Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.06.04.657874

Human microglia in brain assembloids display region-specific diversity and respond to hyperexcitable neurons carrying SCN2A mutation

Wu, J.·Chen, X.·Zhang, J.·Wettschurack, K. W.·Robinson, M. J.·Li, W.·Zhao, Y.·Yoo, Y.-E.·Deming, B. A.·Abeyaratna, A. D.·Que, Z.·Du, D.·Tegtmeyer, M. T.·Yuan, C.·Skarnes, W. C.·Rochet, J.-C.·Wu, L.-J.·Yang, Y.
View original source ↗Export metadata ↓

Abstract

Microglia critically shape neuronal circuit development and function, yet their region-specific properties and roles in distinct circuits of the human brain remain poorly understood. In this study, we generated region-specific brain organoids (cortical, striatal, and midbrain), each integrated with human microglia, to fill this critical gap. Single-cell RNA sequencing uncovered six distinct microglial subtypes exhibiting unique regional signatures, including a subtype highly enriched for the GABAB receptor gene within striatal organoids. To investigate the contributions of microglia to neural circuitry, we created microglia-incorporated midbrain-striatal assembloids, modeling a core circuit node for many neuropsychiatric disorders including autism. Using chemogenetics to activate this midbrain-striatal circuit, we observed increased calcium signaling in microglia involving GABAB receptors. Leveraging this model, we examined microglial responses within neural circuits harboring an SCN2A nonsense (C959X) mutation associated with profound autism. Remarkably, microglia displayed heightened calcium responses to SCN2A mutation-mediated neuronal hyperactivity, and engaged in excessive synaptic pruning. These pathological effects were reversed by pharmacological inhibition of microglial GABAB receptors. Collectively, our findings establish an advanced platform to dissect human neuroimmune interactions in sub-cortical regions, highlighting the important role of microglia in shaping critical circuitry related to neuropsychiatric disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/657874v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@125b36eorg.highwire.dtl.DTLVardef@270079org.highwire.dtl.DTLVardef@903525org.highwire.dtl.DTLVardef@19145c4_HPS_FORMAT_FIGEXP M_FIG C_FIG TeaserModeling regional microglial diversity in sub-cortical regions is challenging. We generated human organoid and assembloid models containing microglia that acquire region-specific heterogeneity. Our work shows dynamic responses of microglia when exposed to hyperexcitable midbrain-striatal circuits, providing an exciting platform to study neuroimmune interactions in human brain development and neuropsychiatric disorders, including SCN2A mutation-mediated monogenic autism. HighlightsO_LI* Single-cell RNA sequencing analyses reveal six distinct microglial subtypes that spontaneously attain unique specialization in human cortical, striatal, and midbrain organoids. C_LIO_LI* Microglia facilitate axonal projections across regional organoids, promoting assembloid formation. C_LIO_LI* Microglia respond to hyperexcitable neurons via calcium signaling and exhibit excessive pruning of neuronal synapses. C_LIO_LI* Blocking microglial GABAB receptors normalizes calcium activity and reduces synaptic pruning, suggesting a potential targeting strategy for synaptic deficits. C_LI

Explore related subjects

neurosciencePreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Wu, J., Chen, X., Zhang, J., Wettschurack, K. W., Robinson, M. J., Li, W., Zhao, Y., Yoo, Y.-E., Deming, B. A., Abeyaratna, A. D., Que, Z., Du, D., Tegtmeyer, M. T., Yuan, C., Skarnes, W. C., Rochet, J.-C., Wu, L.-J., Yang, Y.. 2025-06-04. Human microglia in brain assembloids display region-specific diversity and respond to hyperexcitable neurons carrying SCN2A mutation. https://doi.org/10.1101/2025.06.04.657874

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

CoReg, tracking-based motion compensation for in vivo calcium imaging

In vivo calcium imaging enables the observation of neural activity with high spatial and temporal resolution. However, recordings are frequently affected by motion artifacts caused by animal movement, physiological processes, tissue drift, or instability of the imaging setup. These artifacts make signal extraction harder and reduce the consistency of downstream analyses. Current registration methods can correct rigid and non-rigid motion, but often estimate motion from individual frames or image patches and make limited use of temporal information. In addition, activity-driven fluorescence changes can make it difficult to distinguish changes in image appearance from actual motion. Here, we treat motion correction in calcium imaging as a point tracking problem and introduce CoReg, an open-source Python- based software tool with a graphical user interface. We benchmark CoReg against established registration methods using fluorescence imaging datasets from multiple species. CoReg performs competitively with or better than existing approaches across several settings. We further show that its performance is robust to the choice of tracked points, making the method straightforward to apply. CoReg includes implementations of both our method and the evaluated established methods. Our results show that tracking-based registration provides a simple and reliable approach for motion correction in vivo calcium imaging.

