Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

Ogbonna, E. C.; Talemi, S. R.; Maliga, Z.; Zhao, Z.; Yapp, C.; Pant, S. M.; Lu, Y. D.; Muhlich, J.; Gagne, A.; Martinot, A. J.; Coy, S.; Santagata, S.; Shih, A. R.; Solomon, I. H.; Naidoo, T.; Aldridge, B. B.; Steyn, A. J. C.; Sorger, P. K.

doi:10.64898/2026.06.02.725201

bioRxiv · 10.64898/2026.06.02.725201

Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

Ogbonna, E. C.·Talemi, S. R.·Maliga, Z.·Zhao, Z.·Yapp, C.·Pant, S. M.·Lu, Y. D.·Muhlich, J.·Gagne, A.·Martinot, A. J.·Coy, S.·Santagata, S.·Shih, A. R.·Solomon, I. H.·Naidoo, T.·Aldridge, B. B.·Steyn, A. J. C.·Sorger, P. K.

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Abstract

Tertiary lymphoid structures (TLSs) are sites of immune organization in peripheral tissues that arise from chronic inflammation. They play important roles in infection control and cancer but the mechanisms controlling their formation remain only partly understood. Here, we combine high-plex imaging, serial-section 3D reconstruction, and optimal transport trajectory modeling to reconstruct TLSs in human lungs infected with Mycobacterium tuberculosis. We find that the extended and irregular shape of TLSs is poorly captured by 2D histopathology or spatial profiling, making assessment of developmental stage (early, primary, or secondary) error prone. In contrast, modeling TLS development in 3D using optimal transport reveals two trajectories that differ in the timing and coordination of follicular dendritic cell association, germinal center consolidation, and position within the tissue. These findings highlight the value of volumetric analysis in understanding immune organization and provide new insights into TLS biology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/725201v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@11b4daorg.highwire.dtl.DTLVardef@7871feorg.highwire.dtl.DTLVardef@1840c2dorg.highwire.dtl.DTLVardef@3b6028_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LI3D reconstruction of TB-infected lung reveals TLSs to be extended, heterogeneous structures that are frequently misclassified in 2D C_LIO_LITLS maturation follows continuous trajectories rather than discrete histological stages C_LIO_LIOptimal transport modeling identifies distinct maturation paths with divergent follicular dynamics C_LIO_LIGerminal center organization and Tfh-FDC interactions emerge along maturation trajectories C_LIO_LITLS maturation states are shaped by spatially localized microenvironmental niches. C_LI

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Ogbonna, E. C., Talemi, S. R., Maliga, Z., Zhao, Z., Yapp, C., Pant, S. M., Lu, Y. D., Muhlich, J., Gagne, A., Martinot, A. J., Coy, S., Santagata, S., Shih, A. R., Solomon, I. H., Naidoo, T., Aldridge, B. B., Steyn, A. J. C., Sorger, P. K.. 2026-06-07. Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis. https://doi.org/10.64898/2026.06.02.725201

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