Collaborative Research: Ideas Lab: The Role of Extracellular RNA in Intercellular and Interkingdom Communication

该项目是七个具有不同和互补专业知识的实验室之间的合作。该项目的总体目标是了解细胞外RNA（exRNA）在细胞间通讯中的作用，以及在塑造微生物群落中的作用，特别是生活在植物，昆虫和人类内部的细菌。这些微生物的集合通常被称为微生物组，对植物和动物（包括人类）的健康至关重要。健康的微生物组促进健康的免疫系统，但健康的微生物组如何维持却知之甚少。该项目将测试宿主细胞分泌的RNA通过细胞间的交流和修改微生物组在维持健康方面发挥核心作用的假设。RNA以其在细胞内蛋白质生产中的关键作用而闻名，例如在基于RNA的COVID疫苗中。然而，并非所有的RNA都编码蛋白质，细胞产生的非编码RNA比编码RNA多，其中一些被细胞主动推入环境中。这种分泌的RNA似乎被其他细胞吸收，包括细菌和真菌，可能会影响它们的生长。了解exRNA如何塑造细胞和生物体之间的通信将使农业和医学中的exRNA通信得以操纵，这将导致环境友好型农药的开发，以及促进植物和动物健康微生物组形成的治疗方法。这些知识也将使诊断和治疗工具的发展，早期发现和/或治疗疾病。所有细胞生物分泌RNA。然而，这些胞外RNA（exRNA）的功能知之甚少。两个可能的功能是细胞间和王国间的通信。exRNA生物学中存在大量的开放性问题：exRNA是如何被选择用于分泌的，它们是如何靶向受体细胞的，以及它们在正常健康和生物体健康中的作用是什么？拟南芥叶exRNA分离物在转录后修饰N6-甲基腺苷（m6 A）（与总细胞RNA相比）中高度富集，表明转录后修饰可以标记用于输出的特定RNA。与此一致，人外泌体microRNA富含m6 A（相对于胞质microRNA）。有趣的是，最近发现大量定位于细胞外表面的哺乳动物小非编码RNA（ncRNA）具有特异性唾液酸化聚糖修饰。这些观察结果表明，特定的RNA修饰标记RNA用于细胞输出和直接进入适当的受体细胞。该项目将1）测试exRNA具有特定特征的假设，这些特征标志着它们在物种内和物种之间的分泌和吸收，2）确定exRNA如何从信号细胞转移到接收细胞，以及3）通过检查人类肠道，昆虫肠道和叶面模型来评估exRNA对微生物组健康和组成的影响。该项目由生物科学理事会共同资助，该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project is a collaboration among seven laboratories with diverse and complementary expertise. The overarching goal of the project is to understand the role of extracellular RNA (exRNA) in communication between cells and in shaping the community of microbes, especially bacteria, that live on and inside plants, insects, and humans. These collections of microbes are often referred to as microbiomes and are critical for the health of plants and animals, including humans. A healthy microbiome promotes a healthy immune system, but how healthy microbiomes are maintained is poorly understood. This project will test the hypothesis that RNA secreted by host cells plays a central role in maintaining health both through communication among cells and by modifying the microbiome. RNA is best known for its key role in protein production inside cells, such as in RNA-based COVID vaccines. However, not all RNA encodes proteins, and cells produce more non-coding RNA than coding RNA, some of which is actively pushed into the environment by cells. This secreted RNA appears to be taken up by other cells, including bacteria and fungi, where it could potentially impact their growth. Understanding how exRNAs shape communication between cells and organisms will enable manipulation of exRNA communication in both agriculture and medicine, which will lead to development of environmentally friendly pesticides, as well as treatments that promote formation of healthy microbiomes in both plants and animals. This knowledge will also enable development of diagnostic and therapeutic tools for early detection and/or treatment of disease.All cellular organisms secrete RNAs. The functions of these extracellular RNAs (exRNAs), however, are poorly understood. Two likely functions are intercellular and interkingdom communication. Open questions abound in exRNA biology: how are exRNAs selected for secretion, how are they targeted to recipient cells, and what are their roles in normal health and organismal fitness? Arabidopsis leaf exRNA isolates are highly enriched in the post-transcriptional modification N6-methyladenosine (m6A) (as compared to total cellular RNA) suggesting that post-transcriptional modifications may tag specific RNAs for export. Consistent with this, human exosomal microRNAs are enriched with m6A (relative to cytosolic microRNAs). Interestingly, a large number of mammalian small non-coding RNAs (ncRNAs) that localize to the external cell surface were recently found to harbor specific sialylated glycan modifications. These observations suggest that specific RNA modifications tag RNAs for cellular export and direct entry into appropriate recipient cells. This project will 1) test the hypothesis that exRNAs have specific features marking them for secretion and uptake, both within and among species, 2) determine how exRNAs are transferred from signaler to receiver cells, and 3) assess the impact of exRNA on microbiome health and composition through examining human gut, insect gut, and leaf surface models.This project was co-funded by the Directorate for Biological Sciences, and the Plant Genome Research Program and the Plant Biotic Interactions Program in the Division of Integrative Organismal Systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.