Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancer (RNA-Seq)

KAT6A is a histone acetyltransferase that is emerging as a therapeutic target in cancer, including estrogen receptor positive (ER+) breast cancer. We performed CRISPR screens to identify the chromatin adaptor Menin as a regulator of KAT6A inhibitor response. Co-treatment with KAT6A/B and Menin inhibitors had synergistic anti-proliferative effects in ER+, but not ER-, breast cancer lines. Our data revealed that KAT6A and Menin cooperatively regulate ER-driven gene expression and chromatin accessibility via direct effects on ESR1 expression and at ER target genes. KAT6A and Menin co-localize at promoters of ESR1 and ER-driven genes and combined KAT6A/B and Menin inhibition selectively displaced RNA Pol II from chromatin at these loci. Combined KAT6A/B and Menin inhibition was effective in ER+ patient-derived organoids and in models of endocrine resistance. KAT6A/B and Menin inhibitors are currently in clinical trials and have shown manageable toxicity profiles, underscoring the potential therapeutic relevance for ER+ breast cancer. Gene expression changes were assessed in MCF7 and T47D cells after 8h, 48h, and 96h of KAT6A/B inhibition. Additionally, gene expression changes were assessed in MCF7 cells and patient-derived organoids in response to Menin and/or KAT6A/B inhibition.

KAT6A是一种组蛋白乙酰转移酶（histone acetyltransferase），正逐渐成为包括雌激素受体阳性（estrogen receptor positive, ER+）乳腺癌在内的多种恶性肿瘤的治疗靶点。本研究通过CRISPR筛选（CRISPR screen）鉴定出染色质衔接蛋白Menin为调控KAT6A抑制剂应答的关键调控因子。联合使用KAT6A/B与Menin抑制剂，在ER+乳腺癌细胞系中可产生协同抗增殖效应，而在雌激素受体阴性（estrogen receptor negative, ER-）乳腺癌细胞系中则无此类效应。
研究数据表明，KAT6A与Menin可通过直接调控ESR1基因表达以及作用于雌激素受体靶基因区域，协同调控雌激素受体驱动的基因表达与染色质开放性。二者共同定位于ESR1及雌激素受体靶基因的启动子区域，联合抑制KAT6A/B与Menin可选择性地将RNA聚合酶II（RNA polymerase II, RNA Pol II）从这些基因位点的染色质上解离下来。
联合抑制KAT6A/B与Menin在ER+患者来源类器官（patient-derived organoids, PDO）及内分泌治疗抵抗模型中均展现出显著的治疗活性。目前KAT6A/B与Menin抑制剂已进入临床试验阶段，且毒性谱可控，这进一步凸显了其针对ER+乳腺癌的治疗应用潜力。
本研究分别在KAT6A/B抑制剂处理8h、48h及96h后，检测了MCF7与T47D细胞的基因表达变化；此外，还在经Menin及/或KAT6A/B抑制剂处理的MCF7细胞与患者来源类器官中，评估了基因表达的改变情况。