Systematic morphological profiling of human gene and allele function via Cell Painting
| Autor: | Mark-Anthony Bray, Shantanu Singh, Yashaswi Shrestha, Anne E. Carpenter, Mohammad Hossein Rohban, Julia B Berthet, Xiaoyun Wu, Xaralabos Varelas, Jesse S. Boehm |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Golgi Apparatus Endoplasmic Reticulum Genome Image Processing Computer-Assisted Biology (General) Organism Genetics General Neuroscience Optical Imaging Intracellular Signaling Peptides and Proteins NF-kappa B General Medicine Tools and Resources Mitochondria Cell Transformation Neoplastic Multigene Family Medicine Computational and Systems Biology Human Signal Transduction TBX1 QH301-705.5 Science Systems biology Biology Protein Serine-Threonine Kinases NF-kB pathway General Biochemistry Genetics and Molecular Biology DNA sequencing 03 medical and health sciences gene functional annotation Cell Line Tumor Humans Hippo Signaling Pathway morphological profiling Gene Alleles Adaptor Proteins Signal Transducing Fluorescent Dyes Cell Nucleus Osteoblasts General Immunology and Microbiology Staining and Labeling Gene Expression Profiling YAP-Signaling Proteins Phosphoproteins TNF Receptor-Associated Factor 2 Hippo Pathway Proto-Oncogene Proteins c-rel 030104 developmental biology HEK293 Cells Gene Expression Regulation Transcriptional Coactivator with PDZ-Binding Motif Proteins Trans-Activators Human genome Minimal genome Transcription Factors |
| Zdroj: | eLife eLife, Vol 6 (2017) |
| ISSN: | 2050-084X |
| Popis: | 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. DOI: http://dx.doi.org/10.7554/eLife.24060.001 eLife digest Many human diseases are caused by particular changes, called mutations, in patients’ DNA. A genome is the complete DNA set of an organism, which contains all the information to build the body and keep it working. This information is stored as a code made up of four chemicals called bases. Humans have about 30,000 genes built from DNA, which contain specific sequences of bases. Genome sequencing can determine the exact order of these bases, and has revealed a long list of mutations in genes that could cause particular diseases. However, over 30% of genes in the human body do not have a known role. Genes can serve multiple roles, some of which are not yet discovered, and even when a gene’s purpose is known, the impact of each particular mutation in a given gene is largely uncatalogued. Therefore, new methods need to be developed to identify the biological roles of both normal and abnormal gene sequences. For hundreds of years, biologists have used microscopy to study how living cells work. Rohban et al. have now asked whether modern software that extracts data from microscopy images could create a fingerprint-like profile of a cell that would reflect how its genes affect its role and appearance. While some genes do not necessarily carry a code with instructions of what a cell should look like, they can indirectly modify the structure of the cell. The resulting changes in the shape of the cell can then be captured in images. The idea was that two cells with matching profiles would indicate that their combinations of genes had matching biological roles too. Rohban et al. tested their approach with human cells grown in the laboratory. In each sample of cells, they ‘turned on’ one of a few hundred relatively well-known human genes, some of which were known to have similar roles. The cells were then stained via a technique called ‘Cell Painting’ to reveal eight specific components of each cell, including its DNA and its surface membrane. The stained cells were imaged under a microscope and the resulting microscopy images analyzed to create a profile of each type of cell. Rohban et al. confirmed that turning on genes known to perform similar biological roles lead to similar-looking cells. The analysis also revealed a previously unknown interaction between two major pathways in the cell that control how cancer starts and develops. In the future, this approach could predict the biological roles of less-understood genes by looking for profiles that match those of well-known genes. Applying this strategy to every human gene, and mutations in genes that are linked to diseases, could help to answer many mysteries about how genes build the human body and keep it working. DOI: http://dx.doi.org/10.7554/eLife.24060.002 |
| Databáze: | OpenAIRE |
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