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Prinz, M.

Publications and source records attributed to Prinz, M..

At least 19 recordsLinked to original sources

Coding agents author interpretable single-cell embedding models from the literature

The single-cell literature catalogs cell states as validated marker-gene programs -- a sparse, compositional prior. Conventional embedding methods do not leverage this prior and learn cell-state structure de novo from the expression matrix, producing dense dimensions needing post-hoc interpretation and batch correction. Here we show coding agents can author single-cell embedding models directly from the literature. Given a scenario that focuses this literature lens on a chosen biological subdomain, the agent edits a structured Python template, curating named, literature-cited gene programs and composing them into axes, without a gene-set database, training, or sight of the data. Across mouse and human tissues these zero-shot embeddings are competitive in biological quality with conventional, foundation-model, and program-informed baselines, batch-robust by construction and reproducible across runs, complementing data-driven embeddings. Because each dimension is a named, cited gene program, the embedding is interpretable and auditable, and its composable axes can be steered into a developmental tree.

bioinformatics↗

Spatially confined niches support hypoxia-associated transcriptional plasticity contributing to malignant progression in IDH-mutant gliomas

BackgroundWhile hypoxia is a well-established driver of glioblastoma progression, its role in IDH-mutant gliomas, characterized by localized hypoxic microenvironments rather than overt necrosis, remains poorly understood. Here, we investigate how hypoxia and microenvironmental-adaptations shape cellular heterogeneity and transcriptional plasticity in these tumors. MethodsWe integrated bulk, single-cell, and spatial-transcriptomics datasets from IDH-mutant glioma patients (Astrocytomas and Oligodendrogliomas) to characterize cellular-states and map the localization of hypoxic niches. To uncover tumor microenvironment effects, we established co-culture models using primary IDH-mutant glioma cells with human microglia and astrocytes, maintained under hypoxic and normoxic conditions, followed by bulk RNA-sequencing. ResultsWe identified a hypoxia-associated astrocyte-like (AC-like) program that defines a quiescent, non-cycling population with a distinct transcription factor profile indicative of functional plasticity in IDH-mutant gliomas. These cells harbor glioma stem cell (GSC)-like features and are poised for a quiescent-to-activated (Q-to-A) transition that drives tumor progression. Mechanistically, co-culture models reveal that microglia promote this Q-to-A transition by enhancing HBEGF/EGFR paracrine signaling. Spatial transcriptomics uncovers the co-localization of hypoxic niches within quiescent AC-like cells, whereby the activated subpopulation forms discrete niches defined by localized HBEGF/EGFR communication gradients. Notably, tumors exhibiting elevated EGFR-driven activation signatures correlate with higher histological grade and poorer patient survival, implicating the Q-to-A transition as a critical driver of malignant progression. ConclusionQ-to-A transition within the hypoxic niche represents a critical driver of malignant progression in IDH-mutant gliomas, providing a microenvironment-driven mechanism for the transition to higher-grade disease and identifying targetable-vulnerabilities for therapeutic intervention. Key pointsO_LIHypoxic niches spatially confine quiescent, astrocyte-like cellular state characterized by glioma stem cell features in IDH-mutant gliomas. C_LIO_LIMicroglia triggers the quiescent-to-activated (Q-to-A) transition via paracrine EGFR signaling crosstalk. C_LIO_LIEGFR-driven Q-to-A plasticity serves as a microenvironmentally-regulated driver of malignant progression and adverse patient survival. C_LI Importance of the studyWhile high-grade glioblastomas feature well-defined hypoxic and necrotic regions that drive tumor progression and therapy resistance, IDH-mutant gliomas lack these distinct hallmarks, instead exhibiting disorganized hypoxic niches. Consequently, the functional contribution of these niches to tumor progression has remained poorly understood. Although genetic and epigenetic alterations are established drivers of progression in IDH-mutant gliomas, we provide an additional, essential layer of complexity: microenvironment-driven transcriptional plasticity. By uncovering the relationship between tumor hypoxia and heterogeneous glioma cell states, we uncover that these niches are essential for such plasticity. We also show that the tumor microenvironment provides critical molecular cues necessary to initiate a transcriptional shift enabling glioma cells to transition from a quiescent reservoir into an activated state primed for rapid proliferation. By identifying this paracrine mechanism, our work uncovers a targetable vulnerability that dictates how dormant cell reservoirs are mobilized to fuel malignant transformation.

