A critical hurdle in the clinical translation of nucleic acid drugs is the inefficiency in testing formulations for therapeutic potential. Specifically, the ability to quantitatively predict gene expression is lacking when transitioning between cell culture and animal studies. We address this challenge by developing a mathematical framework that can reliably predict short-interfering RNA (siRNA)-mediated gene silencing with as few as one experimental data point as an input, evaluate the efficacies of existing formulations in an expeditious manner, and ultimately guide the design of nanocarriers with optimized performances. The model herein consisted of only essential rate-limiting steps and parameters with easily characterizable values of the RNA interference process, enabling the easy identification of which parameters play dominant roles in determining the potencies of siRNA formulations. Predictions from our framework were in close agreement with in vitro and in vivo experimental results across a retrospective analysis using multiple published data sets. Notably, our findings suggested that siRNA dilution was the primary determinant of gene-silencing kinetics. Our framework shed light on the fact that this dilution rate is governed by different parameters, i.e., cell dilution (in vitro) versus clearance from target tissue (in vivo), highlighting a key reason why in vitro experiments do not always predict in vivo outcomes. Moreover, although our current effort focuses on siRNA, we anticipate that the framework can be modified and applied to other nucleic acids, such as mRNA, that rely on similar biological processes.

中文翻译：

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加速核酸制剂开发的动力学建模

核酸药物临床转化的一个关键障碍是测试制剂治疗潜力的效率低下。具体来说，在细胞培养和动物研究之间转换时，缺乏定量预测基因表达的能力。我们通过开发一个数学框架来应对这一挑战，该框架可以可靠地预测短干扰 RNA (siRNA) 介导的基因沉默，只需一个实验数据点作为输入，快速评估现有配方的功效，并最终指导具有优化性能的纳米载体的设计。本文的模型仅包含必要的限速步骤和参数，以及易于表征的 RNA 干扰过程值，能够轻松识别哪些参数在确定 siRNA 制剂的效力中起主导作用。我们框架的预测与使用多个已发布数据集进行回顾性分析的体外和体内实验结果。值得注意的是，我们的研究结果表明 siRNA 稀释是基因沉默动力学的主要决定因素。我们的框架阐明了这种稀释率受不同参数控制的事实，即细胞稀释（体外）与靶组织清除率（体内），突出了体外实验并不总是预测体内结果的一个关键原因. 此外，尽管我们目前的工作集中在 siRNA 上，但我们预计该框架可以被修改并应用于其他依赖于类似生物过程的核酸，例如 mRNA。