You are here

Elife DOI:10.7554/eLife.24060

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

Publication TypeJournal Article
Year of Publication2017
AuthorsRohban, MHossein, Singh, S, Wu, X, Berthet, JB, Bray, M-A, Shrestha, Y, Varelas, X, Boehm, JS, Carpenter, AE
Date Published2017 03 18
KeywordsAdaptor Proteins, Signal Transducing, Alleles, Cell Line, Tumor, Cell Nucleus, Cell Transformation, Neoplastic, Endoplasmic Reticulum, Fluorescent Dyes, Gene Expression Profiling, Gene Expression Regulation, Golgi Apparatus, HEK293 Cells, Humans, Image Processing, Computer-Assisted, Intracellular Signaling Peptides and Proteins, Mitochondria, Multigene Family, NF-kappa B, Optical Imaging, Osteoblasts, Phosphoproteins, Protein-Serine-Threonine Kinases, Proto-Oncogene Proteins c-rel, Signal Transduction, Staining and Labeling, TNF Receptor-Associated Factor 2

We hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically meaningful gene clusters consistent with known functional annotation (e.g., the RAS-RAF-MEK-ERK cascade). We used novel subpopulation-based visualization methods to interpret the morphological changes for specific clusters. This unbiased morphologic map of gene function revealed TRAF2/c-REL negative regulation of YAP1/WWTR1-responsive pathways. We confirmed this discovery of functional connectivity between the NF-κB pathway and Hippo pathway effectors at the transcriptional level, thereby expanding knowledge of these two signaling pathways that critically regulate tumor initiation and progression. We make the images and raw data publicly available, providing an initial morphological map of major biological pathways for future study.


Alternate JournalElife
PubMed ID28315521
PubMed Central IDPMC5386591
Grant ListF31 HL132506 / HL / NHLBI NIH HHS / United States
T32 HL007035 / HL / NHLBI NIH HHS / United States