cancer biology↗

An organotypic neocortical slice culture for studying neuroglial interactions

Organotypic slice cultures (OSCs) are widely used to study cellular properties in a functional and developmental tissue context. With the recent advent of transgenic mouse lines and viral tools we postulated that OSCs may enable the study of multicellular glial and neuroglial interactions in development, as well homeostatic and pathological conditions. Here, we made mouse cortical OSCs and used markers for oligodendroglial, microglial states and neuronal types between 1 to 28 days in vitro (DIV). The OSC was characterized by in-vivo like cortical layering, including layer 5 pyramidal neurons and produced highly robust synchronized period bursts resembling Up- and Down states. Glial cells showed a strong cortical layer- and time-dependent development pattern: in the first week (DIV 1-7), slicing-related debris clearance and developmentally restricted sparse oligodendroglial myelination created an environment with highly phagocytic, non-homeostatic microglia (assessed with CD68 and purinergic receptor P2Y12, respectively). Between DIV 14 and 21, however, slices showed stereotypical cortical myelin patterns and the emergence of a homeostatic microglia phenotype while exhibiting continued phagocytosis. Furthermore, live two-photon imaging and morphometric analyses revealed highly ramified microglia and myelinated axons with compact myelination, exceeding lamellae count compared to age-matched in vivo axons. Lastly, from DIV 28 and onwards, myelin integrity became impaired and associated with phagocytic microglia. Together, the results indicate that between DIV14 and 21 cortical OSCs are well suited for live imaging of homeostatic and activity-dependent neuron-glia interactions, bridging the gap between in vivo investigations and primary cell cultures.

neuroscience↗

Socially regulated genes are spatially hyperconnected to enhancers in the ant brain

Caste identity in Harpegnathos saltator ants remains plastic beyond development and throughout adulthood. Adult Harpegnathos workers can become dominant reproductives, known as "gamergates," through a social caste transition that involves extensive transcriptional and cellular remodeling of the brain. To gain insight into the epigenetic regulation of this process, we generated comprehensive, caste-specific epigenomic atlases of the Harpegnathos brain, including chromatin accessibility, histone modifications, and 3D genome architecture. Using these data we refined the genome assembly, annotated enhancers, and linked them to target genes. We then identified candidate 3D-architectural factors, many of which were specifically upregulated in gamergate brains. Promoters of genes upregulated during the worker-gamergate transition formed an unusually high number of 3D chromatin contacts with their regulatory regions, and most of these contacts were already present in workers. We propose that the pre-existing hyper-connectivity of socially regulated genes is essential to adult brain plasticity and behavioral reprogramming.

genomics↗

Postnatal Maturation of Dendritic Epidermal T Cells and Langerhans Cells Follows Distinct Differentiation Trajectories Independent of Microbiota

The mouse epidermis harbors two key resident immune populations--dendritic epidermal T cells (DETCs), a subset of invariant {gamma}{delta} T cells, and Langerhans cells (LCs), specialized tissue-resident macrophages--both of which play critical roles in immune surveillance, barrier integrity, and tissue homeostasis. While the fetal origin of both cell types has been defined, the cellular and molecular mechanisms that govern their postnatal fates following colonization of the epidermis around birth remain incompletely understood. Here, we present a combination of immunophenotyping- and transcriptome-resolved single-cell map of DETC and LC development in the mouse epidermis from late embryogenesis through adulthood. We delineate differentiation trajectories for both cell types, marked by distinct changes in morphology, proliferation, and transcriptional programming. Using mice deficient in {gamma}{delta} T cells, which lack canonical DETCs, we demonstrate that LCs develop independently of canonical DETCs likely due to the presence of {beta}DETCs. Moreover, analysis of germ-free mice and wildlings reveals that the postnatal development of both DETCs and LCs is independent of microbial colonization. Together, our findings define the core principles underlying the establishment of the mouse epidermal immune niche. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/716534v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@18088a0org.highwire.dtl.DTLVardef@189e0f2org.highwire.dtl.DTLVardef@10f37d6org.highwire.dtl.DTLVardef@1ad59c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Vicious circle of amyloid and leptomeningeal macrophages evokes vascular dysfunction in CAA

