2026

C. Li, J. Thijssen, T. Kroes, L. Koorneef, T. Höllt, L. van der Weerd, and B. Lelieveldt, "PathwayFinder enables linked exploration of cell types and gene modules in spatially resolved transcriptomics data," iScience, vol. 29, iss. 11, p. 118043, 2026.

[Bibtex]

@article{bib:li:2026,
title = { PathwayFinder enables linked exploration of cell types and gene modules in spatially resolved transcriptomics data },
journal = { iScience },
volume = { 29 },
number = { 11 },
pages = { 118043 },
year = { 2026 },
doi = { 10.1016/j.isci.2026.118043 },
author = { Chang Li and Julian Thijssen and Thomas Kroes and Lisa Koorneef and Thomas Höllt and Louise {van der Weerd} and Boudewijn Lelieveldt},
abstract = { The rapid development of spatially resolved transcriptomics technologies has provided opportunities and challenges for understanding biological systems. Interpreting these data requires integrated analysis of gene expression and cell types within their spatial context, however, existing tools fall short in scaling this linked interactive exploration to large-scale datasets. We present PathwayFinder, a visual analytics application designed to bridge the gap between gene-centric and cell-centric analysis. Unlike standard workflows that view cells and genes in isolation, PathwayFinder links them through a multi-scale interactive interface. This allows researchers to explore the relationships between transcriptomic profiles and tissue architecture, for example, by selecting a cell type to instantly discover its potential marker genes, or brushing gene modules to identify cell populations expressing them and their spatial distributions. Through this tight integration of gene, cell, and spatial views, PathwayFinder facilitates rapid discovery of co-expressed gene modules, specialized cell subpopulations, and functional hypotheses in spatial contexts. },
pdf = {pdfs/2026-li-iscience.pdf},
images = {images/2026-li-iscience.jpg},
thumbnails = {images/2026-li-iscience.jpg},
}

Q. Jiang, V. A. Merkus, C. Lindelauf, J. Krijgsman, N. Guo, L. F. Ouboter, T. Höllt, P. W. Voorneveld, C. R. Meijer-Boekel, F. Koning, A. E. van der Meulen-de Jong, M. F. Pascutti, and V. van Unen, "Tissue-embedded CD4+ plasticity defines mucosal immunity in inflammatory bowel disease," Mucosal Immunology, p. 100369, 2026.

[Bibtex]

@article{bib:jiang:2026,
author = { Jiang, Qinyue and Merkus, Veerle A. and Lindelauf, Ciska and Krijgsman, Jens and Guo, Nannan and Ouboter, Laura F. and Höllt, Thomas and Voorneveld, Philip W. and Meijer-Boekel, Caroline R. and Koning, Frits and van der Meulen-de Jong, Andrea E and Pascutti, Maria Fernanda and van Unen, Vincent },
title = { Tissue-embedded CD4+ plasticity defines mucosal immunity in inflammatory bowel disease },
journal = { Mucosal Immunology },
year = { 2026 },
pages = { 100369 },
doi = { 10.1016/j.mucimm.2026.100369 },
abstract = {CD4+ T helper (Th) cell responses to commensal microbiota are linked to Inflammatory Bowel Disease (IBD), yet how Th programs coexist and evolve in human tissues remains poorly defined. Here, we profiled CD4+ memory T cells in intestinal biopsies using immunological and histological approaches to map phenotypes, functional states, and spatial relationships across disease states. A marked expansion of CD4+ T cells concomitant with a RORγt+ Th population with elevated T-bet expression was linked to the progression of inflammation. Moreover, Foxp3+ cells co-expressing RORγt emerged within the inflamed niche, indicating regulatory–Th17 plasticity. Trajectory visualization revealed a potential branched differentiation path toward regulatory or tissue-resident Th17-like fates, with both termini expressing activation and proliferation markers. Correlation network analysis connected pro-inflammatory CD4+ states to T-bet+Granzyme-B+ CD8+ subsets, indicating coordination between helper and cytotoxic lineages. Histology revealed increased T-cell infiltration and spatial segregation of tissue-resident subsets, with CD103+CD4+ T cells localized mainly in the lamina propria and CD103+CD8+ T cells near the epithelium. TCR stimulation during active disease revealed broad suppression of CD4+ pro-inflammatory cytokines alongside Foxp3+ expansion. Conversely, HLA-DR+CD38+ memory subset retained multifunctionality, producing elevated levels of pro-inflammatory cytokines. Together, these results define a dynamic, tissue-embedded CD4 T-cell landscape in IBD.},
pdf = {pdfs/2026-Jiang-MucosalImmunology.pdf},
images = {images/2026-Jiang-MucosalImmunology.png},
thumbnails = {images/2026-Jiang-MucosalImmunology-icon.png},
}