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Updated: Jul 25, 2025
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
Published on: February 27, 2015
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis
Monica T Dayao1,2, Alexandro Trevino3, Honesty Kim3
1Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, United States.
Motivation:
Spatial proteomics data have been used to map cell states and improve our understanding of tissue organization. More recently, these methods have been extended to study the impact of such organization on disease progression and patient survival. However, to date, the majority of supervised learning methods utilizing these data types did not take full advantage of the spatial information, impacting their performance and utilization.
Results:
Taking inspiration from ecology and epidemiology, we developed novel spatial feature extraction methods for use with spatial proteomics data. We used these features to learn prediction models for cancer patient survival. As we show, using the spatial features led to consistent improvement over prior methods that used the spatial proteomics data for the same task. In addition, feature importance analysis revealed new insights about the cell interactions that contribute to patient survival.
Availability And Implementation:
The code for this work can be found at gitlab.com/enable-medicine-public/spatsurv.
