Systematic morphological profiling of human gene and allele function via Cell Painting

Area of Science:

• Cell Biology
• Genomics
• Bioinformatics

Background:

• Systematic functional annotation of human genes and disease alleles is crucial for understanding biological processes.
• Morphological profiling using cell-based assays offers a potential avenue for unbiased functional characterization.

Purpose of the Study:

• To develop and validate a microscopy-based Cell Painting assay for systematic functional annotation of genes.
• To create a morphological map of gene function and uncover novel pathway interactions.

Main Methods:

• Utilized a Cell Painting assay to generate morphological profiles for 220 human genes and disease-associated alleles.
• Applied subpopulation-based visualization methods to interpret morphological changes and identify gene clusters.
• Validated discovered functional connections at the transcriptional level.

Main Results:

• Detected significant morphological profiles for 50% of the tested genes, forming biologically meaningful clusters.
• The morphological map revealed a novel negative regulatory interaction between TRAF2/c-REL and YAP1/WWTR1-responsive pathways.
• Confirmed functional connectivity between the NF-κB and Hippo signaling pathways.

Conclusions:

• Morphological profiling is an effective strategy for systematic gene functional annotation.
• The study expands knowledge of the NF-κB and Hippo pathways, critical regulators of tumor initiation and progression.
• Publicly released images and data provide a foundational resource for future research on biological pathways.