The subarachnoid space contains leptomeningeal arteries and resident immune cells known as subarachnoid macrophages (SAMs). In Alzheimers disease (AD) and related cerebral amyloid angiopathy, amyloid-{beta} (A{beta}) frequently accumulates around the leptomeningeal arteries. Nevertheless, the local immune responses and their functional consequences remain poorly understood. Using longitudinal intravital imaging in a mouse model of AD, we tracked A{beta} deposition and identified a distinct SAM population that migrates to and phagocytoses these arterial A{beta} deposits. SAM recruitment correlated with vascular remodeling, including smooth muscle loss, aneurysm formation, and reduced cerebral perfusion. Transcriptomic profiling revealed a distinct SAM population in AD with upregulated CD39 expression. Pharmacological inhibition of CD39 attenuated arterial A{beta} deposition, identifying SAMs as a potential therapeutic target in AD.

neuroscience↗

Csf1r-mediated depletion of midbrain microglia prevents dopaminergic neuron loss during chronic colitis

Inflammatory bowel disease (IBD) predisposes to neuropsychiatric comorbidity and particularly increases the risk of Parkinsons Disease (PD) in later life. Although the gut-immune-brain axis was proposed as a link between IBD and PD and a driver of PD immunopathogenesis, the regional pattern and single-cell landscape of the brain immune response during colitis and its contribution to PD pathology remain poorly defined. Here, we observe a loss of dopaminergic neurons in the substantia nigra pars compacta of adult mice with chronic colitis. By confocal microscopy and integrated multi-omics, we reveal a complex midbrain-centered immune response to chronic colitis in comparison to the cortex, hippocampus, and striatum. Single-cell mapping of the midbrain immune landscape showed an inflammatory shift of microglial clusters including an expansion of interferon-response microglia, CD8+ T cell extravasation, and increased numbers of vessel-associated neutrophils. Selective myeloid cell depletion using a colony stimulating factor 1 receptor (Csf1r) inhibitor after colitis onset reduced midbrain microglia by 67% and led to a complete rescue of dopaminergic neuron loss, without affecting mucosal pathology or T cell and neutrophil migration to the midbrain. Collectively, within the complex innate and adaptive midbrain immune response to chronic colitis, we demonstrate a causal role of Csf1r-dependent microglia for dopaminergic neurodegeneration. Thus, Csf1r inhibition in IBD may not locally ameliorate colitis, but provide neuroprotection to dopaminergic neurons. These results reveal a novel cellular link between chronic gut-derived peripheral inflammation and midbrain vulnerability and thereby substantially enhance our understanding of the risk for PD related to the gut-immune-brain axis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/700559v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1bf7217org.highwire.dtl.DTLVardef@1db66c0org.highwire.dtl.DTLVardef@136ef2eorg.highwire.dtl.DTLVardef@190f641_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. C_FIG

