Isolation of functional supramolecular attack particles (SMAPs)

Jainarayanan, A. K.; Chandrasekar, V.; Almeida, V. P.; Widdess, M. A.; Staton, C. C.; Bernand, A.; Pfannenstill, V.; Flannery, S.; Watson, H.; Wicki, A.; Onupom, O.; Elanchezhian, M.; Capera, J.; Chen, L.; Valvo, S.; Anand, N. M.; Mahla, R. S.; Kurz, E.; Franchet, C.; Dalenc, F.; Ysebaert, L.; Michelet, A.; Gupta, D.; Naismith, J. H.; Dustin, L. B.; Fritzsche, M.; Fischer, R.; Valitutti, S.; Leung, C. S.; Wood, M. J. A.; Dustin, M. L.

doi:10.1101/2025.11.10.687675

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bioRxiv · 10.1101/2025.11.10.687675

Isolation of functional supramolecular attack particles (SMAPs)

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Abstract

High density cultures of the GMP compatible NK-92 natural killer cell line release heterogeneous extracellular particles (EP), notably extracellular vesicles (EV) and non-vesicular extracellular particles (NVEP). The NVEP include a small proportion of supramolecular attack particles (SMAPs), the direct cytotoxic potential of which suggests therapeutic promise, yet scalable enrichment and functional evaluation alongside other extracellular particles (EPs) have been lacking. Here, we develop a high-resolution serial size-exclusion liquid chromatography (SELC) workflow that resolves EPs into 4 fractions F1-F4, in which EV are enriched in F2 and SMAPs are enriched in F3. Multi-modal characterization using Nanoparticle Tracking Analysis (NTA), Nano Flow Cytometry (Nano FCM), Transmission Electron Microscopy (TEM), Total Internal Reflection Microscopy (TIRFM) and Proteomics) demonstrated that F2 NK-92 EVs are [~]130-150 nm particles enriched for complement proteins, whereas SMAPs (F3) are 100-110 nm particles enriched for cytotoxic proteins (PRF1, GZMB) and SMAP shell components (e.g., THBS1, THBS4). Functionally, Ca2+-stabilized SMAPs (F3) trigger caspase-3-dependent apoptosis in tumor cell lines with robust dose responses, while F2 lacks direct cytotoxicity in vitro. Ex vivo, F3 SMAPs kill patient-derived breast cancer and chronic lymphocytic leukaemia cells (CLL) in a concentration-dependent manner. In NSG mice, intra-tumoral treatment with SMAPs (F3) restrains the growth of aggressive B16F10 melanoma and PANC-1 pancreatic cancer, confirming in vivo functionality. These results establish a scalable method to isolate and compare NK-derived particle classes and provide a foundation for targeted SMAP engineering as a promising approach for treatment of solid tumours. Significance StatementCell therapies face barriers in solid tumours, including lack of entry and suppression. NK cells release extracellular particles (EPs), including supramolecular attack particles (SMAPs), that can traffic into tumour tissue. We define a practical, scalable chromatography process that resolves NK-derived SMAPs from other EPs and demonstrate that SMAPs induce caspase mediated apoptosis in vitro and engage in cytotoxic lymphocyte independent anti-tumour activity in vivo. These insights open a route to engineering and testing SMAP-based therapeutics to overcome limitations of whole-cell approaches in solid cancers.

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Jainarayanan, A. K., Chandrasekar, V., Almeida, V. P., Widdess, M. A., Staton, C. C., Bernand, A., Pfannenstill, V., Flannery, S., Watson, H., Wicki, A., Onupom, O., Elanchezhian, M., Capera, J., Chen, L., Valvo, S., Anand, N. M., Mahla, R. S., Kurz, E., Franchet, C., Dalenc, F., Ysebaert, L., Michelet, A., Gupta, D., Naismith, J. H., Dustin, L. B., Fritzsche, M., Fischer, R., Valitutti, S., Leung, C. S., Wood, M. J. A., Dustin, M. L.. 2025-11-12. Isolation of functional supramolecular attack particles (SMAPs). https://doi.org/10.1101/2025.11.10.687675

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