AUTHOR=Tran Thao , Wee Felicia , Joseph Craig Ryan , Zhang Wanqiu , Lim Jeffrey Chun Tatt , Neo Zhen Wei , Chong Li Yen , Yap Francis Hong Xin , Patterson Nathan Heath , Claesen Marc , Ly Alice , Yeong Joe 

TITLE=An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=Volume 12 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2025.1614288

DOI=10.3389/fmolb.2025.1614288

ISSN=2296-889X

ABSTRACT=Recent advances in spatial transcriptomics (ST) and spatial proteomics (SP) technologies have enabled high-dimensional molecular profiling at single-cell resolution, providing deeper insights into the tumour-immune microenvironment. However, these modalities are typically applied to separate tissue sections, limiting direct comparisons across molecular layers. We developed a wet-lab and computational framework to perform and integrate ST and SP from the same tissue section, as demonstrated on human lung cancer samples. Applying ST, SP, and hematoxylin and eosin (H&E) staining from the same section ensured consistency in tissue morphology and spatial context. Computational registration using Weave software allowed accurate alignment and annotation transfer across modalities. This co-registered dataset enabled single-cell level comparisons of RNA and protein expression, revealed segmentation accuracy and transcript-protein correlation analyses within individual cells. Notably, we observed systematic low correlations between transcript and protein levels—consistent with prior findings—now resolved at cellular resolution. Our approach highlights the feasibility and utility of performing spatially-resolved multi-omics analysis on the same section without compromising data quality, facilitating concordance studies and region-specific analysis of immune and tumour markers, and ultimately advancing our understanding of disease heterogeneity at the molecular level.