Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example

Thomas Defard; Auxence Desrentes; Charles Fouillade; Florian Mueller

doi:10.1007/978-1-0716-4184-2_5

Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example

Methods Mol Biol. 2025:2864:77-105. doi: 10.1007/978-1-0716-4184-2_5.

Authors

Thomas Defard^{1

2

3

4

5}, Auxence Desrentes^{6

7

8}, Charles Fouillade⁹, Florian Mueller^{10

11}

Affiliations

¹ Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Paris, France.
² Institut Pasteur, Université Paris Cité, Imaging and Modeling Unit, Paris, France.
³ Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France.
⁴ Institut Curie, PSL University, Paris, France.
⁵ INSERM, U900, Paris, France.
⁶ UMRS1135 Sorbonne University, Paris, France.
⁷ INSERM U1135, Paris, France.
⁸ Team "Immune Microenvironment and Immunotherapy", Centre for Immunology and Microbial Infections (CIMI), Paris, France.
⁹ Institut Curie, Inserm U1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France.
¹⁰ Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Paris, France. [email protected].
¹¹ Institut Pasteur, Université Paris Cité, Imaging and Modeling Unit, Paris, France. [email protected].

PMID: 39527218
DOI: 10.1007/978-1-0716-4184-2_5

Abstract

Spatial transcriptomics methods provide insight into the cellular heterogeneity and spatial architecture of complex, multicellular systems. Combining molecular and spatial information provides important clues to study tissue architecture in development and disease. Here, we present a comprehensive do-it-yourself (DIY) guide to perform such experiments at reduced costs leveraging open-source approaches. This guide spans the entire life cycle of a project, from its initial definition to experimental choices, wet lab approaches, instrumentation, and analysis. As a concrete example, we focus on tertiary lymphoid structures (TLS), which we use to develop typical questions that can be addressed by these approaches.

Keywords: Homebuilt; Open-source; Spatial biology; Spatial transcriptomic; Tertiary lymphoid structure.

MeSH terms

Animals
Gene Expression Profiling* / methods
Humans
Software
Tertiary Lymphoid Structures* / genetics
Tertiary Lymphoid Structures* / pathology
Transcriptome*