neuroscience↗

Iron-Associated Mesenchymal Plasticity and Tumor Invasion in Glioblastoma

Glioblastoma (GBM) recurrence is driven by tumor cells that infiltrate surrounding brain tissue and evade surgical and therapeutic eradication. Although dysregulated iron handling is a recognized feature of the necrotic and hemorrhagic GBM tumor core, its relationship to invasive tumor cell states remains incompletely defined. Here, we investigated how iron-associated microenvironments relate to transcriptional programs of invasion in human GBM. Using multi-regional single-nucleus RNA sequencing of human GBM specimens encompassing tumor core, invasive front, and infiltrated cortex, we found that malignant cells from the tumor core exhibit coordinated upregulation of iron uptake and storage pathways together with invasion-associated gene programs. At the single-cell level, iron metabolism and invasion signatures were strongly correlated, defining a distinct core-enriched malignant subpopulation with mesenchymal-like transcriptional identity, stress-adaptive features, and angiogenic signaling. These iron-high/invasion-high cells aligned with mesenchymal-and astrocyte-like GBM states and were associated with unfavorable patient survival. Despite elevated oxidative stress and ferroptosis-associated transcriptional pressure, this population concurrently expressed anti-apoptotic and anti-ferroptotic regulators, consistent with an iron-tolerant invasive state. To assess functional consequences of iron exposure, we modeled iron-rich conditions using non-cytotoxic particulate iron in patient-derived GBM cell lines and human organotypic cortical slice cultures. Iron exposure induced intracellular iron accumulation, oxidative stress responses, increased tumor cell motility in vitro, and enhanced invasion within intact human brain tissue. Collectively, these findings demonstrate that iron-rich tumor core niches are closely associated with mesenchymal plasticity and invasive behavior in GBM and support a role for iron-associated microenvironmental pressure in shaping invasive tumor cell states. Key PointsO_LITranscriptional profiling reveals that the GBM tumor core harbors malignant cells that strictly couple active iron metabolism with invasive programs. C_LIO_LIThis iron-accumulating, Mesenchymal-like subpopulation is distinctively characterized by angiogenesis and stress resistance. C_LIO_LIIron supplementation in vitro and human ex vivo models are sufficient to drive mesenchymal transition and significantly enhance tumor migration and tissue invasion. C_LI Importance of the StudyGlioblastoma (GBM) recurrence is driven by highly invasive tumor cells that evade resection and resist therapy. Yet the microenvironmental pressures that push GBM cells into an invasive, therapy-resistant state remain poorly defined. Although iron dysregulation has been implicated across cancers, its role as a microenvironmental determinant of GBM invasion has never been demonstrated in physiologically relevant human systems. By integrating multi-regional single-nucleus RNA sequencing with functional validation in patient-derived GBM lines and human organotypic cortical slice cultures, we uncover a core-enriched, iron-associated mesenchymal program that co-segregates with invasion, stress adaptation, and angiogenic signaling. We further show that physiologically relevant iron exposure is sufficient to induce mesenchymal transition, enhance motility, and accelerate tissue invasion within human cortical architecture. These findings position iron as a selective driver that links the hemorrhagic, necrotic GBM core to the emergence of invasive subpopulations that seed recurrence. The data identify iron handling and stress-response pathways as actionable therapeutic vulnerabilities, providing a foundation for strategies that target metabolic resilience and iron-dependent invasive states in GBM. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/695920v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@141cc11org.highwire.dtl.DTLVardef@bcb055org.highwire.dtl.DTLVardef@1dcd332org.highwire.dtl.DTLVardef@ad7cad_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Inflammation-enhanced synapse-specific phagocytosis by adult APP microglia in a microfluidic neuron-microglia co-culture model

