Spatial multi-omics reveal intratumoral humoral immunity niches associated with tertiary lymphoid structures in pancreatic cancer immunotherapy pathologic responders

Sidiropoulos, D. N.; Shin, S. M.; Wetzel, M.; Girgis, A. A.; Bergman, D.; Danilova, L.; Perikala, S.; Shu, D. H.; Montagne, J. M.; Deshpande, A.; Leatherman, J.; Dequiedt, L.; Jacobs, V.; Ogurtsova, A.; Mo, G.; Yuan, X.; Lvovs, D.; Stein-O'Brien, G.; Yarchoan, M.; Zhu, Q.; Harper, E. I.; Weeraratna, A. T.; Kiemen, A. L.; Jaffee, E. M.; Zheng, L.; Ho, W. J.; Anders, R. A.; Fertig, E. J.; Kagohara, L. T.

doi:10.1101/2024.09.22.613714

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bioRxiv · 10.1101/2024.09.22.613714

Spatial multi-omics reveal intratumoral humoral immunity niches associated with tertiary lymphoid structures in pancreatic cancer immunotherapy pathologic responders

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Abstract

Pancreatic adenocarcinoma (PDAC) is a rapidly progressing cancer that responds poorly to immunotherapies. Intratumoral tertiary lymphoid structures (TLS) have been associated with rare long-term PDAC survivors, but the role of TLS in PDAC and their spatial relationships within the context of the broader tumor microenvironment remain unknown. We generated a spatial multi-omics atlas encompassing 26 PDAC tumors from patients treated with combination immunotherapies. Using machine learning-enabled H&E image classification models and unsupervised gene expression matrix factorization methods for spatial transcriptomics, we characterized cellular states within TLS niches spanning across distinct morphologies and immunotherapies. Unsupervised learning generated a TLS-specific spatial gene expression signature that significantly associates with improved survival in PDAC patients. These analyses demonstrate TLS-associated intratumoral B cell maturation in pathological responders, confirmed with spatial proteomics and BCR profiling. Our study also identifies spatial features of pathologic immune responses, revealing TLS maturation colocalizing with IgG/IgA distribution and extracellular matrix remodeling. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/613714v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@d5e1a5org.highwire.dtl.DTLVardef@1d14012org.highwire.dtl.DTLVardef@c57c6corg.highwire.dtl.DTLVardef@16baa56_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIIntegrated multi-modal spatial profiling of human PDAC tumors from neoadjuvant immunotherapy clinical trials reveal diverse spatial niches enriched in TLS. C_LIO_LITLS maturity is influenced by tumor location and the cellular neighborhoods in which TLS immune cells are recruited. C_LIO_LIUnsupervised machine learning of genome-wide signatures on spatial transcriptomics data characterizes the TLS-enriched TME and associates TLS transcriptomes with survival outcomes in PDAC. C_LIO_LIInteractions of spatially variable gene expression patterns showed TLS maturation is coupled with immunoglobulin distribution and ECM remodeling in pathologic responders. C_LIO_LIIntratumoral plasma cell and immunoglobin gene expression spatial dynamics demonstrate trafficking of TLS-driven humoral immunity in the PDAC TME. C_LI SignificanceWe report a spatial multi-omics atlas of PDAC tumors from a series of immunotherapy neoadjuvant clinical trials. Intratumorally, pathologic responders exhibit mature TLS that propagate plasma cells into malignant niches. Our findings offer insights on the role of TLS-associated humoral immunity and stromal remodeling during immunotherapy treatment.

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Sidiropoulos, D. N., Shin, S. M., Wetzel, M., Girgis, A. A., Bergman, D., Danilova, L., Perikala, S., Shu, D. H., Montagne, J. M., Deshpande, A., Leatherman, J., Dequiedt, L., Jacobs, V., Ogurtsova, A., Mo, G., Yuan, X., Lvovs, D., Stein-O'Brien, G., Yarchoan, M., Zhu, Q., Harper, E. I., Weeraratna, A. T., Kiemen, A. L., Jaffee, E. M., Zheng, L., Ho, W. J., Anders, R. A., Fertig, E. J., Kagohara, L. T.. 2024-09-23. Spatial multi-omics reveal intratumoral humoral immunity niches associated with tertiary lymphoid structures in pancreatic cancer immunotherapy pathologic responders. https://doi.org/10.1101/2024.09.22.613714

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