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Quantitative characterization of tissue states using multiomics and ecological spatial analysis

D. Ding,Zeyu Tang,Bokai Zhu,Hongyu Ren,A. Shalek,Robert Tibshirani,GP Nolan

Published 2025 in Nature Genetics

ABSTRACT

The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease. Multiomics and ecological spatial analysis (MESA) calculates ecodiversity-inspired metrics in spatially resolved omics integrated with single-cell data, enabling the quantitative comparison of tissue states across a range of conditions.

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