Microglia play a critical role in synapse remodeling and neuroinflammation, both of which are dysregulated in Alzheimers disease (AD). However, most in vitro models rely on neonatal or immortalized microglia, limiting their relevance to adult pathophysiological context. Here, we present a compartmentalized microfluidic co-culture platform that enables spatially controlled interactions between primary cortical neurons and adult microglia from wild-type (WT) and APP-transgenic mice. This system allows precise functional analysis of microglia-synapse interactions under defined inflammatory conditions. Upon lipopolysaccharide (LPS) stimulation, APP microglia exhibited exaggerated morphological activation, elevated IL-1{beta} secretion, and selectively increased engulfment of synaptic material. In contrast, phagocytosis of non-specific substrates such as pHrodo Zymosan remained unchanged, suggesting a substrate-specific enhancement of microglial phagocytic activity. Blocking the complement receptor CD11b abolished the LPS-induced increase in synaptic uptake, confirming the role of complement-dependent pathways. Transcriptomic profiling revealed robust inflammatory responses in both genotypes, with selectively heightened expression of proinflammatory genes in APP microglia, consistent with a primed immune phenotype. Importantly, increased synaptic uptake occurred without measurable loss of global synaptic connectivity, highlighting the specificity and sensitivity of the system to detect microglial functional changes. This model captures genotype-dependent microglial reactivity (revealing phenotypes not fully captured by transcriptomic rofiling) and provides a physiologically relevant, tractable in vitro platform for dissecting microglial contributions to synaptic pathology in neurodegenerative disease.

neuroscience↗

Distinct and Combined Interferon-α/β-receptor-1 Loss in Neurons and Astrocytes Disrupt Brain Energy Metabolism and Drive Parkinsonian Dementia

Dysregulated interferon-alpha/beta-receptor 1 (IFNAR1) signaling was recently identified to contribute to the development of sporadic Parkinsons Disease (PD) into PD with Dementia (PDD). The molecular, cellular, and phenotypic impacts of brain IFNAR1 loss in aging have not been explored in vivo, which may reveal novel disease mechanisms and therapeutic targets. Here it is shown that baseline IFNAR1 expression varies in the major brain cell types, including neurons and astrocytes, and is differentially affected in PD and Lewy Body Dementia patients compared to unaffected controls. Neuron- and astrocyte-specific transcriptomic and proteomic alterations in Ifnar1-/- mice implicate mitochondrial defects and synergistic dysfunctional neurotransmission upon IFNAR1 loss, leading to glucose hypermetabolism measured by functional metabolic analysis. Consequently, Ifnar1-/- mice exhibited PDD-like pathogenesis, including dopaminergic cell loss in the substantia nigra, cortical neurodegeneration, Lewy-body-like inclusions, neuroinflammation, and progressive PDD-like behavior deficits. Brain cell-specific IFNAR1 loss examined in vivo revealed delayed but distinct development of PDD-like phenotypes, where neuropathology, motor, and cognitive behavior deficits were specifically recapitulated only in mice lacking neuronal IFNAR1, and behavior resembling neuropsychiatric abnormalities recapitulated only in mice lacking astrocytic IFNAR1. This work supports a crucial role of IFNAR1 in brain homeostasis and emphasizes a need for understanding neurodegenerative pathophysiology in cell-specific contexts. HighlightsO_LIIFNAR1 and related type-I IFN genes are differentially expressed among major brain cell types in Parkinsons Disease, Lewy Body Dementia, and unaffected controls C_LIO_LIEarly molecular alterations in Ifnar1-/- mice show lack of immunomodulation contributing to neuroinflammation, mitochondrial defects, and dysregulated energy metabolism C_LIO_LIIfnar1-/- mice develop a progressive Parkinsonian-like disease phenotype, including dopaminergic cell loss in substantia nigra, cortical neurodegeneration, phosphorylated (p)alpha-synuclein+ and pTau+ Lewy-body-like inclusions, neuroinflammation, and progressive motor, cognitive, and neuropsychiatric disturbance-like behavior deficits C_LIO_LINeuropathologies, motor, and cognitive deficits are recapitulated in mice lacking neuronal IFNAR1 (Syn1Cre;Ifnar1fl/fl) whereas neuropsychiatric abnormalities are recapitulated in mice lacking astrocytic IFNAR1 (GFAPCre;Ifnar1fl/fl) C_LI

