Biology subjects

Studer, M.

Publications and source records attributed to Studer, M..

11 recordsLinked to original sources

bioRxiv2026

An NR2F1-dependent retinoic acid network controls retinal specialization in mice and reveals foveal hypoplasia in patients with BBSOAS

The molecular programs that establish specialized retinal regions during development are essential for high-acuity vision, yet how their disruption contributes to human visual disorders remains poorly understood. Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS), caused by pathogenic variants in NR2F1 and characterized by visual impairment, provides an opportunity to investigate these mechanisms. Using single-cell RNA sequencing of three complementary Nr2f1 mouse models, including two carrying patient-specific mutations, we identified a shared Nr2f1-dependent transcriptional program enriched in retinoic acid (RA) pathway genes. Loss or mutation of Nr2f1 disrupted the spatial organization of RA signaling, most prominently by expanding the dorso-equatorial Cyp26a1 expression domain into ventral retina and reducing ventral determinants such as Vax2. These molecular changes were associated with altered dorso-ventral distribution of S- and M-opsin-expressing cone photoreceptors. We further demonstrate that human NR2F1 binds a conserved regulatory region upstream of CYP26A1, supporting its direct role in regulating local RA availability. Finally, high-resolution optical coherence tomography in individuals with BBSOAS revealed reproducible foveal abnormalities, including a smaller and shallower foveal pit and increased central retinal thickness, consistent with foveal hypoplasia. These findings uncover a previously unrecognized retina-intrinsic component of BBSOAS visual pathology and establish an NR2F1-RA/CYP26A1 regulatory axis linking developmental retinal regionalization to human foveal specialization.

developmental biology↗

bioRxiv2025

Human cortico-vascular assembloids reveal a CELF2-AHNAK-dependent switch from neuronal to endothelial tropism in glioblastoma cells

Glioblastoma (GB) remains one of the most aggressive human cancers, driven by profound cellular plasticity and dynamic interactions with the neurovascular niche. Yet, existing preclinical models fail to reproduce the human brain-vascular interface, limiting studies of tumor-host crosstalk and invasion. To overcome this gap, we developed a human induced pluripotent stem cell (hiPSC)-derived cortico-endothelial (CO+EO) assembloid model by fusing cortical and endothelial organoids from the same genetic background. These assembloids spontaneously form branched vascular networks enriched in tight junction proteins (CLDN5, OCLN, ZO-1), thereby recapitulating a key blood-brain barrier (BBB)-like property and providing a physiologically relevant human platform for exploring glioblastoma-neurovascular interactions. Using this system, we uncover a previously unrecognized CELF2-dependent glioblastoma stem cell (GSC) tropism. CELF2-expressing GSCs preferentially infiltrate neural regions, where they trigger neuronal apoptosis and disrupt endothelial tight junction integrity, supporting an aggressive phenotype. Conversely, CELF2-deficient GSCs lose neurotropism, acquire mesenchymal features, and are redirected toward vascular compartments. This endothelial affinity requires the scaffold protein AHNAK, strongly expressed at the plasma membrane of CELF2-deficient cells and enriched at tumor-endothelial interfaces. AHNAK knockdown abolished endothelial infiltration, demonstrating its critical role in vascular tropism. Analysis of patient GB samples confirmed that CELF2-positive tumor cells are enriched in poorly vascularized, mitotically active areas and excluded from vessel-rich zones, closely paralleling assembloid findings. Transcriptomic profiling further revealed that CELF2 promotes a neuronal progenitor-like program while repressing mesenchymal and vascular-associated gene expression, thereby shaping tumor identity, invasive behavior, and tissue preference. Collectively, our study introduces CO+EO assembloids as an original human model of glioblastoma plasticity at the neurovascular interface. We identify CELF2 as a master regulator of GSC tropism and AHNAK as a mediator of vascular affinity, unveiling a novel molecular axis that governs glioblastoma invasion and highlighting new therapeutic opportunities. Key points- Developed cortico-endothelial assembloids mimicking the brain microenvironment. - Identified CELF2 level as a determinant of glioblastoma cell tropism toward neuronal or endothelial niches. - Showed CELF2-positive GB cells disrupt endothelial tight junctions, unlike CELF2-negative cells. Importance of the studyThis study presents a novel, physiologically relevant in vitro model of glioblastoma (GB) that faithfully recapitulates the complex human brain microenvironment, including both vascular and neuronal components. By combining cortical and endothelial organoids derived from human iPSCs into cortico-endothelial assembloids (CO+EOs), the model enables detailed analysis of GB cell behavior, including migration, tissue tropism, and impact on the neurovascular interface. The work identifies CELF2 as a key molecular determinant of GB cell tropism and neurovascular interaction. The discovery that CELF2-expressing GB cells preferentially infiltrate neuronal tissue and disrupt endothelial tight junctions, whereas CELF2-deficient cells favor endothelial regions without compromising tight junction integrity, offers critical insights into tumor heterogeneity and mechanisms of invasiveness. These findings not only enhance our understanding of how GB cells interact with distinct microenvironmental niches but also provide a powerful platform for testing therapeutic strategies targeting tumor-microenvironment interactions. Graphical AbstractSchematic representation of CO+EO assembloids comprising an endothelial (yellow) and a cortical (red) domain. On the left, control CELF2-expressing GB cells preferentialy infiltrate the neuronal compartment, where they trigger neuronal apoptosis and disrupt BBB-like tight junctions upon contact with endothelial cells. On the right, CELF2-deprived GB cells exhibit reduced neural invasion and increased tropism for endothelial cells, consistent with a mesenchymal signature shift partially driven by elevated AHNAK expression. These cells exert limited impact on neuronal viability and BBB integrity, and display partial loss of GSC identity, as indicated by reduced OLIG2 expression. The CO+EO assembloid model thus recapitulates key features of cortico-endothelial human tissue heterogeneity and provides a reliable platform to dissect the molecular mechanisms underlying GSC tropism and their tissue-specific interactions O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/683634v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@26440org.highwire.dtl.DTLVardef@103b93eorg.highwire.dtl.DTLVardef@176ca48org.highwire.dtl.DTLVardef@1da502f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Unravelling the conundrum of nucleolar NR2F1 localization: A comparative analysis of NR2F1 antibody-based approaches in vitro and in vivo.

