Life Sciences Institute, Zhejiang University, Hangzhou, China.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Nat Protoc. 2021 Feb;16(2):1129-1151. doi: 10.1038/s41596-020-00451-8. Epub 2021 Jan 13.
The complexity and dynamics of human diseases are driven by the interactions between internal molecular activities and external environmental exposures. Although advances in omics technology have dramatically broadened the understanding of internal molecular and cellular mechanisms, understanding of the external environmental exposures, especially at the personal level, is still rudimentary in comparison. This is largely owing to our limited ability to efficiently collect the personal environmental exposome (PEE) and extract the nucleic acids and chemicals from PEE. Here we describe a protocol that integrates hardware and experimental pipelines to collect and decode biotic and abiotic external exposome at the individual level. The described protocol has several advantages over conventional approaches, such as exposome monitoring at the personal level, decontamination steps to increase sensitivity and simultaneous capture and high-throughput profiling of biotic and abiotic exposures. The protocol takes ~18 h of bench time over 2-3 d to prepare samples for high-throughput profiling and up to a couple of weeks of instrumental time to analyze, depending on the number of samples. Hundreds to thousands of species and organic compounds could be detected in the airborne particulate samples using this protocol. The composition and complexity of the biotic and abiotic substances are heavily influenced by the sampling spatiotemporal factors. Basic skillsets in molecular biology and analytical chemistry are required to carry out this protocol. This protocol could be modified to decode biotic and abiotic substances in other types of low or ultra-low input samples.
人类疾病的复杂性和动态性是由内部分子活动和外部环境暴露之间的相互作用驱动的。尽管组学技术的进步极大地拓宽了对内部分子和细胞机制的理解，但与内部相比，对外部环境暴露的理解，特别是在个人层面上，仍然很初级。这主要是由于我们收集个人环境暴露组（PEE）并从 PEE 中提取核酸和化学物质的能力有限。在这里，我们描述了一种整合硬件和实验管道的方案，用于在个体水平上收集和解码生物和非生物的外部暴露组。与传统方法相比，该方案具有几个优势，例如在个人水平上进行暴露组监测、通过去污步骤提高灵敏度以及同时捕获和高通量分析生物和非生物暴露物。该方案需要在 2-3 天内准备样品进行高通量分析，大约需要 18 小时的实验时间，具体取决于样品数量。使用该方案可以在空气中颗粒物样品中检测到数百到数千种物种和有机化合物。生物和非生物物质的组成和复杂性受到采样时空因素的严重影响。执行该方案需要具备分子生物学和分析化学的基本技能。该方案可以修改为解码其他类型的低或超低输入样本中的生物和非生物物质。
