Transcriptomic data of BT549 triple negative breast cancer cells treated with 20 μM NU7441,a DNA-dependent kinase inhibitor

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a multifunctional serine-threonine protein kinase that plays pleiotropic roles in cancer.NU7441 is a specific DNA-PKcs inhibitor.We investigated the effect of the DNA-dependent kinase (DNA-PK) inhibitor, NU7441, on the transcriptome of BT549 triple negative breast cancer (TNBC) cells.Total RNA extracted from NU7441 or vehicle-treated cells was processed for preparation of sequencing libraries . Assessment of read quality was performed using fastqc tool. Trimming and filtering low-quality reads were performed using fastp. Reads were aligned by hisat2. SAM files were converted to BAM files using Samtools. Mapped reads were quantified using featureCounts.The RNA sequencing results were also subjected to gene differential expression analysis, Gene Ontology (GO) analysis and KEGG pathway analysis. After NU7441 treatment, total number of 2045 differential genes were selected according to |log2(FoldChange)| >= 1 & padj<= 0.05, among which 1365 genes were down-regulated and 680 genes were up-regulated. The differential genes in pattern recognition receptors (PRRs) immune responses signals, including NOD-like receptor signaling, Toll-like receptor signaling, RIG-I-like receptor signaling and Cytosolic DNA-sensing pathways were noted in this paper .

DNA依赖蛋白激酶催化亚基（DNA-dependent protein kinase catalytic subunit, DNA-PKcs）是一种多功能丝氨酸-苏氨酸蛋白激酶，在癌症中发挥多效性调控作用。NU7441是一种特异性DNA-PKcs抑制剂。本研究探究了DNA依赖蛋白激酶（DNA-dependent kinase, DNA-PK）抑制剂NU7441对BT549三阴性乳腺癌（triple negative breast cancer, TNBC）细胞转录组的影响。从经NU7441处理或溶剂对照处理的细胞中提取总RNA，用于构建测序文库。使用fastqc工具对测序reads进行质量评估，通过fastp工具对低质量reads进行修剪与过滤。采用hisat2工具完成reads比对，借助Samtools将SAM格式文件转换为BAM格式文件，利用featureCounts对比对成功的reads进行定量分析。本研究同时对RNA测序结果开展了基因差异表达分析、基因本体（Gene Ontology, GO）分析及京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路分析。经NU7441处理后，依据|log₂(折叠变化)| ≥1 且校正后P值（padj）≤0.05的筛选标准，共鉴定得到2045个差异表达基因，其中1365个基因表达下调，680个基因表达上调。本研究分析了模式识别受体（pattern recognition receptors, PRRs）免疫应答信号通路相关的差异基因，涵盖NOD样受体信号通路、Toll样受体信号通路、视黄酸诱导基因I样受体（RIG-I样）信号通路及胞质DNA感知通路。