Visium spatial transcriptome analysis add on to the current proposed scRNA seq analysis

Cleveland Clinic Lerner Com-Cwru, Cleveland OH

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Abstract

ABSTRACT: This application is being submitted in response to the Notice of Special Interest (NOSI) identified as NOT-CA-23-045. Cisplatin induced Acute kidney injury (C-AKI) is a complex condition with significant morbidity and mortality. Our research team aims to investigate the cellular and molecular mechanisms involved in AKI and therapy response. We have used single-cell RNA sequencing (scRNA seq) to investigate gene expression levels in individual cells. However, scRNA seq lacks spatial context, which is important for understanding cell-cell interactions and the microenvironment. Therefore, we propose adding Visium Spatial Transcriptomics, a cutting-edge technique that combines histological imaging with RNA sequencing, to our study. We aim to analyze gene expression levels in a spatially resolved manner, identify new cell types and their spatial distribution, and generate high-resolution maps of gene expression patterns in kidney tissue. To investigate the spatial expression patterns of genes involved in the immune response and other processes affected by APE2-ASO treatment, we propose a study using Visium Spatial Transcriptomics in the APE2 ASO-treated cisplatin-induced AKI model. By adding Visium Spatial Transcriptomics to our ongoing AKI study, we aim to gain a deeper understanding of the cellular and molecular mechanisms involved and identify potential therapeutic targets.