scACCorDiON: a clustering approach for explainable patient level cell–cell communication graph analysis

Bioinformatics, vol. 41

Abstract

MOTIVATION: Combining single-cell sequencing with ligand-receptor (LR) analysis paves the way for the characterization of cell communication events in complex tissues. In particular, directed weighted graphs naturally represent cell-cell communication events. However, current computational methods cannot yet analyze sample-specific cell-cell communication events, as measured in single-cell data produced in large patient cohorts. Cohort-based cell-cell communication analysis presents many challenges, such as the nonlinear nature of cell-cell communication and the high variability given by the patient-specific single-cell RNAseq datasets. RESULTS: Here, we present scACCorDiON (single-cell Analysis of Cell-Cell Communication in Disease clusters using Optimal transport in Directed Networks), an optimal transport algorithm exploring node distances on the Markov Chain as the ground metric between directed weighted graphs. Benchmarking indicates that scACCorDiON performs a better clustering of samples according to their disease status than competing methods that use undirected graphs. We provide a case study of pancreas adenocarcinoma, where scACCorDion detects a sub-cluster of disease samples associated with changes in the tumor microenvironment. Our study case corroborates that clusters provide a robust and explainable representation of cell-cell communication events and that the expression of detected LR pairs is predictive of pancreatic cancer survival. AVAILABILITY AND IMPLEMENTATION: The code of scACCorDiON is available at https://scaccordion.readthedocs.io/en/latest/. and https://doi.org/10.5281/zenodo.15267648. The survival analysis package can be found at https://github.com/CostaLab/scACCorDiON.su.

Authors 4

1. James Shiniti Nagai corresponding Aachen Institute for Computational Genomics

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, RWTH Aachen Medical Faculty , Aachen 52074,

   RWTH Aachen Medical Faculty Institute for Computational Genomics, , Pauwelsstr. 19, 52074, Aachen,

2. Tiago Maié Aachen Institute for Computational Genomics

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, RWTH Aachen Medical Faculty , Aachen 52074,

   RWTH Aachen Medical Faculty Institute for Computational Genomics, , Pauwelsstr. 19, 52074, Aachen,

3. Michael T. Schaub corresponding Aachen Department of Computational Science

   RWTH Aachen University

   Affiliation as printed

   Department of Computational Science, RWTH Aachen University , Aachen 52074,

   RWTH Aachen University Department of Computational Science, , Ahornstraße. 55, 52074, Aachen,

4. Ivan G. Costa corresponding Aachen Institute for Computational Genomics

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, RWTH Aachen Medical Faculty , Aachen 52074,

   RWTH Aachen Medical Faculty Institute for Computational Genomics, , Pauwelsstr. 19, 52074, Aachen,