SPaRTAN, a Computational Framework for Linking Cell-Surface Receptors to Transcriptional Regulators

Details

• Personal Author:
  Hartman DJ ; Ma X ; Osmanbeyoglu HU ; Qi Z ; Singh H ; Somasundaram A
• Description:
  The identity and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. Recently single-cell technologies have been developed that enable simultaneous quantitative analysis of cell-surface receptor expression with transcriptional states. To date, these datasets have not been used to systematically develop cell-context-specific maps of the interface between signaling and transcriptional regulators orchestrating cellular identity and function. 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 immune cell types in the blood to predict the coupling of signaling receptors with cell context-specific TFs. Selected predictions are validated by prior knowledge and flow cytometry analyses. SPaRTAN is then used to predict the signaling coupled TF states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN enhances the utility of CITE-seq datasets to uncover TF and cell-surface receptor relationships in diverse cellular states. [Description provided by NIOSH]
• Subjects:
  Cytology Genetics Occupational Health Safety
• Keywords:
  Cell Signaling Cell Type Cytometric Analysis Emerging Technology Gene Regulation Genes Quantitative Analysis
• ISSN:
  0305-1048
• Document Type:
  Text
• Funding:
  Cooperative Agreement
• Genre:
  Journal Article
• Place as Subject:
  OSHA Region 3 ; Pennsylvania
• CIO:
  National Institute for Occupational Safety and Health (NIOSH)
• Topic:
  Workplace Safety & Health
• Location:
  North America
• Volume:
  49
• Issue:
  17
• NIOSHTIC Number:
  nn:20063464
• Citation:
  Nucleic Acids Res 2021 Sep; 49(17):9633-9647
• Contact Point Address:
  Hatice Ulku Osmanbeyoglu, Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
• Email:
  osmanbeyogluhu@pitt.edu
• Federal Fiscal Year:
  2021
• Performing Organization:
  University of Pittsburgh at Pittsburgh
• Peer Reviewed:
  True
• Start Date:
  20060901
• Source Full Name:
  Nucleic Acids Research
• End Date:
  20260831
• Collection(s):
  National Institute for Occupational Safety and Health
• Main Document Checksum:
  urn:sha-512:c84a13c3efefa24b915d6dea7c48e1d0bc5e3250c8f3add19fb9bf6b805bd5d0c50902df9975164a72419180cb3684b3885f40296dbe8189870d364f2d411076
• Download URL:
  https://stacks.cdc.gov/view/cdc/226527/cdc_226527_DS1.pdf
• File Type:
  [PDF - 9.16 MB ]