Biology subjects

Westphal, M.

Publications and source records attributed to Westphal, M..

14 recordsLinked to original sources

bioRxiv2026

Baseline regulatory programs in larval and adult neural progenitors converge towards an injury-induced state after spinal cord injury

Regeneration after spinal cord injury requires progenitor cells to convert injury-associated signals into coordinated remodeling of gene regulatory programs. Mammalian spinal progenitors show limited neurogenic output after injury, whereas zebrafish regenerate spinal neurons and recover motor function. To investigate the regulatory changes that allow ependymo-radial glia (ERG) cells, the progenitor cells of the zebrafish spinal cord, to generate new neurons, we combined single-nucleus gene expression and chromatin accessibility profiling across embryonic, larval, and adult stages with topic-based gene regulatory network (GRN) inference. We found that larval and adult ERGs enter the injury response from distinct regulatory baselines: larval progenitors are characterized by a gliogenic program, whereas adult progenitors maintain a comparatively quiescent state. Following injury, both populations gradually change their baseline programs and shift towards a lesion-associated module marked by stress-responsive and chromatin-associated regulators, including jun, hmga1a, hmga2, ybx1, and foxj1a. The shift away from homeostatic states is supported by decreased expression of the Notch-associated regulators nuclear factor I A (nfia) and hey1 in larvae, while in adults, downregulation of the same nuclear factor and other TFs such as bhlhe41 is associated with quiescence exit. Pathway analysis showed stage-specific alterations after injury, characterized predominantly by extracellular signaling and cytoskeletal reorganization in larvae and by metabolic and translational remodeling in adults. Despite divergence from the homeostatic states, injury-induced larval and adult GRNs remain distinct from embryonic hERG regulatory programs. Thus, larval and adult progenitors follow different trajectories from their baselines towards a related lesion-reactive state, in which shared regeneration-associated features are acquired within respective contexts.

bioinformatics↗

bioRxiv2026

Spinal injury induces a stem cell-like progenitor state that promotes regenerative neurogenesis via clcf1 in zebrafish.

After spinal injury, zebrafish, in contrast to mammals, show regenerative neurogenesis, characterized by enhanced injury-induced proliferation of ependymo-radial glial cells (ERGs) and an increase in injury-induced generation of neurons from these progenitors. It is unclear whether regenerative neurogenesis simply recapitulates development or uses regeneration-specific mechanisms. Using scRNA-seq and in vivo validation we find a spinal injury-induced state in ERGs (iiERGs) in larval zebrafish. This cell state emerges mostly without proliferation and has stem cell characteristics, including weak expression of neurogenic genes and strong expression of stemness factors, such as lin28a. Expression of lin28a is not detectable during ongoing developmental neurogenesis. Following spinal cord lesion, lin28a disruption increases the numbers of ERGs undergoing neuronal differentiation and of newly-generated neurons, at the expense of proliferating ERGs and iiERGs. This supports a stemness-preserving role of lin28a in iiERGs. Importantly, iiERGs secrete growth factors, including the regeneration-specific cytokine clcf1, which depends in part on lin28a expression. Disruption of clcf1 signalling impairs spinal progenitor proliferation and injury-induced generation of new neurons, but does not affect the emergence of iiERGs. Over-expression of clcf1 is sufficient to augment neurogenesis in unlesioned animals without inducing the iiERG state, indicating that clcf1 acts as a generic growth factor. Hence, we describe an injury-specific stem cell-like ERG population that regulates regenerative neurogenesis by attenuating neuronal differentiation via lin28a and promoting progenitor proliferation via clcf1.

neuroscience↗

bioRxiv2024

Tumor-Associated Macrophages in Meningiomas: An Independent Prognostic Factor for Poor Survival Outperforming the Benefits of T cells

