Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.
Cancer Rep (Hoboken). 2023 Jan;6(1):e1686. doi: 10.1002/cnr2.1686. Epub 2022 Jul 30.
Chemotherapeutic drug concentrations vary across different regions of tumors and this is thought to be involved in development of chemotherapy resistance. Insufficient drug delivery to some regions of the tumor may be due to spatial differences in expression of genes involved in the disposition, transport, and detoxification of drugs (pharmacogenes). Therefore, in this study, we analyzed the spatial expression of 286 pharmacogenes in six breast cancer tissues using the recently developed Visium spatial transcriptomics platform to (1) determine if these pharmacogenes are expressed heterogeneously across tumor tissue and (2) to determine which pharmacogenes have the most spatial expression heterogeneity.
The spatial transcriptomics technology sequences the transcriptome of 55 um diameter barcoded sections (spots) across a tissue sample. We analyzed spatial gene expression profiles of four biobank-sourced breast tumor samples in addition to two breast tumor sample datasets from 10× Genomics. We define heterogeneity as the interquartile range of read counts. Collectively, we identified 8887 spots in tumor regions, 3814 in stroma, 44 in lymphocytes, and 116 in normal regions based on pathologist annotation of the tissues. We showed statistically significant differences in expression of pharmacogenes in tumor regions compared to surrounding non-tumor regions. We also observed that the most heterogeneously expressed genes within tumor regions were involved in reactive oxygen species (ROS) handling and detoxification mechanisms. GPX4, GSTP1, MGST3, SOD1, CYP4Z1, CYB5R3, GSTK1, and NAT1 showed the most heterogeneous expression within tumor regions.
The heterogeneous expression of these pharmacogenes may have important implications for cancer therapy due to their ability to impact drug distribution and efficacy throughout the tumor. Our results suggest that chemoresistance caused by expression of GPX4, GSTP1, MGST3, and SOD1 may be intrinsic, not acquired, since the heterogeneity is not specific to chemotherapy-treated samples or cell type. Additionally, we identified candidate chemoresistance pharmacogenes that can be further tested through focused follow-up studies.
化疗药物浓度在肿瘤的不同区域存在差异，这被认为与化疗耐药的发展有关。肿瘤某些区域药物输送不足可能是由于参与药物处置、转运和解毒（药物基因）的基因在空间上的表达差异所致。因此，在这项研究中，我们使用最近开发的 Visium 空间转录组学平台分析了 6 个乳腺癌组织中 286 个药物基因的空间表达，以确定这些药物基因是否在肿瘤组织中存在异质性表达，以及哪些药物基因具有最大的空间表达异质性。
空间转录组学技术对 55μm 直径的带条码的组织切片（点）进行转录组测序。我们分析了来自四个生物库的乳腺癌组织样本的空间基因表达图谱，以及来自 10× Genomics 的两个乳腺癌组织样本数据集。我们将异质性定义为读取计数的四分位距。根据组织病理学家的注释，我们在肿瘤区域鉴定了 8887 个点，在基质中鉴定了 3814 个点，在淋巴细胞中鉴定了 44 个点，在正常区域中鉴定了 116 个点。我们发现与周围非肿瘤区域相比，肿瘤区域中药物基因的表达存在统计学显著差异。我们还观察到，肿瘤区域内表达最不均匀的基因与活性氧（ROS）处理和解毒机制有关。GPX4、GSTP1、MGST3、SOD1、CYP4Z1、CYB5R3、GSTK1 和 NAT1 在肿瘤区域内表达最不均匀。
这些药物基因的异质性表达可能对癌症治疗具有重要意义，因为它们能够影响药物在整个肿瘤中的分布和疗效。我们的研究结果表明，由于 GPX4、GSTP1、MGST3 和 SOD1 的表达导致的化疗耐药可能是内在的，而不是获得性的，因为这种异质性不是特异性的化疗处理样本或细胞类型。此外，我们还鉴定了候选化疗耐药药物基因，可以通过进一步的后续研究进行测试。
