Broad研究所Anne E. Carpenter研究小组在研究中取得进展。他们报道了人类细胞中基因过表达和过表达的形态图谱。2025年8月7日，国际知名学术期刊《自然—方法学》发表了这一成果。

在这里，课题组人员通过严格评估数据处理选项来减轻技术影响，并验证数据集的稳定性和生物学相关性。表型分析揭示了以前未发现的基因簇和功能关系，包括与线粒体功能、癌症和神经过程相关的基因簇和功能关系。JUMP细胞绘画基因数据集是探索基因关系和发现以前未知功能的宝贵资源。

据悉，细胞绘制图像提供了对细胞状态的宝贵见解，并使许多生物学应用成为可能，但公开可用的阵列数据集仅包括数百个受干扰的基因。JUMP细胞绘制联盟干扰了人类U-2 OS细胞中大约75%的蛋白质编码基因组，生成了丰富的单细胞图像和提取的特征。这些图谱捕获了干扰15,243个人类基因的表型影响，包括过度表达12,609个基因（主题化开放阅读框）和敲除7,975个基因（主题化CRISPR-Cas9）。

附：英文原文

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

Author: Chandrasekaran, Srinivas Niranj, Alix, Eric, Arevalo, John, Borowa, Adriana, Byrne, Patrick J., Charles, William G., Chen, Zitong S., Cimini, Beth A., Deng, Boxiong, Doench, John G., Ewald, Jessica D., Fritchman, Briana, Fuller, Colin J., Gaetz, Jedidiah, Goodale, Amy, Haghighi, Marzieh, Han, Yu, Hanifehlou, Zahra, Hennig, Holger, Hernandez, Desiree, Jacob, Christina B., James, Tim, Jetka, Tomasz, Kalinin, Alexandr A., Komalo, Ben, Kost-Alimova, Maria, Krawiec, Tomasz, Marion, Brittany A., Martin, Glynn, McCarthy, Nicola Jane, Miller, Lisa, Monsees, Arne, Moshkov, Nikita, Muoz, Aln F., Ogier, Arnaud, Otrocka, Magdalena, Rataj, Krzysztof, Root, David E., Rubbo, Francesco, Scrace, Simon, Selinger, Douglas W., Senft, Rebecca A., Sommer, Peter, Thibaudeau, Amandine, Trisorus, Sarah, Valiya Veettil, Rahul, Van Trump, William J., Wang, Sui, Warcho, Micha, Weisbart, Erin, Weiss, Amlie, Wiest, Michael, Zaremba, Agata, Zinovyev, Andrei, Singh, Shantanu, Carpenter, Anne E.

Issue&Volume: 2025-08-07

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.

DOI: 10.1038/s41592-025-02753-9

Source: https://www.nature.com/articles/s41592-025-02753-9