Morphological map of under- and overexpression of genes in human cells

Srinivas Niranj Chandrasekaran¹, Eric Alix², John Arevalo¹, Adriana Borowa³, Patrick J Byrne¹, William G Charles⁴, Zitong S Chen¹, Beth A Cimini¹, Boxiong Deng⁵, John G Doench¹, Jessica D Ewald¹, Briana Fritchman¹, Colin J Fuller⁶, Jedidiah Gaetz⁷, Amy Goodale¹, Marzieh Haghighi¹, Yu Han¹, Zahra Hanifehlou⁸, Holger Hennig⁴, Desiree Hernandez¹, Christina B Jacob⁸, Tim James⁴, Tomasz Jetka³, Alexandr A Kalinin¹, Ben Komalo⁶, Maria Kost-Alimova¹, Tomasz Krawiec³, Brittany A Marion¹, Glynn Martin², Nicola Jane McCarthy², Lisa Miller¹, Arne Monsees⁴, Nikita Moshkov¹, Alán F Muñoz¹, Arnaud Ogier⁸, Magdalena Otrocka³, Krzysztof Rataj³, David E Root¹, Francesco Rubbo⁶, Simon Scrace², Douglas W Selinger⁷, Rebecca A Senft¹, Peter Sommer⁸, Amandine Thibaudeau⁸, Sarah Trisorus⁶, Rahul Valiya Veettil⁴, William J Van Trump⁶, Sui Wang⁵, Michał Warchoł³, Erin Weisbart¹, Amélie Weiss⁸, Michael Wiest⁶, Agata Zaremba³, Andrei Zinovyev⁴, Shantanu Singh⁹, Anne E Carpenter¹⁰

Affiliations

¹ Broad Institute, Cambridge, MA, USA.
² Revvity Discovery Limited (formerly known as Horizon Discovery), Cambridge, UK.
³ Ardigen S.A, Kraków, Poland.
⁴ Evotec SE, Hamburg, Germany.
⁵ Stanford University, Stanford, CA, USA.
⁶ Spring Science, San Carlos, CA, USA.
⁷ Plex Research Inc., Cambridge, MA, USA.
⁸ Ksilink, Strasbourg, France.
⁹ Broad Institute, Cambridge, MA, USA. shantanu@broadinstitute.org.
¹⁰ Broad Institute, Cambridge, MA, USA. anne@broadinstitute.org.

PMID: 40775081
PMCID: PMC12439680 (available on 2026-02-07)
DOI: 10.1038/s41592-025-02753-9

Morphological map of under- and overexpression of genes in human cells

Srinivas Niranj Chandrasekaran et al. Nat Methods. 2025 Aug.

. 2025 Aug;22(8):1742-1752.

doi: 10.1038/s41592-025-02753-9. Epub 2025 Aug 7.

Authors

Affiliations

¹ Broad Institute, Cambridge, MA, USA.
² Revvity Discovery Limited (formerly known as Horizon Discovery), Cambridge, UK.
³ Ardigen S.A, Kraków, Poland.
⁴ Evotec SE, Hamburg, Germany.
⁵ Stanford University, Stanford, CA, USA.
⁶ Spring Science, San Carlos, CA, USA.
⁷ Plex Research Inc., Cambridge, MA, USA.
⁸ Ksilink, Strasbourg, France.
⁹ Broad Institute, Cambridge, MA, USA. shantanu@broadinstitute.org.
¹⁰ Broad Institute, Cambridge, MA, USA. anne@broadinstitute.org.

PMID: 40775081
PMCID: PMC12439680 (available on 2026-02-07)
DOI: 10.1038/s41592-025-02753-9

Abstract

Cell Painting images offer valuable insights into a cell's state and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUMP Cell Painting Consortium perturbed roughly 75% of the protein-coding genome in human U-2 OS cells, generating a rich resource of single-cell images and extracted features. These profiles capture the phenotypic impacts of perturbing 15,243 human genes, including overexpressing 12,609 genes (using open reading frames) and knocking out 7,975 genes (using CRISPR-Cas9). Here we mitigated technical artifacts by rigorously evaluating data processing options and validated the dataset's robustness and biological relevance. Analysis of phenotypic profiles revealed previously undiscovered gene clusters and functional relationships, including those associated with mitochondrial function, cancer and neural processes. The JUMP Cell Painting genetic dataset is a valuable resource for exploring gene relationships and uncovering previously unknown functions.

PubMed Disclaimer

Conflict of interest statement

Competing interests: The authors declare the following competing interests: S.S., B.A.C. and A.E.C. serve as scientific advisors for companies that use image-based profiling and Cell Painting (A.E.C., Recursion, SyzOnc, Quiver Bioscience; S.S., Waypoint Bio, Dewpoint Therapeutics, Deepcell and B.A.C., Marble Therapeutics) and receive honoraria for occasional scientific visits to pharmaceutical and biotechnology companies. Authors with affiliations to the pharmaceutical, technology and biotechnology companies listed are or have been employees of those companies and may have real or optional ownership therein. The other authors declare no competing interests.

References

1. Mattiazzi Usaj M et al. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol. 26, 598–611 (2016). - PubMed
1. Bougen-Zhukov N, Loh SY, Lee HK & Loo L-H Large-scale image-based screening and profiling of cellular phenotypes. Cytometry A 91, 115–125 (2017). - PubMed
1. Boutros M, Heigwer F & Laufer C Microscopy-Based High-Content Screening. Cell 163, 1314–1325 (2015). - PubMed
1. Cheng J et al. Massively Parallel CRISPR-Based Genetic Perturbation Screening at Single-Cell Resolution. Adv. Sci 10, e2204484 (2023). - PMC - PubMed
1. Perlman ZE et al. Multidimensional drug profiling by automated microscopy. Science 306, 1194–1198 (2004). - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Morphological map of under- and overexpression of genes in human cells

Affiliations

Morphological map of under- and overexpression of genes in human cells

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources