Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment

PLOS Computational Biology

10.1371/journal.pcbi.1012707

https://doi.org/10.1371/journal.pcbi.1012707

Mai Chan Lau, Jennifer Borowsky, Juha P. Väyrynen, Koichiro Haruki, Melissa Zhao, Andressa Dias Costa, Simeng Gu, Annacarolina da Silva, Tomotaka Ugai, Kota Arima, Minh N. Nguyen, Yasutoshi Takashima, Joe Yeong, David Tai, Tsuyoshi Hamada, Jochen K. Lennerz, Charles S. Fuchs, Catherine J. Wu, Jeffrey A. Meyerhardt, Shuji Ogino, Jonathan A. Nowak

18 February 2025

Lau, M. C., Borowsky, J., Väyrynen, J. P., Haruki, K., Zhao, M., Dias Costa, A., Gu, S., da Silva, A., Ugai, T., Arima, K., Nguyen, M. N., Takashima, Y., Yeong, J., Tai, D., Hamada, T., Lennerz, J. K., Fuchs, C. S., Wu, C. J., Meyerhardt, J. A., … Nowak, J. A. (2025). Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment. PLOS Computational Biology, 21(2), e1012707. https://doi.org/10.1371/journal.pcbi.1012707

Background Growing evidence supports the importance of characterizing the organizational patterns of various cellular constituents in the tumor microenvironment in precision oncology. Most existing data on immune cell infiltrates in tumors, which are based on immune cell counts or nearest neighbor-type analyses, have failed to fully capture the cellular organization and heterogeneity. Methods We introduce a computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), that jointly measures immune cell partitioning between tumor epithelial and stromal areas and immune cell clustering versus dispersion. As proof-of-principle, we applied TIPC to a prospective cohort incident tumor biobank containing 931 colorectal carcinoma cases. TIPC identified tumor subtypes with unique spatial patterns between tumor cells and T lymphocytes linked to certain molecular pathologic and prognostic features. T lymphocyte identification and phenotyping were achieved using multiplexed (multispectral) immunofluorescence. In a separate hepatocellular carcinoma cohort, we replaced the stromal component with specific immune cell types—CXCR3+CD68+ or CD8+—to profile their spatial relationships with CXCL9+CD68+ cells. Results Six unsupervised TIPC subtypes based on T lymphocyte distribution patterns were identified, comprising two cold and four hot subtypes. Three of the four hot subtypes were associated with significantly longer colorectal cancer (CRC)-specific survival compared to a reference cold subtype. Our analysis showed that variations in T-cell densities among the TIPC subtypes did not strictly correlate with prognostic benefits, underscoring the prognostic significance of immune cell spatial patterns. Additionally, TIPC revealed two spatially distinct and cell density-specific subtypes among microsatellite instability-high colorectal cancers, indicating its potential to upgrade tumor subtyping. TIPC was also applied to additional immune cell types, eosinophils and neutrophils, identified using morphology and supervised machine learning; here two tumor subtypes with similarly low densities, namely ‘cold, tumor-rich’ and ‘cold, stroma-rich’, exhibited differential prognostic associations. Lastly, we validated our methods and results using The Cancer Genome Atlas colon and rectal adenocarcinoma data (n = 570). Moreover, applying TIPC to hepatocellular carcinoma cases (n = 27) highlighted critical cell interactions like CXCL9-CXCR3 and CXCL9-CD8. Conclusions Unsupervised discoveries of microgeometric tissue organizational patterns and novel tumor subtypes using the TIPC algorithm can deepen our understanding of the tumor immune microenvironment and likely inform precision cancer immunotherapy.

Attribution 4.0 International (CC BY 4.0)

This research / project is supported by the National Medical Research Council - Open Fund–Young Individual Research Grant
Grant Reference no. : OFYIRG23jan-0049

This research is supported by core funding from: Bioinformatics Institute (BII)
Grant Reference no. :

This research is supported by core funding from: Singapore Immunology Network (SIgN)
Grant Reference no. :

https://oar.a-star.edu.sg/communities-collections/articles/21566

1553-7358

Bioinformatics Institute