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Mining Spatial Transcriptomics Datasets using DeepSpaceDB
Published on: September 5, 2025
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A spatial atlas of the complement system uncovers unique expression patterns in postnatal brain development in mice
Yingying Zhang1, Brianna Watson1,2, Ajitanuj Rattan1
1Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Nature Communications
|December 2, 2025
Summary
The brain utilizes the complement system, beyond its immune functions, for development. This study reveals the alternative pathway
Area of Science:
- Neuroscience
- Molecular Biology
- Genetics
Background:
- Non-immunological roles of the classical complement pathway (CP) in brain development and disease are emerging.
- Expression and function of other complement pathways in the brain are largely unknown.
Purpose of the Study:
- To create a comprehensive spatial transcriptomic atlas of the complement system in the mouse brain.
- To investigate the expression patterns and functional roles of different complement pathways during brain development.
Main Methods:
- Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) was employed.
- Spatial transcriptomics was used to map complement gene expression in mouse brains from embryonic to adult stages.
Main Results:
- Most complement genes exhibit localized expression with significant cellular, spatial, and temporal heterogeneity.
- Endogenous expression of the alternative pathway (AP), including the activator Masp3, was detected in immature brains.
- Masp3 deficiency resulted in altered brain molecular structure and impaired working spatial memory.
Conclusions:
- The brain possesses distinct complement regulatory mechanisms compared to the periphery.
- Masp3 plays a crucial role in brain maturation, potentially through modulating AP activity.
- These findings highlight novel roles for the complement system, particularly the AP, in neurodevelopment.

