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Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

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Cancer Systems and Integrative Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2660))

Abstract

Complex signaling and transcriptional programs control the development and physiology of specialized cell types. Genetic perturbations in these programs cause human cancers to arise from a diverse set of specialized cell types and developmental states. Understanding these complex systems and their potential to drive cancer is critical for the development of immunotherapies and druggable targets. Pioneering single-cell multi-omics technologies that analyze transcriptional states have been coupled with the expression of cell-surface receptors. This chapter describes SPaRTAN (Single-cell Proteomic and RNA-based Transcription factor Activity Network), a computational framework, to link transcription factors with cell-surface protein expression. SPaRTAN uses CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) data and cis-regulatory sites to model the effect of interactions between transcription factors and cell-surface receptors on gene expression. We demonstrate the pipeline for SPaRTAN using CITE-seq data from peripheral blood mononuclear cells.

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Acknowledgments

This study was funded by support from the National Institutes of Health (R00 CA207871 and R35GM146989 to H.U.O., T15 LM007059-35 to A.S.) and the Innovation in Cancer Informatics Funds (to H.U.O.). Figures 1 and 2 were created with BioRender.com.

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Correspondence to Hatice Ulku Osmanbeyoglu .

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Sagan, A., Ma, X., Ramjattun, K., Osmanbeyoglu, H.U. (2023). Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes. In: Kasid, U.N., Clarke, R. (eds) Cancer Systems and Integrative Biology. Methods in Molecular Biology, vol 2660. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3163-8_11

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  • DOI: https://doi.org/10.1007/978-1-0716-3163-8_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3162-1

  • Online ISBN: 978-1-0716-3163-8

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