目的：雌激素受体乳腺癌（BC）的特点是雌激素受体的表达。它是女性中最常见的癌症，全球发病率为 226 万例。本研究的目的是确定雌激素受体阳性和三阴性 BC 样本之间的差异表达基因和亚型转换。方法：从 ArrayExpress 收集数据，然后从 HISAT2 进行预处理和后续映射。通过StringTie进行Read定量，然后使用R包ballgown进行差异表达分析。使用Enrichr进行功能富集分析，然后根据ScType标记数据库筛选免疫基因。还使用 IsoformSwitchAnalyzeR 软件包进行异构体开关分析。结果：共鉴定出9,771个差异表达基因，其中上调表达基因86个，下调表达基因117个。六个基因被鉴定为主要与雌激素受体阳性 BC 相关，同时发现了一组新的十个基因，这些基因以前在雌激素受体阳性 BC 中未曾报道过。此外，还确定了免疫系统相关基因中的选择性剪接和随后的亚型使用。结论：本研究确定了癌细胞中免疫系统相关基因中亚型的差异使用，表明由于 CXCR 趋化因子受体结合、铁离子结合和细胞因子活性的失调而导致免疫抑制。版权所有 © 2023 Khan、Hanif、Alsakhen、Jabbar 、沙姆赫、阿尔萨伊阿里、阿尔迈马迪、阿尔加姆迪、沙库里、阿尔法拉吉、阿尔穆塔里、侯赛因·伊萨·穆罕默德、阿布齐德、雷赫曼和胡瓦梅尔。

Objective: Estrogen receptor breast cancer (BC) is characterized by the expression of estrogen receptors. It is the most common cancer among women, with an incidence rate of 2.26 million cases worldwide. The aim of this study was to identify differentially expressed genes and isoform switching between estrogen receptor positive and triple negative BC samples. Methods: The data were collected from ArrayExpress, followed by preprocessing and subsequent mapping from HISAT2. Read quantification was performed by StringTie, and then R package ballgown was used to perform differential expression analysis. Functional enrichment analysis was conducted using Enrichr, and then immune genes were shortlisted based on the ScType marker database. Isoform switch analysis was also performed using the IsoformSwitchAnalyzeR package. Results: A total of 9,771 differentially expressed genes were identified, of which 86 were upregulated and 117 were downregulated. Six genes were identified as mainly associated with estrogen receptor positive BC, while a novel set of ten genes were found which have not previously been reported in estrogen receptor positive BC. Furthermore, alternative splicing and subsequent isoform usage in the immune system related genes were determined. Conclusion: This study identified the differential usage of isoforms in the immune system related genes in cancer cells that suggest immunosuppression due to the dysregulation of CXCR chemokine receptor binding, iron ion binding, and cytokine activity.Copyright © 2023 Khan, Hanif, Alsakhen, Jabbar, Shamkh, Alsaiari, Almehmadi, Alghamdi, Shakoori, Al Farraj, Almutairi, Hussein Issa Mohammed, Abouzied, Rehman and Huwaimel.