Abstract
The developmental pathways and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. We present SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network), a computational method to link cell-surface receptors to transcription factors (TFs) by exploiting cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets with cis-regulatory information. SPaRTAN is applied to peripheral blood mononuclear cells (PBMCs) to predict the coupling of signaling receptors with cell context-specific TF activities. The predictions are validated by flow cytometry analyses. SPaRTAN is then used to analyze the signaling coupled TF activity states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN greatly enhances the utility of CITE-seq datasets to probe signaling coupled TF networks that regulate developmental or functional transitions in cellular states.
Competing Interest Statement
The authors have declared no competing interest.
