Spatially resolved host-fungal transcriptomics profiling by fungal-DBiT
- 1Yale School of Medicine
Abstract
Hosts and their associated fungi coexist within a shared tissue environment, engaging in dynamic interactions that influence immune regulation, tissue homeostasis, and disease progression. Dissecting these interactions requires spatially resolved and unbiased approaches capable of capturing gene expression from both host and fungal cells within intact tissue architecture. Here, we present fungal-DBiT, a spatial transcriptomic platform that enables simultaneous, high-resolution mapping of host and fungal RNAs, directly in tissue sections. Using fungal-DBiT, we profiled the spatial distribution of host and fungal transcripts in a fungal infection mouse model, and review pronounced spatial heterogeneity in fungal localization and activity, accompanied by region-specific host transcriptional responses. We further applied fungal-DBiT to intestinal tissues under physiological conditions, demonstrating its sensitivity in detecting low-abundance fungal species in the absence of overt inflammation. Together, these results demonstrate the ability of fungal-DBiT to resolve host-fungal interactions in situ and highlight its utility for studying mycobiome associated immune responses and disease processes with spatial precision.
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BibTeX
@misc{yu2026spatially,
title = {{Spatially resolved host-fungal transcriptomics profiling by fungal-DBiT}},
author = {X. Yu and F. Gao and D. Song and G. Li and D. Wang and S. Wang and X. Di and S. He and L. Lin and J. Xu and D. Zhang and Y. Jin and J. Du and N. W. Palm and Y. Liu},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.19.760099},
url = {https://www.biorxiv.org/content/10.64898/2026.10.19.760099v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Spatially resolved host-fungal transcriptomics profiling by fungal-DBiT
AU - X. Yu
AU - F. Gao
AU - D. Song
AU - G. Li
AU - D. Wang
AU - S. Wang
AU - X. Di
AU - S. He
AU - L. Lin
AU - J. Xu
AU - D. Zhang
AU - Y. Jin
AU - J. Du
AU - N. W. Palm
AU - Y. Liu
PY - 2026
DA - 2026/10/19
PB - bioRxiv
DO - 10.64898/2026.10.19.760099
UR - https://www.biorxiv.org/content/10.64898/2026.10.19.760099v1
AB - Hosts and their associated fungi coexist within a shared tissue environment, engaging in dynamic interactions that influence immune regulation, tissue homeostasis, and disease progression. Dissecting these interactions requires spatially resolved and unbiased approaches capable of capturing gene expression from both host and fungal cells within intact tissue architecture. Here, we present fungal-DBiT, a spatial transcriptomic platform that enables simultaneous, high-resolution mapping of host and fungal RNAs, directly in tissue sections. Using fungal-DBiT, we profiled the spatial distribution of host and fungal transcripts in a fungal infection mouse model, and review pronounced spatial heterogeneity in fungal localization and activity, accompanied by region-specific host transcriptional responses. We further applied fungal-DBiT to intestinal tissues under physiological conditions, demonstrating its sensitivity in detecting low-abundance fungal species in the absence of overt inflammation. Together, these results demonstrate the ability of fungal-DBiT to resolve host-fungal interactions in situ and highlight its utility for studying mycobiome associated immune responses and disease processes with spatial precision.
ER -