固定的,嵌入的活检的单细胞空间转录学揭示了结肠炎相关的细胞网络
Elvira Mennillo1, Madison L Lotstein2,3, Gyehyun Lee1
1Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
bioRxiv : the preprint server for biology
|November 28, 2024
概括
在存档的FFPE活检上,基于成像的单细胞空间转录学 (iSCST) 确定了与炎症相关的纤维细胞和单细胞是性结肠炎的关键. 这一框架有助于发现用于患者风险分层的生物标志物.
科学领域:
- 生物技术是生物技术.
- 基因组学就是基因组学.
- 免疫学 免疫学 免疫学
背景情况:
- 归档的甲固定,嵌 (FFPE) 组织为翻译研究提供了巨大的潜力.
- 为FFPE样本开发强大的基于成像的单细胞空间转录学 (iSCST) 对于分析临床标本至关重要.
研究的目的:
- 建立一个可靠的iSCST框架来分析从炎症性肠病 (IBD) 患者的存档的FFPE粘膜活检.
- 为了对不同的iSCST平台进行FPE组织分析进行比较.
主要方法:
- 使用57个FFPE粘膜活检 (9名健康对照组,11名性结肠炎患者) 进行了3个iSCST平台的基准测试.
- 应用统一的数据处理管道,包括细胞细分,转录检测,注释,差异基因表达和邻里丰富.
- 用外部批量转录基因数据集验证iSCST的发现.
主要成果:
- 一个定制的290个复数的Xenium基因组显示出在FFPE组织中检测转录的高灵敏度和特异性.
- 确定了与炎症相关的纤维细胞 (IAF) 和单细胞作为结肠炎相关的细胞社区.
- 发现与Vedolizumab (VDZ) 响应相关的独特的转录组签名,区分了响应者与非响应者.
结论:
- 优化的iSCST框架可以在常规临床FFPE样本中研究结肠炎相关的细胞网络.
- 来自iSCST的基于FFPE的生物标志物可以集成到临床工作流程中,以实现潜在的患者风险分层.
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