neuroscience↗

Tissue imprinting defines functional mosaic of dermal macrophages

Dermal macrophages (macs) protect the skin from invading pathogens. They are derived from embryonic as well as hematopoietic progenitors. However, the functional impact of their diverse origin and the control networks defining different subsets remain unclear. Here, using multidimensional analysis of dermal macs, we reveal that the absence of circulating monocytes in interferon regulatory factor 8 (Irf8) deficient mice delays mac renewal during the steady state. Yet, the functional mosaic of dermal macs remains largely intact, i.e., major dermal mac subsets develop independently of monocyte replenishment. Thus, the tissue microenvironment is sufficient to induce alternative differentiation pathways and functional specialization of resident cells. Mycobacterial skin infection induces a steep increase in mac density due to monocyte-derived macs which execute urgent antibacterial functions and differentiate into site-adapted mac subsets in wildtype but not Irf8-/-mice, while long-term resident macs are required to initiate a tissue repair program already in early stages of infection. In summary, we introduce a model, where an intricate network of specialized mac subsets develops to meet microanatomical needs and external cellular input is required only during immunological emergency situations. HighlightsO_LIIrf8-/--driven monocytopenia has negligible impact on homeostatic dermal macrophage diversity. C_LIO_LIResident dermal macrophages have diverse specializations but remain flexible to adapt to challenges such as lacking monocyte influx C_LIO_LIBone marrow-derived macrophages differentiate into specialized resident cells, with microenvironmental cues overriding origin-dependent programming. C_LIO_LIIn chronic bacterial infections, distinct specialized bone-marrow-derived macrophages mount the defense, while resident macrophages activate a tissue-modifying program from early on. C_LI

immunology↗

Single-cell, spatial, and fate-mapping analyses uncover niche dependent diversity of cochlear myeloid cells.

Recent advances in fate mapping and single-cell technologies have revealed how the dynamics and function of tissue-resident macrophages are shaped by their environment. However, macrophages in sensory organs such as the cochlea where the central nervous system and peripheral nervous system meet remain understudied. Combining single-cell transcriptomics, fate mapping, and parabiosis experiments, we show that five types of myeloid cells including three tissue-resident macrophage subpopulations, coexist in the mouse cochlea. The three macrophage subsets showed different potential functions in relationship with their specific topography across cochlear compartments. Further analysis revealed that they were partially derived from yolk sac progenitors during development, while in adulthood, most cochlear macrophages were long-term resident. Finally, we showed that cochlear macrophage morphology and density changed during aging. Our findings show that cochlea is a microenvironment with a unique heterogeneity of macrophages in terms of gene expression, spatial distribution, ontogeny, and function.

immunology↗

Personality and MB-COMT gene: molecular-genetic and epigenetic associations with NEO-PI-R personality domains and facets in monozygotic twins

This study investigates the relationship between MB-COMT DNA methylation (DNAm) and the personality traits outlined in the NEO-PI-R model through an epigenetic study of monozygotic twins. DNAm, a critical epigenetic mechanism, regulates gene expression and has been linked to various biological processes and disorders. By leveraging the genetic similarities of monozygotic twins, this research explores how epigenetic variations influenced by environmental factors correlate with personality differences. The study utilized the Five-Factor Model (FFM) to categorize personality traits into five domains: Neuroticism, Extraversion, Conscientiousness, Agreeableness, and Openness to Experience. Each domain comprises six facets, providing a granular view of personality. The research centered on the catechol-O-methyltransferase (COMT) gene, focusing on its role in dopamine metabolism, which is hypothesized to influence personality traits through the dopaminergic system. DNAm status in the promoter region of the MB-COMT gene, was examined to determine its association with personality facets. Preliminary findings suggest a complex interaction between MB-COMT DNAm patterns and personality traits. Specific methylation patterns at different CpG sites were linked to varying expressions of traits such as impulsivity and aggression, highlighting the nuanced impact of epigenetics on personality. This study underscores the potential of integrating genetic, epigenetic, and environmental data to enhance our understanding of personality formation. The results contribute to a broader understanding of how genetic predispositions shaped by environmental factors manifest in complex trait differences, paving the way for future research in genetic psychiatry and personalized medicine.