BackgroundTumor-associated macrophages (TAMs) represent the main immune cell population in various brain malignancies. To elucidate their biological impact in the tumor microenvironment (TME) of meningiomas (MGMs), we assessed TAM numbers, activation state, malignancy- and survival-associated changes, as well as their association with tumor-infiltrating T lymphocytes (TILs). MethodsTAM infiltration was analyzed in a multicenter cohort of 195 clinically well-annotated cases (follow-up >5 years, n=120 newly-diagnosed and n=75 recurrent MGMs) enriched for higher-grade MGMs. TAMs and M2-TAMs were quantified by tissue cytometry on whole-tumor sections. Further, we assessed levels of 27 cyto- and chemokines in a subset of tissues (n=46 cases), and re-analyzed our previously published T cell infiltration (n=94 cases) and expanded microarray (n=97 cases) datasets. ResultsNewly-diagnosed MGMs showed a substantial but highly heterogeneous TAM infiltration that was four times higher than for TILs. Anti-inflammatory M2-TAMs were increased in higher WHO grade tumors and in recurrent MGMs. Importantly, high M2-TAM infiltration was associated with poor progression-free survival independent of other prognostic confounders and even mitigated the beneficial prognostic effect of TIL infiltration. Additional cytokine, gene expression and pathway analyses corroborated the presence of an immunosuppressive niche in M2-TAM-enriched MGMs. ConclusionsAltogether, higher numbers of TAMs and M2-TAMs appear to be a hallmark of clinically aggressive behavior in newly-diagnosed and recurrent MGMs. Unlike TILs, immunosuppressive TAMs seem to play a dominant negative role in the immunological landscape of MGMs, highlighting M2-TAMs to be an attractive treatment target for immunotherapeutic approaches. Translational Relevance of the StudyMeningiomas (MGMs) are typically regarded as benign neoplasms, however there is a substantial proportion of clinically aggressive tumors that are refractory to standard treatment modalities and demand for the development of novel therapeutic approaches such as immunotherapy. This is the first comprehensive study reporting malignancy- and progression-associated changes of tumor-associated macrophages (TAMs), their polarization state, their association with tumor-infiltrating T lymphocytes (TILs), and their impact on patient survival in a large multicenter cohort of 195 tumors containing substantial numbers of clinically aggressive cases. Notably, we identified higher numbers of immunosuppressive M2-TAMs as an independent prognostic factor for poor survival, overriding the beneficial prognostic effects of TILs. Thus, our data highlight an important role of immunosuppressive M2-TAMs on tumor malignancy and progression, and further suggest targeting macrophages as a treatment strategy to improve the success of immunotherapeutic approaches in MGMs. Key pointsO_LIMeningiomas are highly infiltrated by immunosuppressive M2-TAMs. C_LIO_LIHigh M2-TAM numbers are an independent negative prognostic factor for patient survival. C_LIO_LIHigh TAM infiltration mitigates the beneficial prognostic impact of TILs. C_LI

cancer biology↗

bioRxiv2024

Wound closure after brain injury relies on force generation by microglia in zebrafish

Wound closure after a brain injury is critical for tissue restoration but this process is still not well characterised at the tissue level. We use live observation of wound closure in larval zebrafish after inflicting a stab wound to the brain. We demonstrate that the wound closes in the first 24 hours after injury by global tissue contraction. Microglia accumulation at the point of tissue convergence precedes wound closure and computational modelling of this process indicates that physical traction by microglia could lead to wound closure. Indeed, genetically or pharmacologically depleting microglia leads to defective tissue repair. Live observations indicate centripetal deformation of astrocytic processes contacted by migrating microglia. Severing such contacts leads to retraction of cellular processes, indicating tension. Weakening tension by disrupting the F-actin stabilising gene lcp1 in microglial cells, leads to failure of wound closure. Therefore, we propose a previously unidentified mechanism of brain repair in which microglia has an essential role in contracting spared tissue. Understanding the mechanical role of microglia will support advances in traumatic brain injury therapies Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/597300v3_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@112aorg.highwire.dtl.DTLVardef@6712c4org.highwire.dtl.DTLVardef@101179borg.highwire.dtl.DTLVardef@b4ecb6_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies

Epigenome-wide association studies (EWAS) are transforming our understanding of the interplay between epigenetics and complex human traits and phenotypes. We introduce the Methylation Screening Array (MSA), a new iteration of the Infinium technology for scalable and quantitative screening of trait associations of nuanced ternary-code cytosine modifications in larger, more inclusive, and stratified human populations. MSA integrates EWAS, single-cell, and cell-type-resolved methylome profiles, covering diverse human traits and diseases. Our first MSA applications yield multiple biological insights: we revealed a previously unappreciated role of 5-hydroxymethylcytosine (5hmC) in trait associations and epigenetic clocks. We demonstrated that 5hmCs complement 5-methylcytosines (5mCs) in defining tissues and cells epigenetic identities. In-depth analyses highlighted the cell type context of EWAS and GWAS hits. Using this platform, we conducted a comprehensive human 5hmC aging EWAS, discovering tissue-invariant and tissue-specific aging dynamics, including distinct tissue-specific rates of mitotic hyper- and hypomethylation rates. These findings chart a landscape of the complex interplay of the two forms of cytosine modifications in diverse human tissues and their roles in health and disease.

genomics↗

bioRxiv2024

NSCLC patients with oligo-metastatic brain disease show an altered CD4 T-cells immune profile