As a transcription factor, NR2F1 regulates spatiotemporal gene expression during development and in adulthood. Aberrant NR2F1 causes a rare neurodevelopmental disorder known as Bosch-Boonstra- Schaaf Optic Atrophy Syndrome. In addition, altered NR2F1 expression is frequently observed in various cancers and is considered a prognostic marker or potential therapeutic target. In this context, NR2F1 has been shown to localize not only in the nucleus but also in the nucleoli, suggesting a novel non-canonical role in this compartment. Hence, we studied this phenomenon employing various in vitro and in vivo models in different antibody-dependent approaches. Examination of seven commonly used anti-NR2F1 antibodies in different human cancer and stem cells as well as in wild type and null mice revealed that the nucleolar localization of NR2F1 is artificial and does not play a functional role. Our subsequent comparative analysis demonstrated for the first time which anti-NR2F1 antibody best fits which approach. As our data allow for correct data interpretation, making them publicly available may have far-reaching implications for NR2F1 research in health and disease. More generally, the study also underlines the need to optimize any antibody-mediated technique.

cell biology↗

bioRxiv2023

FGF8-mediated gene regulation affects regional identity in human cerebral organoids

The morphogen FGF8 establishes graded positional cues imparting regional cellular responses via modulation of early target genes. The roles of FGF signaling and its effector genes remain poorly characterized in human experimental models mimicking early fetal telencephalic development. We used hiPSC-derived cerebral organoids as an in vitro platform to challenge the effect of FGF8 signaling on neural identity and differentiation. We found that FGF8 treatment increases cellular heterogeneity leading to distinct telencephalic and mesencephalic-like domains that co-develop in multi-regional organoids. Within telencephalic domains, FGF8 affects the anteroposterior and dorsoventral identity of neural progenitors, the balance between GABAergic and glutamatergic neurons, thus impacting spontaneous neuronal network activity. Moreover, FGF8 efficiently modulates key regulators responsible for several human neurodevelopmental disorders. Overall, our results show that FGF8 signaling is directly involved in both regional patterning and cellular diversity in human cerebral organoids and in modulating genes associated with normal and pathological neural development.