genetics↗

Ubiquitin-specific protease 8 controls B cell proteostasis and cell survival in multiple myeloma

Ubiquitin-specific protease 8 (USP8) is a multifunctional deubiquitinating enzyme that plays a pivotal role in the regulation of endosomal and lysosomal trafficking. Several studies showed that USP8 is critically involved in the pathogenesis of various tumor entities. Recently, USP8 emerged as a vulnerability gene in multiple myeloma (MM), suggesting a functional role in the B- and plasma cell compartment. Here we have comprehensively analyzed mice with deletion of Usp8 at different stages of B-cell development. Furthermore, we evaluated the function of USP8 in proteasome inhibition susceptible and Bortezomib (BTZ) resistant patient derived MM cells using depletion of USP8 and treatment with DUB-IN-2, a widely used inhibitor published to target USP8. Usp8 depletion in Usp8f/fCd19-Cre mice affected B-cell survival and development favoring immature, innate-like B cells, and germinal center and plasma cells, while also elevating immune-responses and causing Roquin depletion. Cells expressing catalytically inactive USP8 accumulated proteins modified with mixed ubiquitin/NEDD8 chains, indicating proteotoxic stress. Moreover, we identified these modifications as preferred substrates of USP8. In MM cells, efficient USP8 knockdown reduced survival by inducing lysosomal dysfunction. In contrast, DUB-IN-2 induced an enhanced ER stress response to treatment with BTZ. Our results highlight the potential of targeting USP8 and the combination of DUB-IN-2 and BTZ in treating BTZ-resistant MM. However, our biochemical and cellular analyses raise fundamental concerns about the function of DUB-IN-2 as a USP8 inhibitor.

molecular biology↗

Focal cortical dysplasia type II-dependent maladaptive myelination in the human frontal lobe

Focal cortical dysplasias (FCDs) are local malformations of the human neocortex and a leading cause of intractable epilepsy. FCDs are classified into different subtypes including FCD IIa and IIb, characterized by a blurred gray-white matter boundary or a transmantle sign indicating abnormal white matter myelination. Recently, we have shown that myelination is also compromised in the gray matter of FCD IIa of the temporal lobe. Since myelination is key for brain function which is imbalanced in epilepsy, in the current study we investigated myelination in the gray matter of FCD IIa and IIb from the frontal lobe. We found that in particular FCD IIb showed myelination disturbances such as increased numbers of myelinating oligodendrocytes (OLs) and an irregular and disorganized myelination pattern covering an enlarged area in comparison to FCD IIa and controls. Interestingly, both FCD types presented with larger axon diameters when compared to controls. A significant correlation of axon diameter and myelin sheath thickness was found for FCD IIb and controls, whereas in FCD IIa large caliber axons were less myelinated. On the level of gene expression, FCD IIb presented with a significant up-regulation of myelin-associated mRNA synthesis in comparison to FCD IIa and by enhanced binding-capacities of the transcription factor MYRF to promoters of myelin-associated genes reflecting the need for more myelin due to increased axon diameters. These data show that FCD IIa and IIb are characterized by divergent signs of maladaptive myelination which may contribute to the epileptic phenotype. Main pointsO_LIIn the gray matter of the frontal lobe, FCD IIa and FCD IIb are characterized by divergent signs of maladaptive myelination. C_LIO_LIFCD IIa presents with an ordinary radial fiber pattern, but with a reduced thickness of the myelin sheath around large diameter axons and with an attenuation of the myelin synthesis machinery. C_LIO_LIFCD IIb is characterized by an irregular and disorganized myelin fiber pattern, a higher density of myelinating oligodendrocytes and an elevated transcriptional turnover of myelin-associated genes. C_LI

neuroscience↗

Dynamic role of monocytes and meningeal macrophages in bacterial meningoencephalitis

