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7-UP: generating in silico CODEX from a small set of immunofluorescence markers
- Source :
- PNAS Nexus.
- Publication Year :
- 2023
- Publisher :
- Oxford University Press (OUP), 2023.
-
Abstract
- Multiplex immunofluorescence (mIF) assays multiple protein biomarkers on a single tissue section. Recently, high-plex CODEX (co-detection by indexing) systems enable simultaneous imaging of 40+ protein biomarkers, unlocking more detailed molecular phenotyping, leading to richer insights into cellular interactions and disease. However, high-plex data can be slower and more costly to collect, limiting its applications, especially in clinical settings. We propose a machine learning framework, 7-UP, that can computationally generate in silico 40-plex CODEX at single-cell resolution from a standard 7-plex mIF panel by leveraging cellular morphology. We demonstrate the usefulness of the imputed biomarkers in accurately classifying cell types and predicting patient survival outcomes. Furthermore, 7-UP’s imputations generalize well across samples from different clinical sites and cancer types. 7-UP opens the possibility of in silico CODEX, making insights from high-plex mIF more widely available.
Details
- ISSN :
- 27526542
- Database :
- OpenAIRE
- Journal :
- PNAS Nexus
- Accession number :
- edsair.doi...........76d38f5e84f168d2f7724ceee569c832