Systematic morphological profiling of human gene and allele function via Cell Painting.
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.
Broad Institute of MIT and Harvard, Cambridge, United States.
Mohammad Hossein
0000-0001-6589-850X
MH
Rohban
Broad Institute of MIT and Harvard, Cambridge, United States.
Shantanu
0000-0003-3150-3025
S
Singh
Broad Institute of MIT and Harvard, Cambridge, United States.
Xiaoyun
X
Wu
Department of Biochemistry, Boston University School of Medicine, Boston, United States.
Julia B
0000-0002-6549-8116
JB
Berthet
Broad Institute of MIT and Harvard, Cambridge, United States.
Mark-Anthony
0000-0002-9748-3592
MA
Bray
Broad Institute of MIT and Harvard, Cambridge, United States.
Yashaswi
Y
Shrestha
Department of Biochemistry, Boston University School of Medicine, Boston, United States.
Xaralabos
0000-0002-2882-4541
X
Varelas
Broad Institute of MIT and Harvard, Cambridge, United States.
Jesse S
0000-0002-6795-6336
JS
Boehm
Broad Institute of MIT and Harvard, Cambridge, United States.
Anne E
0000-0003-1555-8261
AE
Carpenter
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D000483:Alleles; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000378:metabolism / Q000648:ultrastructure; D002471:Cell Transformation, Neoplastic / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D004721:Endoplasmic Reticulum / Q000378:metabolism / Q000648:ultrastructure; D005456:Fluorescent Dyes / Q000737:chemistry; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006056:Golgi Apparatus / Q000378:metabolism / Q000648:ultrastructure; D057809:HEK293 Cells; D000090683:Hippo Signaling Pathway; D006801:Humans; D007091:Image Processing, Computer-Assisted; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism; D008928:Mitochondria / Q000378:metabolism / Q000648:ultrastructure; D005810:Multigene Family; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism; D061848:Optical Imaging; D010006:Osteoblasts / Q000378:metabolism* / Q000473:pathology; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism; D020569:Proto-Oncogene Proteins c-rel / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D013194:Staining and Labeling / Q000379:methods*; D047992:TNF Receptor-Associated Factor 2 / Q000235:genetics / Q000378:metabolism; D015534:Trans-Activators; D014157:Transcription Factors; D000091364:Transcriptional Coactivator with PDZ-Binding Motif Proteins; D000091102:YAP-Signaling Proteins
D048868:Adaptor Proteins, Signal Transducing; D005456:Fluorescent Dyes; D047908:Intracellular Signaling Peptides and Proteins; D016328:NF-kappa B; C101338:PSMD2 protein, human; D010750:Phosphoproteins; D020569:Proto-Oncogene Proteins c-rel; C068059:REL protein, human; D047992:TNF Receptor-Associated Factor 2; D015534:Trans-Activators; D014157:Transcription Factors; D000091364:Transcriptional Coactivator with PDZ-Binding Motif Proteins; C551991:WWTR1 protein, human; D000091102:YAP-Signaling Proteins; C088374:YAP1 protein, human; D017346:Protein Serine-Threonine Kinases
Hippo Pathway; NF-kB pathway; computational biology; gene functional annotation; human; morphological profiling; systems biology