Single-cell spatial multi-omic characterization of the tumour microenvironment in transformed follicular lymphoma

Wu, S.; Lee, E.; Fratzscher, A.-S.; Lytle, A.; Martin, S. D.; Hsu, T.; Telenius, A.; Yin, Y.; Fong, A.; Rai, S.; Fujisawa, M.; Cheung, H.; Aparicio, S.; Huntsman, D. G.; Aoki, T.; Scott, D. W.; Steidl, C.; Roth, A.

doi:10.64898/2026.08.11.743383

bioRxiv · 10.64898/2026.08.11.743383

Single-cell spatial multi-omic characterization of the tumour microenvironment in transformed follicular lymphoma

Wu, S.·Lee, E.·Fratzscher, A.-S.·Lytle, A.·Martin, S. D.·Hsu, T.·Telenius, A.·Yin, Y.·Fong, A.·Rai, S.·Fujisawa, M.·Cheung, H.·Aparicio, S.·Huntsman, D. G.·Aoki, T.·Scott, D. W.·Steidl, C.·Roth, A.

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Abstract

Histological examination of follicular lymphoma (FL) biopsies remains the cornerstone for diagnostic grading of FL. Single-cell sequencing approaches, while transcriptomically rich, require tissue dissociation and lose the native spatial context that underpins FL transformation to diffuse large B-cell lymphoma (DLBCL). To investigate the spatial interplay between malignant B-cells and the tumour microenvironment (TME) across disease states, we performed subcellular single-cell spatial transcriptomics and spatial proteomics on 12 paired pre/post-transformation samples and 10 non-transforming FL controls, integrated with matched single-cell whole genome sequencing (scWGS). Our analysis reveals that transformation is accompanied by a shift toward B-cell-predominant stromal and immunosuppressive cellular neighbourhoods, where the magnitude of expansion correlates with time to transformation. Prior to transformation, immunomodulatory Galectin-9 interactions move from the intra-follicular core to the extra-follicular space. Integration with scWGS demonstrates that high copy-number instability in malignant B-cells is associated with reduced supportive T-cell niches and intensified immunoregulatory crosstalk at the transformed state. Collectively, our multi-omic analysis characterizes TME remodeling during FL transformation, contributing to a refined disease evolution model.

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Wu, S., Lee, E., Fratzscher, A.-S., Lytle, A., Martin, S. D., Hsu, T., Telenius, A., Yin, Y., Fong, A., Rai, S., Fujisawa, M., Cheung, H., Aparicio, S., Huntsman, D. G., Aoki, T., Scott, D. W., Steidl, C., Roth, A.. 2026-08-18. Single-cell spatial multi-omic characterization of the tumour microenvironment in transformed follicular lymphoma. https://doi.org/10.64898/2026.08.11.743383

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