Biology subjects

Herrmann, U. S.

Publications and source records attributed to Herrmann, U. S..

2 recordsLinked to original sources

bioRxiv2025

An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut

The gastrointestinal environment is home to a massive diversity of diet-, host-, and microbiota-derived small molecules, collectively sensed by a remarkable variety of cells. To explore the cellular and spatial organization of sensation, we used MERFISH to profile receptor expression across 2.1 million cells in multiple regions of the murine gut under specific-pathogen-free (SPF) and germ-free (GF) conditions. This atlas revealed expected and novel cell types--including a candidate murine homolog of human BEST4 enterocytes--demonstrated cell-type regional specialization, discovered extensive location-dependent spatial fine-tuning in mucosal cell expression, and suggested cell-type specific mediators of the effects of microbiota-derived small molecules. In addition, this atlas revealed that, aside from immune cell abundance, many aspects of the murine gut are host-intrinsic and modified only modestly in the absence of a microbiota. Collectively, this atlas provides a valuable resource for understanding the cellular and spatial organization underlying small molecule sensation in the gut.

genomics↗

bioRxiv2025

In situ profiling of plasma cell clonality with image-based single-cell transcriptomics

Image-based single-cell transcriptomics can identify diverse cell types within intact tissues. However, in adaptive immunity, V(D)J recombination generates unique immune receptors within cells of the same type, leading to important functional variation that is not yet defined by these methods. Here we introduce B-cell-receptor multiplexed error robust fluorescence in situ hybridization (BCR-MERFISH), which distinguishes plasma cell clones based on V-gene usage in combination with transcriptome profiling. We demonstrate that BCR-MERFISH accurately identifies V-gene usage in cell culture and in mice with restricted or native plasma cell diversity. We then use BCR-MERFISH to reveal the microbiota-dependent changes in plasma cell abundance, clonal diversity, and public clonotype usage in the mouse gut and the non-uniform distribution of plasma cell clones along the mouse ileum. As tissue context is an essential modulator of plasma cell dynamics, we anticipate that BCR-MERFISH may offer new insights into a wide range of immunological questions.

immunology↗