Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment

Avery Pong; Clarence K Mah; Gene W Yeo; Nathan E Lewis

doi:10.1016/j.copbio.2023.103048

Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment

Curr Opin Biotechnol. 2024 Feb:85:103048. doi: 10.1016/j.copbio.2023.103048. Epub 2023 Dec 23.

Authors

Avery Pong¹, Clarence K Mah², Gene W Yeo³, Nathan E Lewis⁴

Affiliations

¹ Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
² Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
³ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
⁴ Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: nlewisres@ucsd.edu.

PMID: 38142648
PMCID: PMC11168798 (available on 2025-02-01)
DOI: 10.1016/j.copbio.2023.103048

Abstract

Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the TME remains a stubborn barrier to complete drug responses. This review outlines recent advances in the study of CCIs that leverage single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies that can clarify TME dynamics. We anticipate that these strategies will promote discovery of CCIs critical to the tumor-immune interface and will, by extension, expand the repertoire of druggable tumor biomarkers.

Publication types

Review
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Biomarkers
Biomedical Research*
Cell Communication
Communication
Single-Cell Analysis
Tumor Microenvironment*

Substances

Biomarkers

Abstract

Publication types

MeSH terms

Substances

Grants and funding