Khoroshkin Matvei, Zinkevich Arsenii, Aristova Elizaveta, Yousefi Hassan, Lee Sean B, Mittmann Tabea, Manegold Karoline, Penzar Dmitry, Raleigh David R, Kulakovskiy Ivan V, Goodarzi Hani
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
bioRxiv. 2024 Dec 31:2024.12.31.630783. doi: 10.1101/2024.12.31.630783.
mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains a challenge. To address this, we measured the regulatory activity of 60,000 5' and 3' untranslated regions (UTRs) across six cell types and developed PARADE (Prediction And RAtional DEsign of mRNA UTRs), a generative AI framework to engineer untranslated RNA regions with tailored cell type-specific activity. We validated PARADE by testing 15,800 de novo-designed sequences across these cell lines and identified many sequences that demonstrated superior specificity and activity compared to existing RNA therapeutics. mRNAs with PARADE-engineered UTRs also exhibited robust tissue-specific activity in animal models, achieving selective expression in the liver and spleen. We also leveraged PARADE to enhance mRNA stability, significantly increasing protein output and therapeutic durability in vivo. These advancements translated to notable increases in therapeutic efficacy, as PARADE-designed UTRs in oncosuppressor mRNAs, namely PTEN and P16, effectively reduced tumor growth in patient-derived neuroglioma xenograft models and orthotopic mouse models. Collectively, these findings establish PARADE as a versatile platform for designing safer, more precise, and highly stable mRNA therapies.
信使核糖核酸（mRNA）递送通过指导细胞产生治疗性蛋白质，为疾病治疗提供了新的机遇。然而，设计具有可编程细胞类型特异性的高度稳定的mRNA仍然是一项挑战。为了解决这一问题，我们在六种细胞类型中测量了60000个5'和3'非翻译区（UTR）的调控活性，并开发了PARADE（mRNA UTR的预测与合理设计），这是一个生成式人工智能框架，用于设计具有定制细胞类型特异性活性的非翻译RNA区域。我们通过在这些细胞系中测试15800个从头设计的序列来验证PARADE，并鉴定出许多与现有RNA疗法相比具有更高特异性和活性的序列。具有PARADE工程化UTR的mRNA在动物模型中也表现出强大的组织特异性活性，在肝脏和脾脏中实现了选择性表达。我们还利用PARADE来提高mRNA的稳定性，显著增加体内的蛋白质产量和治疗持久性。这些进展转化为治疗效果的显著提高，因为在肿瘤抑制mRNA（即PTEN和P16）中由PARADE设计的UTR在患者来源的神经胶质瘤异种移植模型和原位小鼠模型中有效降低了肿瘤生长。总的来说，这些发现确立了PARADE作为一个通用平台，用于设计更安全、更精确和高度稳定的mRNA疗法。
