Multiplexed In Vivo Screen Pinpoints Drivers of Breast Cancer Aneuploidies

Many cancers exhibit gross copy number alterations (CNA) that are considered characteristic of disease. However, the extensive number of genes encoded on these aberrant chromosome segments makes it challenging to disentangle the specific loci that may drive malignancy. To address this, Al-Zahrani and colleagues developed a CRISPR-based knockout- and activation-linked assay, CRISPR-KOALA, to study complex genetic events in vivo in murine models of basal-like breast cancer (BLBC). First, the authors identified 10 chromosome arms that are frequently and specifically altered in human BLBCs. Then, using the CRISPR-KOALA system, libraries of guide RNAs designed to either knock down or overexpress the orthologous genes encoded on each of the 10 segments were transduced into the mammary epithelium of Trp53- and Pten- or Rb1-floxed mice. In both genetic models, tumor-free survival was markedly reduced in the presence of any given CNA library, suggesting that targeted genes on each altered arm may actively drive tumorigenesis. Next-generation sequencing of the resulting tumors identified a small number of highly enriched guide RNAs within each CNA cohort. Independent validation of select high-penetrance hits (Fbxw7, Mettl14, Csnk1a1, Plgrkt, Mrps18b) revealed accelerated tumorigenesis in each setting. Hit-bearing tumors also maintained normal genomes when compared with controls, further supporting the notion that particular loci are responsible for the selective advantage observed amongst aneuploid BLBCs. Interestingly, the majority of hits from this screen had not yet been characterized as oncogenes or tumor suppressors. One such hit, Plgrkt, accelerated tumor onset when overexpressed in several BLBC models and was initially hypothesized to act through its canonical role as a plasminogen receptor. However, functional studies revealed that PLGRKT overexpression instead supports protumorigenic metabolic reprogramming, thereby suggesting an oncogenic function for PLGRKT independent of plasminogen activity. Taken together, leveraging CRISPR-KOALA to conduct a bidirectional genetic screen led to the identification of targetable drivers of disease like PLGRKT that have previously been overlooked amongst large-scale CNAs in BLBC.Al-Zahrani KN, Langille ER, Nurtanto J, Obersterescu A, Teng K, Lowden C, et al. Aneuploidy selects for the acquisition of driver genes in breast cancer. Nature 2026 July 8 [Epub ahead of print].Note: Research Watch is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details. For more Research Watch, visit Cancer Discovery online at https://aacrjournals.org/cdnews.