BackgroundLung cancer is the leading cause of cancer-related deaths worldwide, with brain metastasis (BM) occurring in 40% of advanced non-small cell lung cancer (NSCLC) patients. In 15% of these patients, the brain is the only affected organ (oligo-metastasis), corresponding to improved prognosis compared to widespread disease. Thus far, it is unknown if the metastatic dissemination to the brain without systemic metastases is a consequence of the immune systems ability to control systemic tumor outgrowth. MethodsHere, we investigated the local and peripheral immune cell composition in NSCLC BM patients, and identified new immune patterns related to the occurrence of brain metastases either as oligo- or poly-metastatic disease. ResultsThe multi-parametric immune phenotyping of peripheral blood revealed a downregulation of KLRG1 in CD8+ T-cells and an increase in CD4+ TH17 cells and elevated IL-17 levels in the blood of all NSCLC BM patients compared to healthy individuals. In addition, BM patients CD4+ T cells showed less CD73 expression with reduced effector memory differentiation. Furthermore, we observed less intra-tumoral infiltration in tumor tissues and a distinctive CD4+ T-cell profile in oligo-synchronous BM, both in the tumor microenvironment and peripheral blood compared to poly-metastatic BM patients. Moreover, 5'-ectonucleotidase CD73 was significantly upregulated in CD4 and T-regulatory cells of oligo-synchronous BM. ConclusionsThese results indicate that oligo-synchronous BM exhibits a more pronounced alteration in the CD4 T-cell immune profile both locally at the tumor site and systemically. Key PointsO_LIBM patients exhibit a skewed systemic immune profile, characterized by downregulation of KLRG1 in CD8+ and induction of TH17/IL-17 axis and CD73 in CD4+ T-cells. C_LIO_LIOligo-synchronous BM displayed a distinct CD4+ T-cell profile in both TME and peripheral blood. C_LI Importance of the StudyThis study presents a novel insight into immune profiles of brain metastasis types in NSCLC patients. Examining tissues and PBMCs sheds light on the disease and uncovers unique immune responses within distinct brain metastasis patterns. This research offers valuable knowledge for improved understanding and identifying potential prognosis markers.

cancer biology↗

bioRxiv2023

Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability

Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is nascent. We present an epigenetically defined neural signature of glioblastoma that independently affects patients survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals high abundance of stem cell-like malignant cells classified as oligodendrocyte precursor and neural precursor cell-like in high-neural glioblastoma. High-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature associates with decreased survival as well as increased functional connectivity and can be detected via DNA analytes and brain-derived neurotrophic factor in plasma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant.

neuroscience↗

bioRxiv2021

Integrated phospho-proteogenomic and single-cell transcriptomic analysis of meningiomas establishes robust subtyping and reveals subtype-specific immune invasion

Meningiomas are the most frequent primary intracranial tumors. They can follow a wide clinical spectrum from benign to highly aggressive clinical course. No specific therapy exists for refractory cases or cases not amenable to resection and radiotherapy. Identification of risk of recurrence and malignant transformation for the individual patients is challenging. However, promising molecular markers and prognostic subgrouping by DNA methylation are emerging. Still, the biological underpinnings of these diagnostic subgroups are elusive, and, consequently, no novel therapeutic options arise thereof. Here we establish robust subgroups across the full landscape of meningiomas, consistent through DNA methylation, mutations, the transcriptomic, proteomic and phospho-proteomic level. Pronounced proliferative stress and DNA damage repair signals in malignant cells and in clusters exclusive to recurrent tumors are in line with their higher mitotic activity, but also provide an explanation for the accumulation of genomic instability in anaplastic meningiomas. Although homozygous deletion of CDKN2A/B is a diagnostic marker of high-grade meningioma, the expression of its gene product increased from low to non-deleted high-grade cases. Differences between subgroups in lymphocyte and myeloid cell infiltration, representing a majority of tumor mass in low-grade NF2 tumors, could be assigned to cluster-specific interaction with tumor cells. Activation to a more proinflammatory phenotype and decreased infiltration of myeloid cells in high-grade cases correlated with lower expression of CSF1, located on chromosome arm 1p, whose deletion is known as prognostic marker, with no proposed mechanism before. Our results demonstrate a robust molecular subclassification of a tumor type across multiple layers, provide insight into heterogeneous growth dynamics despite shared pathognomonic mutations, and highlight immune infiltration modulation as a novel target for meningioma therapy.

genomics↗

bioRxiv2021

OPA1 Deletion in Brown Adipose Tissue Improves Thermoregulation and Systemic Metabolism via FGF21