developmental biology↗

bioRxiv2023

SOX2 and NR2F1 coordinate the gene expression program of the early postnatal visual thalamus

The thalamic dorsolateral geniculate nucleus, (dLGN) receives visual input from the retina via the optic nerve, and projects to the cortical visual area, where eye-derived signals are elaborated. The transcription factors SOX2 and NR2F1 are directly involved in the differentiation of dLGN neurons, based on mouse work and patient mutations leading to vision defects. However, whether they regulate each other, or control common targets is still unclear. By RNA-seq analysis of neonatal dLGN from thalamo-specific Sox2 and Nr2f1 mouse mutants, we found a striking overlap of deregulated genes. Among them, VGF, a cytokine transported along thalamic-cortical axons is strongly downregulated in both mutants. CUT&RUN analysis of SOX2 binding in dLGN chromatin identified a binding pattern characteristic of the dLGN. Collectively, the SOX2 and NR2F1- coregulated genes, and cognate SOX2 binding sites, contribute as a basis to understand the gene regulatory network driving the differentiation and connectivity of thalamic neurons.

developmental biology↗

bioRxiv2023

Structural analysis and genetic code expansion reveal the functional impact of NR2F1 mutations associated with BBSOA-Syndrome

Deciphering the structural effects of variants is essential for understanding the pathophysiological mechanisms of genetic diseases. Using a neurodevelopmental disorder called Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) as a genetic disease model, we applied a combined Genetic Code Expansion (GCE) and structural bioinformatics strategy to assess the pathogenic impact of several human NR2F1 variants. Nonsense mutations in the ligand binding domain (LBD) resulted in truncated proteins, while missense variants significantly affected the folding of NR2F1 monomers as well as its supramolecular complexes. The GCE-enabled covalent and site-specific capture of transient supramolecular interactions in living cells revealed the variable quaternary conformations of NR2F1 variants and pinpointed the disrupted interplay with dimeric partners and the newly identified cofactor, CRABP2, while the computational analyses of the NR2F1 structure delineated the molecular basis of the impact of the variants on the isolated and complexed structures. The revealed consequence of the pathogenic mutations on the conformation, supramolecular interplay, and alterations in the cell cycle, viability, and subcellular localization of the different variants reflect the heterogeneous disease spectrum and establish the foundation for further understanding the complexity of BBSOAS.

biochemistry↗

bioRxiv2023

Genetic identification of novel medullary neurons underlying congenital central hypoventilation syndrome

Congenital Central Hypoventilation Syndrome (CCHS) is a rare, but life-threatening, respiratory disorder that is classically diagnosed in children. This disease is characterized by pronounced alveolar hypoventilation and diminished chemoreflexes, particularly to abnormally high levels of arterial pCO2. Mutations in the transcription factors PHOX2B and LBX1 have been identified in CCHS patients, but the dysfunctional circuit responsible for this disease remains unknown. Here, we show that distinct sets of medullary neurons co-expressing both transcription factors (dB2 neurons) account for specific respiratory functions and phenotypes seen in CCHS. By combining murine intersectional chemogenetics, intersectional labeling, and the selective targeting of the CCHS disease-causing Lbx1FS mutation to specific subgroups of dB2 neurons, we uncovered novel sets of these cells key for i) respiratory tidal volumes and the hypercarbic reflex, ii) neonatal respiratory stability and iii) neonatal survival. These data provide functional evidence for the essential role of dB2 neurons in neonatal respiratory physiology and will be instrumental for the development of therapeutic strategies for the management of CCHS. In summary, our work uncovers new neural components of the central circuit regulating breathing and establishes dB2 neuron dysfunction to be causative of CCHS.

neuroscience↗

bioRxiv2022

Targeted high throughput mutagenesis of the human spliceosome reveals its in vivo operating principles

