Spatiotemporal Multiomics Analysis to Reveal the Cell-Specific Immune Response in Arabidopsis

Project: Research project

Project Details


Upon recognition of an invading pathogen, plant cells employ a multi-tiered immune response, characterized by intricate gene expression and metabolic reprogramming. Traditional bulk omics technologies, such as transcriptomics and metabolomics approaches, have been extensively used to understand the complex defense mechanisms by dissecting the interactions of various biomolecules. However, bulk omics data are measurement of average signals from whole tissues and often overlook the heterogeneity and diversity of different cells’ responses in infected tissues.

Recently, single-cell omics technologies have been employed in understanding how different cell types exhibit distinct responses to pathogen invasions. However, these techniques face some challenges, particularly in plant research. Some plant cells resist easy separation, and the protoplast preparation process can significantly modify transcriptomes, proteomes, and metabolomes. Furthermore, crucial spatial contexts of cells within tissues are often lost due to cell separation. A promising advancement in this field is the emergence of spatial transcriptomics technologies, which allow for the analysis of transcriptomes at the single cell or subcellular resolution from whole tissue sections, without the need for cell separation. One notable technology in this area is stereo-RNA-sequencing, developed by the Beijing Genome Institute (BGI), which offers high resolution and sensitivity for spatial transcriptome analysis. In addition to spatial transcriptome analysis, mass spectrometry imaging (MSI) technologies have emerged for label-free, spatially resolved in situ profiling of small molecules in tissue sections again at the single-cell/subcellular resolution. These innovations offer unprecedented potential to map the spatiotemporal transcriptomes and metabolomes across tissues, allowing for a more comprehensive understanding of the molecular dynamics in important biological processes.

In this project, a collaborative team of scientists specializing in plant-pathogen interaction, stereo-seq, MSI, and spatial omics data analysis will work together to utilize stereo-seq and MSI technologies to conduct a spatially resolved analysis of transcriptomes and metabolomes in cells across Arabidopsis leaves affected by pathogens to provide a more comprehensive view of cell-specific immune responses. Additionally, our objective is to develop protocols that combine stereo-seq and MALDI-MSI analyses. This will enable us to perform a spatially resolved multimodal analysis of transcriptomes and metabolomes from the same cells. This study will gain a holistic view of the cellspecific interplay between gene expression and small molecules and inter-cellular communication underlying the local and systemic immune responses. Ultimately, the insights gained from our research may identify key regulatory molecules that can be targeted to enhance the durable disease resistance of crops.
StatusNot started
Effective start/end date1/01/2531/12/27


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