Adrenergic stimulation of brown adipocytes alters mitochondrial dynamics, including proteolytic processing of the mitochondrial fusion protein optic atrophy 1 (OPA1). However, direct mechanisms linking OPA1 to brown adipose tissue (BAT) physiology are incompletely understood. By deleting OPA1 selectively in BAT (OPA1 BAT KO), we demonstrate that OPA1 is required for cold-induced thermogenesis. Unexpectedly, OPA1 deficiency induced fibroblast growth factor 21 (FGF21) as a BATokine in an activating transcription factor 4 (ATF4)- dependent manner. BAT-derived FGF21 mediates an adaptive response in OPA1 BAT KO mice, by inducing browning of white adipose tissue (WAT), increasing resting metabolic rates, and improving thermoregulation. However, FGF21 does not mediate the resistance to diet-induced obesity observed in these animals. These findings reveal a requirement for OPA1 in BAT thermogenesis, and uncovers a homeostatic mechanism of BAT-mediated metabolic protection governed by an ATF4-FGF21 axis, that is activated independently of BAT thermogenic function.

physiology↗

bioRxiv2020

The shrub Ephedra californica facilitates arthropod communities along a regional desert climatic gradient.

Arthropods underpin arid community dynamics and provide many key ecosystem services. In arid ecosystems, the key habitat components that influence arthropod community structure are relatively understudied. Ephedra californica is a common and widespread shrub with established positive effects on plant and vertebrate animal communities within the drylands of Southern California. The capacity for these positive effects to further support arthropod communities has not been examined. We tested the hypothesis that the physical structure and cover vegetation enhances key measures of arthropod community assembly at nine Californian desert sites that comprise an extensive regional aridity gradient. We contrasted the effects of shrub canopies with ground-covering vegetation on structuring ground-active arthropod communities by surveying ground-active arthropods with pitfall traps and collecting vegetation on the soil surface in the form of residual dry matter (RDM). We collected a total of 5868 individual arthropod specimens for a total of 184 morphospecies. Arthropod abundance and morphospecies richness and RDM biomass and cover were significantly greater beneath the canopy of E. californica throughout the region. Total biomass of RDM did not significantly influence arthropod communities, but cover of RDM on the soil surface negatively influenced arthropod abundance. Neither climatic aridity nor downscaled evaporative stress estimates were significant mediators of the arthropodvegetation association patterns. Vegetation thus likely has direct and indirect physical effects on arthropod communities. These canopy versus soil surface vegetation differences will refine sampling of fine-scale patterns of arthropod diversity in drylands. Regional land managers can support arthropod diversity by maintaining populations of foundation shrub species such as E. californica.

ecology↗

bioRxiv2019

Parkinsons disease uncovers an underlying sensitivity of subthalamic nucleus neurons to beta-frequency cortical input

Abnormally sustained beta-frequency synchronisation between the motor cortex and subthalamic nucleus (STN) is associated with motor symptoms in Parkinsons disease (PD). It is currently unclear whether STN neurons have a preference for beta-frequency input (12-35Hz), rather than cortical input at other frequencies, and how such a preference would arise following dopamine depletion. To address this question, we combined analysis of cortical and STN recordings from awake PD patients undergoing deep brain stimulation surgery with recordings of identified STN neurons in anaesthetised rats. In PD patients, we demonstrate that a subset of STN neurons are strongly and selectively sensitive to fluctuations of cortical beta oscillations over time, linearly increasing their phase-locking strength with respect to full range of instantaneous amplitude. In rats, we probed the frequency response of STN neurons more precisely, by recording spikes evoked by short bursts of cortical stimulation with variable frequency (4-40Hz) and constant amplitude. In both healthy and dopamine-depleted animals, only beta-frequency stimulation selectively led to a progressive reduction in the variability of spike timing through the stimulation train. We hypothesize, that abnormal activation of the indirect pathway, via dopamine depletion and/or cortical stimulation, could trigger an underlying sensitivity of the STN microcircuit to beta-frequency input.

neuroscience↗

bioRxiv2018

Temporal evolution of beta bursts in the parkinsonian cortico-basal ganglia network

