequently, we performed qPCR experiments to test the effect of 5AzaC (DNMT1 inhibitor) on FOXN3-AS1 expression AML cell lines (THP1 and OCI-AML3). We leveraged the "OncoPredict" R package in conjunction with the Genomics of Drug Sensitivity (GDSC) database to predict drug response in AML patients expressing FOXN3-AS1.
We observed a significant upregulation of FOXN3-AS1 expression in AML patients compared to healthy controls using clinical samples. The TCGA database revealed an association between high FOXN3-AS1 expression and adverse prognosis. In our subsequent analysis, genes with poor prognostic implications in AML patients were exclusively identified in the FOXN3-AS1 high-expression group, further corroborating this relationship. AML patients with higher FOXN3-AS1 expression levels may respond less optimally to immunotherapy than patients with lower levels. Besides, we computationally predicted the interaction of FOXN3- AS1 and DNMT1 protein and experimentally confirmed that DNMT1i (GSK-3484862) affects the expression level of FOXN3-AS1. We also found that the chemotherapy drugs (5-Fluorouralic, Cisplatin, Dactolisib, Sapitinib, Temozolomide, Ulixertinib, Vinorelbine, Ruxolitinib, Osimertinib and Cisplatin) showed favorable responses in AML patients with high FOXN3-AS1 expression levels.
Our candidate approach identifies FOXN3-AS1 as a prognostic indicator of survival in AML with a potential immune-related role. The preliminary observations we made on FOXN3-AS1/DNMT1 crosstalk warrant more in-depth invested immunotherapeutic approaches in AML.
我们聚焦于FOXN3基因并选择其反义转录本（FOXN3-AS1），以研究其在急性髓系白血病（AML）中的潜在作用。
多个整合的多组学数据集拓展了癌症研究的视野。随着新高通量技术的出现，大量非编码RNA已被证实参与不同类型血液系统恶性肿瘤的发病机制。
我们使用来自AML患者的骨髓标本，通过定量聚合酶链反应（qPCR）进行实验验证。然后，利用Kaplan-Meier（KM）曲线和受试者工作特征（ROC）曲线，在TCGA数据库中证实FOXN3-AS1与AML患者的预后相关性。使用Spearman相关性分析FOXN3-AS1表达与基因突变、免疫及免疫功能之间的相关性。为探索FOXN3-AS1与DNMT1蛋白之间的物理和功能相互作用，我们使用了爱荷华州立大学的RPISeq网络工具。随后，我们进行qPCR实验，以测试5-氮杂胞苷（DNMT1抑制剂）对AML细胞系（THP1和OCI-AML3）中FOXN3-AS1表达的影响。我们利用“OncoPredict”R包结合药物敏感性基因组学（GDSC）数据库，预测表达FOXN3-AS1的AML患者的药物反应。
使用临床样本，我们观察到与健康对照相比，AML患者中FOXN3-AS1表达显著上调。TCGA数据库显示高FOXN3-AS1表达与不良预后相关。在我们随后的分析中，在FOXN3-AS1高表达组中专门鉴定出对AML患者预后有不良影响的基因，进一步证实了这种关系。FOXN3-AS1表达水平较高的AML患者对免疫治疗的反应可能不如水平较低的患者。此外，我们通过计算预测了FOXN3-AS1与DNMT1蛋白的相互作用，并通过实验证实DNMT1抑制剂（GSK-3484862）会影响FOXN3-AS1的表达水平。我们还发现化疗药物（5-氟尿嘧啶、顺铂、达可替尼、沙帕替尼、替莫唑胺、乌利替尼、长春瑞滨、鲁索替尼、奥希替尼和顺铂）在FOXN3-AS1表达水平较高的AML患者中显示出良好的反应。
我们的候选方法将FOXN3-AS1鉴定为AML生存的预后指标，具有潜在的免疫相关作用。我们对FOXN3-AS1/DNMT1相互作用的初步观察结果，值得在AML中进行更深入的免疫治疗方法研究。
