ArticleGenome research2025
Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids.
Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Brain organoids as models of extracellular vesicle-mediated human neural communication.Neural regeneration research · 2026Article
- Modeling Epilepsies with Human Brain Organoids: Recent Advances and Ongoing Challenges.Epilepsy currents · 2026Review
- Developmental signaling reveals functionally enriched human-specific gene regulation in telencephalic progenitors.bioRxiv : the preprint server for biology · 2026Article
- Disease modelling with in vitro vascularised organoids.Disease models & mechanisms · 2026Review
- Beyond the baseline: mapping the context-specific regulatory landscape of disease.Trends in genetics : TIG · 2026Review
- Cell type-agnostic transcriptomic signatures enable uniform comparisons of neural maturation.PLoS biology · 2026Article
- Air-liquid interface-centered oxygen engineering in human brain organoids: intact, sliced, and microfluidic extensions.Frontiers in cell and developmental biology · 2026Review
- Non-negative matrix factorization algorithms generally improve topic model fits.Statistics and computing · 2026Article
- Context-dependent regulatory variants in Alzheimer's disease.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
- Update of
Authors and funding
2 authors.
Funding
Abstract
The interaction between genetic variants and environmental stressors is key to understanding the mechanisms underlying neurological diseases. In this study, we use human brain organoids to explore how varying oxygen levels expose context-dependent gene regulatory effects. By subjecting a genetically diverse panel of 21 brain organoids to hypoxic and hyperoxic conditions, we identify hundreds of gene regulatory changes that are undetectable under baseline conditions, with 148 trait-associated genes showing regulatory effects only in response to oxygen stress. To capture more nuanced transcriptional patterns, we employ topic modeling, which reveals context-specific gene regulation linked to dynamic cellular processes and environmental responses, offering a deeper understanding of how gene regulation is modulated in the brain. These findings underscore the importance of genotype-environment interactions in genetic studies of neurological disorders and provide new insights into the hidden regulatory mechanisms influenced by environmental factors in the brain.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.