Macrophages in the meninges, especially in the dura mater sheathing the brain from the skull, are involved in the immune defense of the central nervous system (CNS). However, their site-specific origin and function, both in steady state and in bacterial CNS infections are incompletely understood. Using an intravenous model of streptococcal meningoencephalitis that mimics hematogenous dissemination in humans, we found that bacteria accumulated predominantly in the leptomeninges and dura, whereas invasion into the brain parenchyma was rare. However, monocyte infiltration into the leptomeninges and parenchyma strongly correlated with disease severity. In the dura, infection triggered activation and loss of resident macrophages, followed by rapid engraftment of inflammatory monocytes that transiently replenished the dural macrophage niche. Under homeostasis, dural monocytes were supplied independently of CCR2 from adjacent skull bone marrow. In infection, however, this local reservoir was rapidly exhausted, and the markedly increased demand for monocytes required mobilization from peripheral bone marrow sources, revealing context-dependent heterogeneity in monocyte origin. Infection also reshaped ontogeny of this differential monocyte output, with an increase in Monocyte-Dendritic Cell Progenitor - derived monocytes (MDP-Mo). MDP-Mo exhibited enhanced MHC-II expression and persisted in the brain during the resolution phase together with CD4 T cells, suggesting a role in antigen presentation after bacterial clearance. Together, these findings reveal a highly dynamic and compartment-specific remodeling of monocyte ontogeny, recruitment, and differentiation across CNS borders during bacterial meningoencephalitis. These mechanisms may offer opportunities for therapeutic interventions in the future. One Sentence SummaryStreptococcal meningoencephalitis disrupts homeostatic, skull bone marrow-derived monocyte and macrophage trajectories in the dura.

immunology↗

Brain resident macrophages regulate sleep, with repopulated ones being unable to reestablish the original sleep circuits

Sleep is a complex behavior regulated by various brain cell types. However, the roles of brain-resident macrophages, including microglia and CNS-associated macrophages (CAMs), particularly those derived postnatally, in sleep regulation remain poorly understood. Here, we investigated the effects of natural (embryo-derived) and repopulated (postnatally derived) brain-resident macrophages on the regulation of vigilance states. We found that depletion in embryonically-derived brain macrophages caused increased sleep in the active period, but reduced its quality, reflected in reduced power of brain sleep oscillations. This was observed both for the Non-REM and REM sleep stages. Subsequent repopulation by postnatal brain macrophages unexpectedly failed to reestablish normal sleep-wake patterns and additionally induced sleep fragmentation. Furthermore, brain macrophage depletion caused excitatory-inhibitory synaptic imbalance, which was resistant to repopulation, and led to increased inhibitory synapses. At the metabolite level, the distinct metabolite profile induced by brain macrophage depletion largely returned to normal after repopulation. Our findings suggest a so far largely unknown interaction between brain-resident macrophages and sleep and emphasizes striking functional differences between embryonic and postnatally-derived brain macrophages, paving the way to future exploration of the role of brain macrophages of different origin in sleep disorders and synaptic connectivity.

neuroscience↗

Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.

Normal hematopoiesis requires constant prolific production of different blood cell lineages by multipotent hematopoietic stem cells (HSC). Stem- and progenitor- cells need to balance dormancy with proliferation. How genetic alterations impact frequency, lineage potential, and metabolism of HSC is largely unknown. Here, we compared induced expression of KRASG12D or RasGRP1 to normal hematopoiesis. At low-resolution, both Ras pathway lesions result in skewing towards myeloid lineages. Single-cell resolution CyTOF proteomics unmasked an expansion of HSC- and progenitor- compartments for RasGRP1, contrasted by a depletion for KRASG12D. SCENITH quantitates protein synthesis with single-cell precision and corroborated that immature cells display low metabolic SCENITH rates. Both RasGRP1 and KRASG12D elevated mean SCENITH signals in immature cells. However, RasGRP1-overexpressing stem cells retain a metabolically quiescent cell-fraction, whereas this fraction diminishes for KRASG12D. Our temporal single cell proteomics and metabolomics datasets provide a resource of mechanistic insights into altered hematopoiesis at single cell resolution.

developmental biology↗