Schiebout Courtney, Lust Hannah, Huang Yina, Frost H Robert
Department of Biomedical Data Science, Dartmouth College, Hanover, NH 03755, United States.
MDI Biological Laboratory, Bar Harbor, ME 04609, United States.
Bioinform Adv. 2023 Sep 6;3(1):vbad120. doi: 10.1093/bioadv/vbad120. eCollection 2023.
Doublets are usually considered an unwanted artifact of single-cell RNA-sequencing (scRNA-seq) and are only identified in datasets for the sake of removal. However, if cells have a juxtacrine interaction with one another and maintain this association through an scRNA-seq processing pipeline that only partially dissociates the tissue, these doublets can provide meaningful biological information regarding the intercellular signals and processes occurring in the analyzed tissue. This is especially true for cases such as the immune compartment of the tumor microenvironment, where the frequency and the type of immune cell juxtacrine interactions can be a prognostic indicator. We developed Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA) as a pipeline for identifying and analyzing biologically meaningful doublets in scRNA-seq data. CIcADA identifies putative doublets using multi-label cell type scores and characterizes interaction dynamics through a comparison against synthetic doublets of the same cell type composition. In performing CIcADA on several scRNA-seq tumor datasets, we found that the identified doublets were consistently upregulating expression of immune response genes.
An R package implementing the CIcADA method is in development and will be released on CRAN, but for now it is available at https://github.com/schiebout/CAMML.
双峰通常被视为单细胞RNA测序（scRNA-seq）中不需要的伪像，仅在数据集中被识别以便去除。然而，如果细胞彼此存在旁分泌相互作用，并通过仅部分解离组织的scRNA-seq处理流程维持这种关联，这些双峰可以提供有关被分析组织中发生的细胞间信号和过程的有意义的生物学信息。对于肿瘤微环境的免疫区室等情况尤其如此，其中免疫细胞旁分泌相互作用的频率和类型可能是一个预后指标。我们开发了scRNA-seq中使用双峰的细胞类型特异性相互作用分析（CIcADA）作为在scRNA-seq数据中识别和分析具有生物学意义的双峰的流程。CIcADA使用多标签细胞类型分数识别推定的双峰，并通过与相同细胞类型组成的合成双峰进行比较来表征相互作用动态。在对几个scRNA-seq肿瘤数据集进行CIcADA分析时，我们发现识别出的双峰始终上调免疫反应基因的表达。
一个实现CIcADA方法的R包正在开发中，将在CRAN上发布，但目前可在https://github.com/schiebout/CAMML获取。
