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Eric Wu1,2, Alexandro E Trevino1, Zhenqin Wu1,3

  • 1Enable Medicine, Menlo Park, CA 94025, USA.

PNAS Nexus
|June 5, 2023
PubMed
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This summary is machine-generated.

A new machine learning method, 7-UP, computationally generates high-plex CODEX data from standard multiplex immunofluorescence (mIF) panels. This approach enables detailed cellular analysis and disease insights from more accessible mIF data.

Area of Science:

  • Biomedical Imaging
  • Computational Biology
  • Pathology

Background:

  • Multiplex immunofluorescence (mIF) allows simultaneous detection of multiple protein biomarkers on tissue sections.
  • High-plex CODEX systems enable imaging of over 40 biomarkers for detailed molecular phenotyping and cellular interaction analysis.
  • The cost and time associated with high-plex data acquisition limit its clinical applicability.

Purpose of the Study:

  • To develop a machine learning framework (7-UP) to computationally generate high-plex CODEX data from standard 7-plex mIF panels.
  • To leverage cellular morphology for imputing missing biomarker information.
  • To assess the utility of imputed data for cell type classification and patient outcome prediction.

Main Methods:

  • Development of the 7-UP machine learning framework.

Related Experiment Videos

  • Application of 7-UP to standard 7-plex mIF data to generate in silico 40-plex CODEX data.
  • Validation of imputed biomarkers for cell type classification and survival prediction.
  • Assessment of imputation generalization across different clinical sites and cancer types.

    • Main Results:

    • The 7-UP framework successfully generated in silico 40-plex CODEX data at single-cell resolution from 7-plex mIF panels.
    • Imputed biomarkers accurately classified cell types and predicted patient survival outcomes.
    • 7-UP imputations demonstrated robust generalization across diverse clinical samples and cancer types.

    Conclusions:

    • The 7-UP method enables the generation of high-plex CODEX data computationally, making advanced molecular phenotyping more accessible.
    • This approach democratizes insights from high-plex imaging, facilitating broader applications in research and potentially clinical settings.
    • 7-UP opens avenues for in silico CODEX, expanding the utility of standard mIF assays.