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Identification of cilia-localized proteins of brain organoids using proximity labelling

ABSTRACT: Primary cilium is a cellular organelle. To identify proteins enriched in primary cilia of brain organoids, we performed proximity labelling followed by LC-Mass spectrometry analysis.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yoichi Kato

PROVIDER: PXD063951 | JPOST Repository | Fri Apr 10 00:00:00 BST 2026

REPOSITORIES: jPOST

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			Action	DRS
	20241226_dia_12048_01.raw	Raw
	20241226_dia_12049_01.raw	Raw
	20250122_dia_2501042_01.raw	Raw
	20250122_dia_2501043_01.raw	Raw
	20250122_dia_2501045_01.raw	Raw

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Project description:<p>Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an <em>in vitro</em> system. Over the past decade, with the advent of spatial technologies, mass spectrometry imaging (MSI) has become a prominent tool for metabolic microscopy, providing label-free, non-targeted molecular and spatial distribution information of the metabolites within tissue, including lipids. This technology has never been used for studies of brain organoids and here, we set out to develop a standardized protocol for preparation and mass spectrometry imaging of human brain organoids. We present an optimized and validated sample preparation protocol, including sample fixation, optimal embedding solution, homogenous deposition of matrices, data acquisition and processing to maximize the molecular information derived from mass spectrometry imaging. We focus on lipids in organoids, as they play critical roles during cellular and brain development. Using high spatial and mass resolution in positive- and negative-ion modes, we detected 260 lipids in the organoids. Seven of them were uniquely localized within the neurogenic niches or rosettes as confirmed by histology, suggesting their importance for neuroprogenitor proliferation. We observed a particularly striking distribution of ceramide-phosphoethanolamine CerPE 36:1; O2 restricted within rosettes and of phosphatidyl-ethanolamine PE 38:3, which was distributed throughout the organoid tissue but not in rosettes. This suggests that ceramide in this particular lipid species might be important for neuroprogenitor biology, while its removal may be important for terminal differentiation of their progeny. Overall, our study establishes the first optimized experimental pipeline and data processing strategy for mass spectrometry imaging of human brain organoids, allowing direct comparison of lipid signal intensities and distributions in these tissues. Further, our data shed new light on the complex processes that govern brain development by identifying specific lipid signatures that may play a role in metabolic cell fate trajectories. mass spectrometry imaging thus has great potential in advancing our understanding of early brain development as well as disease modeling and drug discovery.</p>

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Identification of cilia-localized proteins of brain organoids using proximity labelling

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