WU-SN-TMC Bio-Analysis Core

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Biological Analysis Core Summary/Abstract Senescence is implicated in many human diseases and the elimination of senescent cells in model organisms slows, and in some cases reverses many diseases. These findings raise hope that a detailed mechanistic understanding of senescence will lead to novel therapies to treat human disease. Despite the importance of cellular senescence, we lack robust methods to identify, isolate, and manipulate senescent cells. New approaches and technologies position our team to comprehensively identify senescent cells. This, in turn, will enable in-depth analyses of biomarkers, spatial distribution, behavior, and function of senescent cells across human tissues and time in a high throughput manner. The primary goal for the Biological Analysis Core (BAC) within Washington University Senescence Mapping Center (WU-SN-TMC) is to generate multi-omics and imaging data to build high resolution, multi-dimensional atlases of cellular senescence across tissue types and lifespan to facilitate basic and translational research. Although senescent cells are tracked by several known markers, it is increasingly clear that not all senescent cells express the same set of markers and the usefulness of individual senescent markers may be limited. Static universal tissue agnostic senescence markers may not exist. Instead, there are likely dynamic senescence signatures (gene expression patterns anchored by frequent, but unobligated presence of some of the “known” markers and others yet to be identified), that may differ with cell type, age, and environmental stimuli. We propose using cutting edge enabling technologies at necessary scale, depth, and resolution to identify such signatures while mapping senescent cells in various tissue environments at different ages. We will map senescent cells and their associated phenotypes in four tissues (bone marrow, breast, liver, and colon), chosen for their clinical importance, diversity, relevance to senescence, and availability. We will utilize the highly successful infrastructure we have developed for several large-scale projects as a springboard, combined with in-house expertise in senescence research, to generate cellular senescence atlases with transcriptome-wide coverage, single cell resolution, and spatial registration. We will use our experience in single cell omics to establish a comprehensive epigenetic and transcriptomic landscape in targeted tissues. We will add the spatial dimension to build 2D and 3D molecular atlases by incorporating spatial transcriptomics, CODEX, and light sheet microscopy. We will also use proteomics to study the biomarkers and secretome of senescent cells. To validate our results, we will use established and newly developed mouse models to track senescent cells at different ages with or without perturbations. These studies will allow us to improve detection methods for senescent cells and validate biomarker signatures identified in human studies. BAC will work closely with the other Cores within WU-SN-TMC to produce multi-dimensional molecular and cellular senescence tissue atlases at unprecedented cellular resolution and gene coverage with the highest efficiency possible.