Prevalence and temporal dynamics of transient oscillations in the beta frequency band (15-35 Hz), referred to as beta bursts, are correlated with motor performance and tactile perception. Disturbance of these activities is a candidate mechanism for motor impairment in Parkinsons disease (PD), where the excessively long bursts correlate with symptom severity and are reduced by pharmacological and surgical treatments. To date, characterization of beta bursts in PD has been limited to the local field potentials in the subthalamic nucleus (STN) and cortical EEG. Here, we describe the changes that take place in spiking activity across the cortico-basal ganglia circuit, providing a unique insight into the network dynamics of these transient oscillations. Firstly, we demonstrate that rhythmic subthalamic spiking activity emerges at a fixed phase relationship with respect to cortical beta bursts in PD patients. Using multichannel recordings of ensembles of neurons in the 6-OHDA rat model of PD, we then dissect the beta burst dynamics across the sensorimotor cortex and several basal ganglia structures: striatum (Str), globus pallidus externus (GPe) and STN. Each subcortical structure exhibits enhanced rhythmic activity in the beta band locked to the onset of cortical beta bursts and longer cortical bursts lead to stronger subcortical rhythmicity. Crucially, enhanced subcortical rhythmic activity emerges at a fixed phase relationship with respect to the motor cortex, comparable to the relationship observed in PD patients. Striatal beta bursts terminate prior to the recruitment of those in the STN and GPe, suggesting that while they could play an important role in establishing synchrony in the beta band, they do not extensively contribute to its maintenance in other basal ganglia structures. Critically, changes in cortico-subcortical phase coupling precede the onset of a cortical beta burst, supporting the hypothesis that phase alignment across the cortico-basal ganglia network could recruit these structures into synchronous network oscillations. We provide a powerful approach that not only examines pathophysiology of PD across the motor circuit, but also offer insights that could aid in the design of novel neuromodulation strategies to manipulate the state of the motor system before pathological activities emerge.

neuroscience↗

bioRxiv2018

Synchronised spiking activity underlies phase amplitude coupling in the subthalamic nucleus of Parkinson’s disease patients

Both phase-amplitude coupling (PAC) and beta-bursts in the subthalamic nucleus have been significantly linked to symptom severity in Parkinsons disease (PD) in humans and emerged independently as competing biomarkers for closed-loop deep brain stimulation (DBS). However, the underlying nature of subthalamic PAC is poorly understood and its relationship with transient beta burst-events has not been investigated. To address this, we studied macro- and micro electrode recordings of local field potentials (LFPs) and single unit activity from 15 hemispheres in 10 PD patients undergoing DBS surgery. PAC between beta phase and high frequency oscillation (HFO) amplitude was compared to single unit firing rates, spike triggered averages, power spectral densities and phase-spike locking, and was studied in periods of beta-bursting. We found a significant synchronisation of spiking to HFOs and correlation of mean firing rates with HFO-amplitude when the latter was coupled to beta phase (i.e. in the presence of PAC). In the presence of PAC, single unit power spectra displayed peaks in the beta and HFO frequency range and the HFO frequency was correlated with that in the LFP. Finally, PAC significantly increased with beta burst-duration. Our findings offer new insight in the pathology of Parkinsons disease by providing evidence that subthalamic PAC reflects the locking of spiking activity to network beta oscillations and that this coupling progressively increases with beta-burst duration. These findings suggest that beta-bursts capture periods of increased subthalamic input/output synchronisation in the beta frequency range and have important implications for therapeutic closed-loop DBS.\n\nSignificance statementIdentifying biomarkers for closed-loop deep brain stimulation (DBS) has become an increasingly important issue in Parkinsons Disease (PD) research. Two such biomarkers, phase-amplitude coupling (PAC) and beta-bursts, recorded from the implanted electrodes in subthalamic nucleus in PD patients, correlate with motor impairment. However, the physiological basis of PAC, and it relationship to beta bursts, is unclear. We provide multiple lines of evidence that PAC in the human STN reflects the locking of spiking activity to network beta oscillations and that this coupling progressively increases with the duration of beta-bursts. This suggests that beta-bursts capture increased subthalamic input/output synchronisation and provides new insights in PD pathology with direct implications for closed-loop DBS therapy strategies.

neuroscience↗

bioRxiv2018

Phase-dependent suppression of beta oscillations in Parkinson’s disease patients

Synchronized oscillations within and between brain areas facilitate normal processing, but are often amplified in disease. A prominent example is the abnormally sustained beta-frequency (~20Hz) oscillations recorded from the cortex and subthalamic nucleus of Parkinson's Disease patients. Computational modelling suggests that the amplitude of such oscillations could be modulated by applying stimulation at a specific phase. Such a strategy would allow selective targeting of the oscillation, with relatively little effect on other activity parameters. Here we demonstrate in awake, parkinsonian patients undergoing functional neurosurgery, that electrical stimulation arriving on consecutive cycles of a specific phase of the subthalamic oscillation can suppress its amplitude and coupling to cortex. Stimulus-evoked changes in spiking did not have a consistent time course, suggesting that the oscillation was modulated independently of net output. Phase-dependent stimulation could thus be a valuable strategy for treating brain diseases and probing the function of oscillations in the healthy brain.

neuroscience↗