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Publications

Journal Article Ppublish

PubMed: 40674581 DOI: 10.1093/bioinformatics/btaf409

SpatioMark: quantifying the impact of spatial proximity on cell phenotype.

Bioinformatics 41(8)

Authors: Sourish S Iyengar, Alex R Qin, Nicholas Robertson, Andrew N Harman, Ellis Patrick

Affiliations

  • Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia. Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia. School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia.
  • Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia.
  • School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia.
  • Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia.
  • School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.

Abstract

MOTIVATION

As research advances in spatially resolving the biological archetype of various diseases, technologies that capture the spatial relationships between cells are demonstrating increasing value. Whilst there are an increasing number of analytical methods being developed to identify the complex web of interactions between cells, the downstream impacts of these cell-cell relationships are under explored.

RESULTS

We present SpatioMark, a statistical framework that simplifies the assessment of gene or protein expression changes within a cell type that are associated with the spatial proximity to other cell types. We demonstrate its performance across spatial proteomics and transcriptomics datasets. We link identified relationships with differences in patient survival. We highlight key challenges in identifying changes in molecular markers associated with the localization of cells. We propose correction strategies that reduce artefact-induced relationships.

AVAILABILITY AND IMPLEMENTATION

SpatioMark is implemented in the Statial R package on Bioconductor: https://bioconductor.org/packages/release/bioc/html/Statial.html.

MeSH

Cells, Phenotype