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bioRxiv · 10.1101/2024.01.12.574349

Delineation of signaling routes that underlie differences in macrophage phenotypic states

Totu, T.·Bossart, J.·Hast, K.·Li, C.·Rottmar, M.·Sobottka, B.·Yu, G.·Ayala-Nunez, V.·Buljan, M.
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Abstract

Macrophages represent a major immune cell type in tumor microenvironments, they exist in multiple functional states and are of a strong interest for therapeutic reprogramming. While signaling cascades defining pro-inflammatory macrophages are better characterized, pathways that drive polarization in immunosuppressive macrophages are incompletely mapped. Here, we performed an in-depth characterization of signaling events in primary human macrophages in different functional states using mass spectrometry-based proteomic and phosphoproteomic profiling. Analysis of direct and indirect footprints of kinase activities has suggested PAK2 and PKC kinases as important regulators of in vitro immunosuppressive macrophages (IL-4/IL-13 or IL-10 stimulated). Network integration of these data with the corresesponding transcriptome profiles has further highlighted FOS and NCOR2 as central transcription regulators in immunosuppressive states. Furthermore, we retrieved single cell sequencing datasets for tumors from cancer patients and found that the unbiased signatures identified here through proteomic analysis were able to successfully separate pro-inflammatory macrophage populations in a clinical setting and could thus be used to expand state-specific markers. This study contributes to in-depth multi-omics characterizations of macrophage phenotypic landscapes, which could be valuable for assisting future interventions that therapeutically alter immune cell compartments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/574349v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1234713org.highwire.dtl.DTLVardef@10f4999org.highwire.dtl.DTLVardef@a8dd60org.highwire.dtl.DTLVardef@5dfb33_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGlobal proteomic characterization of primary human macrophages in different states C_LIO_LIMapping of main signaling events through in-depth data analysis C_LIO_LIPKC and PAK2 kinases are important regulators of immunosuppressive macrophages C_LIO_LIProteomic signatures enable accurate detection of pro-inflammatory macrophages in patient tumors C_LI

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Totu, T., Bossart, J., Hast, K., Li, C., Rottmar, M., Sobottka, B., Yu, G., Ayala-Nunez, V., Buljan, M.. 2024-01-14. Delineation of signaling routes that underlie differences in macrophage phenotypic states. https://doi.org/10.1101/2024.01.12.574349

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