Bioinformatic analysis of Protein Disulfide Isomerase A1 (PDIA1)-associated pathways towards developing stratified breast cancer therapies

The oxidoreductase protein disulfide isomerase A1 (PDIA1) functions as a cofactor for many transcription factors including the estrogen receptor alpha (ERa), the NF-??, the nuclear factor erythroid 2-like 2 (NRF2) and regulates the protein stability of the tumor suppressor p53. Taking this into account we hypothesized that PDIA1, by differentially modulating the gene expression of diverse subsets of genes in the ERa positive versus the ERa negative breast cancer cells, modifies dissimilar pathways in the two types of breast cancer. This hypothesis was investigated using RNA-seq data from PDIA1-silenced MCF-7 (ERa+) and MDA-MB-231 (ERa-) breast cancer cells treated with either interferon gamma (IFN-?) or etoposide (ETO) and the obtained data were further analyzed using a variety of bioinformatic tools alongside clinical relevance assessment via Kaplan-Meier patient survival curves. The results highlighted the dual role of PDIA1 in suppressing carcinogenesis in the ERa+ breast cancer patients by negatively regulating the response to reactive oxygen species and promoting carcinogenesis by inducing cell cycle progression. In the ERa- breast cancer patients PDIA1 prevents tumor development by regulating the NF-kappa B and p53 by modulating cell migration and inducing breast cancer progression through control of cytokine signaling and the immune response. The findings reported in this study shed light on the differential pathways regulating carcinogenesis in the ERa+ and ERa- breast cancer patients and could help identify therapeutic targets selectively effective in the ERa+ versus the ERa- patients. Overall design: RNA-sequencing study. 24 samples. Two cell lines. Three replicates per condition. Cells were treated with either etoposide (ETOP) or Interferon-Gamma (INF/IFN) and either with scramble siRNA or siRNA against P4HB (PDIA1).

氧化还原酶蛋白质二硫键异构酶A1（oxidoreductase protein disulfide isomerase A1, PDIA1）可作为多种转录因子的辅因子，包括雌激素受体α（estrogen receptor alpha, ERα）、核因子κB（NF-κB）、核因子红细胞2相关因子2（nuclear factor erythroid 2-like 2, NRF2），并可调控肿瘤抑制因子p53的蛋白稳定性。基于此，我们提出假说：PDIA1可在雌激素受体α阳性（ERα+）与阴性（ERα-）乳腺癌细胞中，差异性调控不同基因子集的表达，进而对两种乳腺癌的信号通路产生差异化影响。本研究通过分析经γ干扰素（interferon gamma, IFN-γ）或依托泊苷（etoposide, ETO）处理的、敲低PDIA1的ERα+乳腺癌细胞系MCF-7与ERα-乳腺癌细胞系MDA-MB-231的转录组测序（RNA-seq）数据，结合多种生物信息学工具与基于卡普兰-迈耶患者生存曲线的临床相关性分析，对该假说进行了验证。研究结果显示，PDIA1在ERα+乳腺癌患者中发挥双重作用：一方面通过负调控活性氧（reactive oxygen species, ROS）应答抑制癌变，另一方面通过促进细胞周期进程推动癌变；而在ERα-乳腺癌患者中，PDIA1可通过调控核因子κB与p53的功能、调节细胞迁移以抑制肿瘤发生，并通过调控细胞因子信号通路与免疫应答促进乳腺癌进展。本研究阐明了调控ERα+与ERα-乳腺癌患者癌变的差异化通路，可为两类患者分别筛选具有选择性疗效的治疗靶点提供理论依据。实验设计概述：转录组测序研究，共纳入24例样本，涵盖2种细胞系，每种处理条件设置3次生物学重复。细胞分别经依托泊苷（ETOP）或γ干扰素（INF/IFN）处理，并转染阴性对照siRNA或靶向P4HB（PDIA1）的siRNA。