Cancer Research Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Genome Biol. 2023 Mar 29;24(1):59. doi: 10.1186/s13059-023-02898-w.
Genome-wide association studies (GWAS) have identified > 200 loci associated with breast cancer risk. The majority of candidate causal variants are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, pinpointing the exact target of the association, and identifying the phenotype it mediates, is a major challenge in the interpretation and translation of GWAS.
Here, we show that pooled CRISPR screens are highly effective at identifying GWAS target genes and defining the cancer phenotypes they mediate. Following CRISPR mediated gene activation or suppression, we measure proliferation in 2D, 3D, and in immune-deficient mice, as well as the effect on DNA repair. We perform 60 CRISPR screens and identify 20 genes predicted with high confidence to be GWAS targets that promote cancer by driving proliferation or modulating the DNA damage response in breast cells. We validate the regulation of a subset of these genes by breast cancer risk variants.
We demonstrate that phenotypic CRISPR screens can accurately pinpoint the gene target of a risk locus. In addition to defining gene targets of risk loci associated with increased breast cancer risk, we provide a platform for identifying gene targets and phenotypes mediated by risk variants.
全基因组关联研究（GWAS）已经确定了与乳腺癌风险相关的超过 200 个位点。大多数候选因果变异位于非编码区域，可能通过调节基因表达来调节癌症风险。然而，确定关联的确切靶标，并确定其介导的表型，是 GWAS 解释和转化的主要挑战。
在这里，我们表明， pooled CRISPR 筛选在鉴定 GWAS 靶基因和定义其介导的癌症表型方面非常有效。在 CRISPR 介导的基因激活或抑制后，我们在 2D、3D 和免疫缺陷小鼠中测量增殖，以及对 DNA 修复的影响。我们进行了 60 次 CRISPR 筛选，确定了 20 个具有高可信度的基因，这些基因被预测为 GWAS 靶点，通过驱动增殖或调节乳腺癌细胞中的 DNA 损伤反应来促进癌症。我们验证了其中一部分基因受乳腺癌风险变异的调控。
我们证明了表型 CRISPR 筛选可以准确地确定风险位点的基因靶标。除了定义与乳腺癌风险增加相关的风险位点的基因靶标外，我们还提供了一个平台，用于识别由风险变体介导的基因靶标和表型。
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