GeoMx digital spatial profiler: expanding the capabilities of the CVR Virus Genomics and Bioinformatics platform

CVR病毒基因组和生物信息学是一个科学家团队，他们使用测序技术和计算方法来了解病毒感染。从事基因组和生物信息学工作的科学家使用DNA测序来确定DNA分子中的核苷酸序列。每个生物体都有一个独特的核苷酸序列，包括病毒，我们可以使用这个序列来了解它们生物学的许多方面。在CVR，病毒基因组和生物信息学团队还进行RNA测序(RNA-seq)。这是一种测量基因表达的实验。换句话说，我们决定由我们的DNA编码的哪些基因被打开或关闭，以及在多大程度上被打开或关闭。这对于了解我们的细胞在被病毒感染时如何反应特别有用，最终导致关于病毒致病机制的线索。我们知道，组织是由不同细胞类型组成的复杂群体，每种细胞类型对病毒感染的反应可能不同。我们还知道，组织可能有隔间，空间信息在感染过程中很重要。然而，研究界最经常使用的方案要求将组织均质化在包含所有RNA分子的单一混合物中。这意味着每个单元提供的所有信息以及空间上下文都会丢失。在这项应用中，我们正在申请资金，以投资于一种保留空间信息的新技术。使用纳米串中的GeoMx，我们在保持空间上下文的同时，从组织中检索RNA-seq信息。这一点很重要，因为它使我们能够可视化不同的细胞或组织区域如何开启和关闭他们的基因，并将这些信息与图像重叠，这些图像指示组织中的哪里发生感染或是否有任何损害，以及其他特征。总体而言，这一新仪器将使我们能够基于来自不同细胞类型、空间数据和组织的其他特征的RNA-SEQ数据来了解病毒如何感染我们，从而使我们能够更全面地了解感染和我们如何应对感染。

The CVR Viral Genomics and Bioinformatics is a team of scientists which use sequencing techniques and computational methods to understand viral infections.Scientists working on genomics and bioinformatics use DNA sequencing to determine the sequence of nucleotides within a DNA molecule. Every organism has a unique sequence of nucleotides, including viruses, and we can use that sequence to understand many aspects of their biology. At the CVR, the Viral Genomics and Bioinformatics team also does RNA sequencing (RNA-seq). This is a type of experiment that measures the expression of genes. In other words, we determine which of the genes encoded by our DNA are turned on or off and at what extent. This is particularly useful to understand how our cells respond when they become infected by viruses, ultimately leading to clues on the mechanisms by which viruses cause disease. We know that tissues are a complex grouping of different cell types, and that each cell type may respond differently to a viral infection. We also know that tissues can have compartments and that spatial information is important during infection. However, the protocols most frequently used by the research community require homogenisation of tissues in a single mixture, containing all the RNA molecules. This means that all the information provided by each individual cell, as well as the spatial context is lost.In this application, we are applying for funds to invest in a new technology that retains the spatial information. With the GeoMx from NanoString, we retrieve RNA-seq information from the tissues while maintaining the spatial context. This is important because it enables us to visualise how different cells or areas of a tissue are turning their genes on and off and overlap that information with images which indicate where in the tissue is the infection taking place or if are there any lesions, amongst other features.Overall, this new instrument will enable us to understand how viruses infect us based on RNA-seq data from different cell types, spatial data and other characteristics of the tissues, enabling a more complete view of infections and how we respond to them.