The spliceosome is a staggeringly complex machine comprising, in humans, 5 snRNAs and >150 proteins. We scaled haploid CRISPR-Cas9 base editing to target the entire human spliceosome and interrogated the mutants using the U2 snRNP/SF3b inhibitor, pladienolide B. Hypersensitive substitutions define functional sites in the U1/U2-containing A-complex but also in components that act as late as the second chemical step after SF3b is dissociated. Viable resistance substitutions map not only to the pladienolide B binding site but also to the G-patch (ATPase activator) domain of SUGP1, which lacks orthologs in yeast. We used these mutants and biochemical approaches to identify the spliceosomal disassemblase DHX15/hPrp43 as the ATPase ligand for SUGP1. These and other data support a model in which SUGP1 promotes splicing fidelity by triggering early spliceosome disassembly in response to kinetic blocks. Our approach provides a template for the analysis of essential cellular machines in humans.

molecular biology↗

bioRxiv2022

Nr2f1-dependent shaping of mitochondrial architecture in newborn mouse hippocampal neurons unravels novel insights into the neurodevelopmental disorder BBSOAS

The nuclear receptor Nr2f1 plays a key role during cortical development by acting as a strong transcriptional regulator in embryonic and postnatal neural cells. In humans, its mutations cause the Bosch-Boonstra-Schaaf optic atrophy-intellectual syndrome (BBSOAS), a rare neurodevelopmental disorder characterized by multiple clinical features including optic nerve atrophy, intellectual disability, and autistic traits. In this study by genome-wide and in silico analyses we found that key factors for mitochondrial function and dynamics represent potential genomic targets under direct Nr2f1 transcriptional control in neurons. Although mitochondrial dysfunction is increasingly implicated in neurodevelopmental disorders, whether and how Nr2f1 can regulate mitochondria function in neural cells is still completely unknown. To address these questions, we have combined mouse genetics, neuroanatomical and imaging approaches. To genetically manipulate Nr2f1 function in newborn neurons we focused on the adult mouse hippocampal dentate gyrus, a site of persistent neurogenesis where Nr2f1 is highly expressed. We showed that conditional Nr2f1 loss-of-function within the hippocampal neurogenic niche lead to a reduced mitochondrial mass associated to mitochondrial fragmentation in newborn neurons, likely reflecting alteration in mitochondrial dynamics. Accordingly, we showed that the fusion factor Mfn2, which is as a putative Nr2f1 target, is downregulated following both Nr2f1 adult depletion and embryonic haploinsufficiency in mice. Overall, our study provides the first evidence of a crucial role of Nr2f1 in shaping mitochondria in neurons and opens a promising avenue for the identification of new mechanisms implicated in BBSOAS pathogenesis involving mitochondrial dysfunction.

neuroscience↗

bioRxiv2021

Topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1

Axonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. Combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines, and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei. Summary statementCortical gradient expression of the area patterning gene Nr2f1 spatially and temporally controls corticopontine topographic connectivity in layer V projection neurons.

neuroscience↗

bioRxiv2019

Intrinsic neuronal excitability and spontaneous activity underlie cortical abnormalities upon Nr2f1/COUP-TFI deficiency

The formation of functional cortical maps in the cerebral cortex results from a timely regulated interaction between intrinsic genetic mechanisms and electrical activity. To understand how transcriptional regulation influences network activity and neuronal excitability within the neocortex, we used mice deficient for the area mapping gene Nr2f1 (also known as COUP-TFI), a key determinant of somatosensory area specification during development. We found that cortical loss of Nr2f1 impacts on spontaneous network activity and synchronization at perinatal stages. In addition, we observed alterations in the intrinsic excitability and morphological features of layer V pyramidal neurons. Accordingly, we identified distinct voltage-gated ion channels regulated by Nr2f1 that might directly influence intrinsic bioelectrical properties during critical time windows of somatosensory cortex specification. Together, our data suggest a tight link between Nr2f1 and neuronal excitability in the developmental sequence that ultimately sculpts the emergence of cortical network activity within the immature neocortex.

neuroscience↗