Biology subjects

Brand, A. H.

Publications and source records attributed to Brand, A. H..

8 recordsLinked to original sources

bioRxiv2026

Sex Steroid Hormone Signaling Tunes Metabolic and Neuronal Programs in Human Cortical Development

Autism spectrum disorder (ASD) exhibits a profound male biased sex ratio. While numerous genes have been implicated in ASD, the functional basis of this sex difference is unclear. One enticing hypothesis is genome-wide transcriptional regulation through estrogens and androgens. While hormone-mediated transcription is well-studied in reproductive tissues, its role in cortical development is poorly defined. Thus, we profiled androgen (AR) and estrogen (ESR1/ESR2) receptor expression in primary human cortex and developmental stage-matched organoid models by single-cell RNA-seq. AR was primarily expressed in radial glia and intermediate progenitors while ESR1/ESR2 was more broadly distributed across multiple cell types of the developing cortex, although with the highest expression in radial glia. To study their genetic effects, we exposed iNeurons and cortical organoids to physiological levels of dihydro-testosterone (DHT) and estradiol (E2). DHT consistently up-regulated oxidative metabolism programs enriched in progenitor cells and down-regulated neuronal maturation pathways, while E2 exhibited a much more attenuated effect. The presence of DHT reduced NTRK2 (TrkB) expression, correlating with expression in developing cortex where NTRK2 had significantly higher expression in progenitor cells of the female cortex, which is also reflected in the increased expression of AR in radial glia. Together, these data indicate that in developing human cortical lineages, sex hormones act as selective, cell-state- dependent modulators that tune metabolic and maturation programs rather than broadly reprogramming the genome. Thus, the effects of variation in transcriptional regulation through estrogens and androgens are likely to be minor, but not absent, in ASD.

genomics↗

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗

bioRxiv2025

Neural stem cell quiescence is actively maintained by the epigenome

Homeostasis and repair of the nervous system is maintained by a population of resident neural stem cells (NSCs) retained in a state of reversible cell cycle arrest called quiescence. quiescent NSCs can resume proliferation in response to different physiological stimuli, such as diet or injury. Reactivation of NSCs requires changes in gene expression, much of which is regulated at the epigenomic level. We mapped, comprehensively and in vivo, the dynamic epigenomic changes in NSC chromatin during stem cell quiescence and reactivation in Drosophila. Contrary to expectations, we found that chromatin accessibility is increased in quiescent NSCs, remodelling extensively within both euchromatin and heterochromatin. Surprisingly, genes crucial for cell cycle progression are repressed whilst remaining within permissive H3K36me3-bound euchromatin. At the same time, genes necessary for cell-cell communication are derepressed by eviction of histone H1 and transition to a SWI/SNF-enriched active state. Our results reveal global expansion of accessible chromatin in quiescent NSCs without concomitant activation of transcription. Strikingly, this process reverses upon reactivation, indicating that opening of chromatin is a quiescence-specific event.

developmental biology↗

bioRxiv2025

A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum

Understanding the molecular mechanisms driving lineage decisions and differentiation during development is challenging in complex systems with a diverse progenitor pool, such as the mammalian cerebellum. Importantly, how different transcription factors cooperate to generate neural diversity and the gene regulatory mechanisms that drive neuron production, especially during the late stages of cerebellar development are poorly understood. Here, we used single cell RNA-sequencing (scRNA-seq) to investigate the developmental trajectories of Nestin-expressing progenitors (NEPs) in the neonatal mouse cerebellum. We identified FOXO1 as a key regulator of NEP-to-inhibitory neuron differentiation, acting directly downstream of ASCL1. Genome occupancy and functional experiments using primary NEPs showed that both ASCL1 and FOXO1 regulate neurogenesis genes during differentiation while independently regulating proliferation and survival, respectively. Furthermore, we demonstrated that WNT signalling promotes the transition from an ASCL1+ to a FOXO1+ cellular state. Finally, we showed that the role of WNT signalling in promoting neuron production via FOXO1 is conserved in primary human NEPs. By resolving how cerebellar interneurons differentiate, our findings could have implications for cerebellar disorders such as spinocerebellar ataxia, where cerebellar interneurons are overproduced.

developmental biology↗

bioRxiv2024

Quiescent neural stem cells transiently become 'neurons' to coordinate reactivation

