Abstract 5953: Unlocking new frontiers in mouse research by exploring the whole-transcriptome in space and time with mouse embryo stages E11 - E14

Abstract Bruker Spatial Biology introduces the CosMx® Mouse Whole Transcriptome Assay: a 21,242 gene panel that covers the entirety of the protein-coding mouse transcriptome. CosMx Spatial Molecular Imager (SMI) is a first-in-class instrument that offers spatially resolved, single-cell transcriptomic analysis at a scale an order of magnitude greater than any other commercially available system. This study profiles four FFPE mouse embryo sections - E11, E12, E13, and E14 - using a development lot of CosMx Mouse Whole Transcriptome (WTX) Assay. Each slide was stained with a 5-channel segmentation cocktail of PanCK, CD3, CD45, CD298/B2M, and DAPI prior to RNA profiling. Cells are segmented according to presence of DAPI and a combined overlay of all four segmentation markers using a machine learning algorithm based on the open-source platform CellPose, trained on staining information collected on over a dozen human and mouse tissue types on CosMx SMI. RNA transcripts are decoded using a multiplexed barcoding strategy where individual ISH probes are assigned unique barcode across 39 reporter sequences, a strategy that is key to allowing over twenty-thousand targets to be detected simultaneously in space. The CosMx Mouse WTX Assay unveils an unprecedented depth of information on each mouse sample. Cell typing was performed on each embryo to identify each developing organ, and niche analysis was used to identify spatial neighborhoods unique to each timepoint. The development of specific organs during these timepoints, such as the retina, liver, gonads, and heart, are interrogated in detail by comparing localized gene expression across the whole transcriptome throughout timepoints, offering a unique four-dimensional window (three spatial dimensions, one time dimension) into embryonic development with the unparalleled resolution of spatial transcriptomics. Capitalizing on the high number of genes available per cell, single cell pathway scores were assigned to each slide, and differential expression was used to quantify which pathways are upregulated at each timepoint. Unbiased spatial algorithms such as Insitucor were used to identify localized gene module expression based on normalized expression across nearby cells, and disease/control perturbation algorithms such as Insitudiff revealed spatial domains defined by gene perturbations of later timepoints relative to E11. CosMx Mouse WTX Assay delivers a first-of-its-kind opportunity to examine the development of mouse embryos in four dimensions using 20,000 spatially resolved genes. This study on mouse embryo development provides a first look at the limitless applications that a whole-transcriptome mouse panel can unlock for researchers including cancer research. Citation Format: Michael Patrick, Liang Zhang, Isabel Lee, Shanshan He, Martin Shelton, John Lyssand, Joseph M. Beechem. Unlocking new frontiers in mouse research by exploring the whole-transcriptome in space and time with mouse embryo stages E11 - E14 abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5953.