neuroscience↗
bioRxiv2026

A shared slowing axis and phenotype-specific rhythms link clinical EEG to FDG-PET dementia phenotypes

Early and accurate identification of neurodegenerative disorders has notable implications for treatment and quality of life. Whereas neuroimaging-based biomarkers can accurately identify neurodegenerative subtypes, EEG represents a low-cost alternative that could expand access to dementia care. Here, we investigated whether six data-driven EEG latent factors, derived by nonnegative tensor decomposition of clinical EEGs, differ systematically across FDG-PET-defined neurodegenerative phenotypes. In 455 patients with EEG and FDG-PET acquired within one year of each other, factor expression was compared across 14 diagnostic classes assigned by StateViewer, a validated artificial intelligence framework for FDG-PET interpretation. To separate disease-general severity from phenotype-specific topography, each factor was also regressed on a subject-level slowing index. Finally, we related the factors to regional FDG uptake and to neuropsychological performance (n = 98) and assessed their potential utility for single-subject classification. Four factors reflecting neurophysiological oscillations (posterior alpha, Rolandic beta, frontotemporal delta-theta and posterior theta-slow alpha) varied significantly across phenotypes, with attenuation of faster and augmentation of slower rhythms most pronounced in dementia with Lewy bodies (DLB), dysexecutive Alzheimer disease (AD) and posterior cortical atrophy, whereas factors dominated by eye-movement and muscle artifact showed no robust phenotypic association. Alpha and beta effects were largely attributable to overall slowing, whereas posterior theta-slow alpha became more phenotype-specific after adjustment (eta-squared 0.082 to 0.147), dissociating the Alzheimer disease spectrum from frontotemporal syndromes. The slowing index tracked with an FDG-PET pattern highly associated with DLB across the cohort, irrespective of assigned phenotype (r = 0.51, P < 0.001). Consistent with a model in which dementia phenotypes reflect altered hippocampal-neocortical oscillatory coupling (stochastic latent oscillatory diffusion), frontotemporal delta-theta tracked a limbocortical axis of metabolic pattern expression, rising with neocortical and falling with limbic-predominant involvement, independent of overall slowing and phenotype. Each factor mapped onto a distinct metabolic topography, with frontotemporal delta-theta resembling Alzheimer-type hypometabolism and posterior theta-slow alpha the medial occipital hypometabolism of DLB. In terms of neuropsychological performance, Rolandic beta was associated with executive functions, and frontotemporal delta-theta with memory, visuospatial and global performance. Using these four factors alone, an exploratory logistic regression classifier separated cognitively unimpaired participants from DLB, posterior cortical atrophy, typical AD, and dysexecutive AD (area under the curve > 0.8) but poorly discriminated frontotemporal dementia phenotypes canonically associated with 4-repeat tau. Thus, data-driven decomposition of clinical EEG separates oscillatory activity from artifact into factors that track metabolic phenotype, regional metabolism and cognition, capturing both overall slowing and phenotype-specific patterns. This work informs the further development of scalable, biology-informed EEG-based phenotyping of neurodegenerative disease.

neuroscience↗
bioRxiv2026

An application of fNIRS for the prediction of hearing thresholds in sleeping infants: a proof of principle

This study applied a two-component-response modelling approach to fNIRS recordings obtained from naturally sleeping infants presented with auditory stimuli at different sound intensities. We investigated whether the relationship between fNIRS response measures and stimulus intensity could be modelled to estimate individual auditory hearing thresholds. In the normal-hearing group, 75% of infants had threshold estimates for the sound /ba/ within the expected normal-hearing range, with an estimated mean equivalent normal loudness (ENL) of 10.72 dB HL (SD 8.64 dB HL). A case study further explored the potential application of this approach in an infant with hearing impairment, highlighting the importance of reliable responses at lower stimulus intensities and appropriate regression model selection. These findings provide preliminary evidence that cortical haemodynamic responses can be quantitatively related to sound intensity for estimating auditory sensitivity.

neuroscience↗