Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome and secretome analysis of human dorsal forebrain organoids reveals a time-dependent shift in the abundance of cell adhesion and extracellular matrix proteins

ABSTRACT: Temporal dynamics of prenatal brain development are influenced by changes in the microenvironment. Particularly, extracellular proteins contribute to the dynamic niche that balances neural stem cell proliferation and differentiation. Here, we present a resource for proteome and secretome analysis of human induced pluripotent stem cell-derived dorsal forebrain organoids over the early developmental period. We used liquid chromatography-mass spectrometry to identify proteins found in whole organoid and secreted proteins at days 20, 35, and 50 of dorsal forebrain organoid differentiation. We show that the whole organoid proteome demonstrates progression in the neurodevelopmental trajectory with reduced proliferation and increased neural differentiation over time. However, secretome analysis revealed a unique signature for developmental progression. Cell adhesion molecules are enriched in the secretome of day 35 organoids, while secretome of day 50 organoids is enriched with extracellular matrix proteins, demonstrating a change in the extracellular interactions over time of organoid differentiation and maturation. We, therefore, show the relevance of secretome analysis for the thorough study of extracellular matrix-related proteins and the importance of time course study of neural organoids to understand the subtle changes that guide human neurodevelopment.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Mohamed Ali Jarboui

PROVIDER: MSV000094878 | MassIVE | Mon May 27 23:53:00 BST 2024

SECONDARY ACCESSION(S): PXD052612

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-Cell RNA Sequencing Analysis of Human Embryonic Stem Cell-Derived Neural Organoids

Project description:Human pluripotent stem cell-derived 3D neural organoids have been shown to recapitulate the major features and cytoarchitecture of early human brain development. We used three commercially available kits: STEMdiff™ Cerebral Organoid Kit, STEMdiff™ Dorsal Forebrain Organoid Differentiation Kit, and STEMdiff™ Ventral Forebrain Organoid Differentiation Kit. These neural organoids contain unique and diverse cell types which model the early brain and are patterned with developmental cues. Here, we sought to investigate the cellular diversity of these organoids using single-cell RNA sequencing.

2023-02-23 | GSE218457 | GEO

Gene expression profilling of day 30 cerebral organoids at the single cell level

Project description:To characterize cerebral organoids generated using STEMdiff Dorsal Forebrain Organoid Differentiation Kit were flash frozen on Day 30, we performed single cell RNA sequencing

2024-12-19 | GSE280812 | GEO

Transcription profiling of human dorsal forebrain organoids treated with Hyper-IL-6

Project description:Description: RNA-seq of total RNA isolated from dorsal forebrain organoids at days 50 and 55 of differentiation. The study aimed at investigating the effects of 5 or 10 days of Hyper-IL-6 exposure on transcriptional profiles of dorsal forebrain organoids.

2023-03-08 | E-MTAB-12702 | biostudies-arrayexpress

Single-cell transcription profiling human dorsal forebrain organoids treated with Hyper-IL-6

Project description:We performed single-cell RNA sequencing of dorsal forebrain organoids at day 53 of differentiation upon treatment with Hyper-IL-6. The study aimed at investigation of the effects of Hyper-IL-6 on transcriptional profiles of dorsal forebrain organoids at single-cell level.

2023-03-08 | E-MTAB-12743 | biostudies-arrayexpress

Human fetal brain self-organizes into long-term expanding organoids (scRNA-Seq)

Project description:Human brain development involves an orchestrated, massive neural progenitor expansion while a multi-cellular tissue architecture is established. Continuously expanding organoids can be grown directly from multiple somatic tissues, yet to date brain organoids can solely be established from pluripotent stem cells. Here, we show that healthy human fetal brain in vitro self-organizes into organoids (FeBOs), phenocopying aspects of in vivo cellular heterogeneity and complex organization. FeBOs can be expanded over long time periods. FeBO growth requires maintenance of tissue integrity, which ensures production of a tissue-like extracellular matrix (ECM) niche, ultimately endowing FeBO expansion. FeBO lines derived from different areas of the central nervous system (CNS), including dorsal and ventral forebrain, preserve their regional identity and allow to probe aspects of positional identity. Using CRISPR-Cas9, we showcase the generation of syngeneic mutant FeBO lines for the study of brain cancer. Taken together, FeBOs constitute a complementary CNS organoid platform.

2024-01-08 | GSE248480 | GEO

Human fetal brain self-organizes into long-term expanding organoids (bulk RNA-Seq)

2024-01-08 | GSE248479 | GEO

Trans-omic Profiling Uncovers Molecular Controls of the Early Human Cerebral Organoid Formation

Project description:Defining molecular controls that orchestrate human brain development is essential for uncovering the complexity behind neurodevelopment and the pathogenesis of neurological disorders. Due to the difficulties in accessing embryonic and fetal brain tissues, the differentiation of human pluripotent stem cell (hPSC)-derived three-dimensional neural organoids has made it possible to recapitulate this developmental process in vitro and provide a unique opportunity to investigate human brain development and disease. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the initial stages of pluripotency and neural differentiation towards the formation of cerebral organoids. Our integrative analysis uncovers key phospho-signalling events underlying neural lineage differentiation, and their convergence on transcriptional (co-)factors and chromatin remodellers that govern downstream gene regulatory networks (GRNs). Comparative analysis with developing human and mouse embryos using these GRNs demonstrates the fidelity of our early cerebral organoids in modelling embryonic brain development. Finally, we demonstrate biochemical modulation of the AKT signalling as a key molecular switch for controlling human cerebral organoid formation. Our data provides a comprehensive resource to gain insight into the molecular controls in human embryonic brain development and also provide a guide for future development of protocols for human cerebral organoid differentiation.

2024-04-23 | PXD047423 | Pride

Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex

Project description:Stem cell-derived human brain organoids hold an unprecedented degree of promise as experimental models of the human brain. They are, however, plagued by poor reproducibility and high organoid-to-organoid variability. Here, we show that a human organoid model pre-patterned to form the dorsal forebrain and cultured for over six months can achieve reproducible generation of a rich diversity of cell types appropriate for the human cerebral cortex. Using single-cell RNA-sequencing of 166,242 cells isolated from 21 individual organoids, we find that 95% of the organoids generated a virtually indistinguishable compendium of cell types, through the same temporal trajectories, and with organoid-to-organoid variability that is comparable to that of individual endogenous brains. The data demonstrate that reproducible development of complex central nervous system (CNS) cellular diversity does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments.

2019-06-05 | GSE129519 | GEO

Induction of inverted morphology in brain organoids by vertical-mixing bioreactors

Project description:Organoid technology provides an opportunity to generate brain-like structures by recapitulating developmental steps in the manner of self-organization. We examined the vertical-mixing effect on brain organoid structures using bioreactors and established inverted brain organoids. The organoids generated by vertical mixing showed neurons that migrated from the outer periphery to the inner core of organoids, in contrast to orbital mixing. To uncover the mechanisms of the inverted structure, we investigated the direction of primary cilia, a cellular mechanosensor. Primary cilia of neural progenitors by vertical mixing were aligned in a multidirectional manner, and those by orbital mixing in a bidirectional manner. Single-cell RNA sequencing revealed that neurons of inverted brain organoids presented a GABAergic character of the ventral forebrain.

2021-10-27 | GSE184409 | GEO

Guided self-organization recapitulates tissue architecture in a bioengineered brain organoid model

Project description:Engineered brain organoids (enCORs) exhibit reproducible neural differentiation and forebrain regionalization.

2017-05-29 | GSE80538 | GEO