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Related Experiment Video

Updated: Aug 11, 2025

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Published on: January 19, 2017

Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation.

Thomas Krausgruber¹, Anna Redl², Daniele Barreca³

¹CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria.

|February 7, 2023

Summary

Granulomas, immune cell lumps, surprisingly mimic lymphoid organ development. Researchers found these structures repurpose gene programs, suggesting granulomas are aberrant lymphoid organs.

Keywords:

cellular interactions cytokine signaling extracellular matrix remodeling granuloma immunometabolism single-cell transcriptomics spatial transcriptomics

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Last Updated: Aug 11, 2025

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Published on: January 19, 2017

Generation of Lymph Node-fat Pad Chimeras for the Study of Lymph Node Stromal Cell Origin

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Visualizing Lymph Node Structure and Cellular Localization using Ex-Vivo Confocal Microscopy

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Published on: August 9, 2019

Area of Science:

Immunology
Systems Biology
Genomics

Background:

Granulomas are immune cell aggregates found in various organs.
While often unstructured, granulomas share features with lymphoid organs.

Purpose of the Study:

To investigate the cellular and molecular mechanisms of granuloma formation in sarcoidosis.
To understand how granulomas develop and potentially mimic lymphoid organ structures.

Main Methods:

Single-cell sequencing and spatial transcriptomics of human sarcoidosis granulomas.
Bioinformatic reconstruction of gene regulatory networks.
In vivo validation using a sarcoidosis mouse model.

Main Results:

Granulomas exhibit an immune-stimulatory environment that repurposes lymphoid organ development programs.
Characteristic spatial patterns and gene expression profiles were identified, involving immunometabolism, cytokine signaling, and extracellular matrix remodeling.
Key cell types include reprogrammed macrophages, Th17.1 cells, and fibroblasts.

Conclusions:

Human granulomas develop by aberrantly combining aspects of normal lymphoid organ development.
Granulomas can be considered aberrant lymphoid organs due to their developmental pathways and cellular composition.