Reactivation of quiescent neural stem cells (qNSCs) is a coordinated process that generates new neurons and glia. Here, we show that during development reactivation follows a hierarchical sequence, whereby anteriorly located qNSCs control the reactivation of more posterior qNSCs in the central nervous system (CNS). Electrical communication between qNSCs and neurons enables this precise spatial and temporal control of reactivation throughout the entire span of the CNS. Using single-cell RNA-seq we discovered that, remarkably, qNSCs switch on a host of neuronal genes while maintaining a stem cell identity. This transient mixed identity is specific to qNSCs, as neuronal genes are turned off after stem cells resume proliferation. Our results uncover long-range communication between qNSCs to coordinate reactivation, enabled by a transient stem cell-neuron fate.

cell biology↗

bioRxiv2024

Targeted DamID detects cell-type specific histone modifications in vivo

Histone modifications play a key role in regulating gene expression and cell fate during development and disease. Current methods for cell-type specific genome-wide profiling of histone modifications require dissociation and isolation of cells and are not compatible with all tissue types. Here we adapt Targeted DamID to recognise specific histone marks, by fusing chromatin binding proteins or single-chain antibodies to Dam, an E. coli DNA adenine methylase. When combined with Targeted DamID (TaDa), this enables cell-type specific chromatin profiling in intact tissues or organisms. We first profiled H3K4me3, H3K9ac, H3K27me3 and H4K20me1 in vivo in neural stem cells of the developing Drosophila brain. Next, we mapped cell-type specific H3K4me3 distribution in neural stem cells of the developing mouse brain. Finally, we injected RNA encoding DamID constructs into 1-cell stage Xenopus embryos to profile H3K4me3 distribution during gastrulation and neurulation. These results illustrate the versatility of Targeted DamID to profile cell-type specific histone marks throughout the genome in diverse model systems. Summary statementTargeted DamID enables genome-wide cell-type specific detection of histone modifications in vivo in Drosophila, mouse and Xenopus.

molecular biology↗

bioRxiv2022

An organoid CRISPRi screen revealed that SOX9 primes human fetal lung tip progenitors to receive WNT and RTK signals

The balance between self-renewal and differentiation in human fetal lung epithelial progenitors controls the size and function of the adult organ. Moreover, progenitor cell gene regulation networks are employed by both regenerating and malignant lung cells, where modulators of their effects could potentially be of therapeutic value. Details of the molecular networks controlling human lung progenitor self-renewal remain unknown. We performed the first CRISPRi screen in primary human lung organoids to identify transcription factors controlling progenitor self-renewal. We show that SOX9 promotes proliferation of lung progenitors and inhibits precocious airway differentiation. Moreover, by identifying direct transcriptional targets using Targeted DamID we place SOX9 at the centre of a transcriptional network which amplifies WNT and RTK signalling to stabilise the progenitor cell state. In addition, the proof-of-principle CRISPRi screen and Targeted DamID tools establish a new approach for using primary human organoids to elucidate detailed functional mechanisms underlying normal development and disease. HighlightsO_LIA pooled CRISPRi screen in human fetal lung organoids identified transcription factors controlling progenitor cell self-renewal. C_LIO_LISOX9 promotes tip progenitor cell proliferation and supresses precocious airway differentiation. C_LIO_LITargeted DamID (TaDa) identified SOX9 direct binding targets, revealing that SOX9 lies at the intersection of WNT and RTK signalling. C_LIO_LISOX9 and ETVs co-regulate the human fetal lung progenitor self-renewal programme. C_LI

developmental biology↗

bioRxiv2021

Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

Genetic studies of autism spectrum disorder (ASD) have revealed a causal role for mutations in chromatin remodeling genes. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with one of the highest de novo mutation rates in sporadic ASD. However, the relationship between CHD8 genomic function and autism-relevant biology remains poorly elucidated. CHD8 binding studies have relied on Chromatin Immunoprecipitation followed by sequencing (ChIP-seq), however, these datasets exhibit significant variability. ChIP-seq has technical limitations in the context of weak or indirect protein-DNA interactions or when high-performance antibodies are unavailable. Thus, complementary approaches are needed overall, and, specifically, to establish CHD8 genomic targets and regulatory function. Here we used Targeted DamID in utero to characterize CHD8 binding in developing embryonic mouse cortex. CHD8 Targeted DamID followed by sequencing (CHD8 TaDa-seq) revealed binding at previously identified targets as well as loci sensitive to Chd8 haploinsufficiency. CHD8 TaDa-seq highlighted CHD8 binding distal to a subset of genes specific to neurodevelopment and neuronal function. These studies establish TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provide insights into the relationship between chromatin remodeling by CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.

genomics↗