|
| Status |
Public on Aug 16, 2021 |
| Title |
SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
The identity and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. Recently single-cell technologies such as CITE-seq 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. The 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 greatly enhances the utility of CITE-seq datasets to uncover TF and cell-surface receptor relationships in diverse cellular states.
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| |
|
| Overall design |
Human malignant mesotheliomas were profiled using CITE-seq
|
| Web link |
https://pubmed.ncbi.nlm.nih.gov/34500467/
|
| |
|
| Contributor(s) |
Osmanbeyoglu HU, Somasundaram A, Qi Z, Ma X |
| Citation(s) |
34500467 |
| |
| Submission date |
Apr 15, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Hatice Ulku Osmanbeyoglu |
| E-mail(s) |
osmanbeyoglulhu@pitt.edu
|
| Phone |
4126237789
|
| Organization name |
University of Pittsburgh
|
| Department |
Biomedical Informatics
|
| Lab |
Osmanbeyoglu Lab
|
| Street address |
5117 Centre Ave. G27c
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (4)
|
| GSM5242790 |
Gene expression from malignant pleural mesothelioma patient |
| GSM5242791 |
Antibody-derived tags from malignant pleural mesothelioma patient |
| GSM5242792 |
Gene expression from malignant peritoneal mesothelioma patient |
| GSM5242793 |
Antibody-derived tags from malignant peritoneal mesothelioma patient |
|
| Relations |
| BioProject |
PRJNA722248 |
| SRA |
SRP314970 |
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