Biology subjects

Blum, R.

Publications and source records attributed to Blum, R..

12 recordsLinked to original sources

bioRxiv2026

Deep brain stimulation of the mesencephalic locomotor centre induces stimulation-dependent behavioural states beyond locomotion

Deep brain stimulation (DBS) of the mesencephalic locomotor region (MLR) has been explored to treat gait disturbances. However, clinical outcomes of MLR-DBS have been disappointing overall, with only modest benefits in some individuals and unwanted effects, including anxiety, reported in others. Preclinical studies in several species, by contrast, show that MLR-DBS can improve locomotor and gait deficits, although defensive behaviours in response to stimulation have also been reported in some species. To investigate this discrepancy, we examined frequency- and amplitude-dependent effects of MLR-DBS in healthy rats, combining semi-supervised and unsupervised behavioural analyses. High-frequency, high-amplitude DBS (80-130 Hz), but not low-frequency stimulation (20-60 Hz), elicited hyperlocomotion intermixed with acute defensive-like behaviours. Low-frequency stimulation instead promoted phases of immobility. Consistently, only high-frequency DBS induced region-specific c-Fos expression in the MLR. Complex behaviours, including hyperlocomotion, rearing, tail rattling, and periods of immobility, were most pronounced in animals with the DBS electrode tip localized to the cuneiform nucleus (CnF) of the MLR. Using AAV tracer constructs for bright labelling of CaMKII-positive neurons and their axons, we identified prominent ascending projections from the CnF to the thalamus, substantia nigra pars compacta, zona incerta, hypothalamus, subthalamic nucleus, and central amygdala (CeA). Retrograde tracing confirmed the CnF-to-CeA projection independently. These findings show that the MLR is anatomically connected to higher-order centres linking motor and defensive networks, with DBS frequency and amplitude critically shaping behavioural outcomes that extend beyond locomotion.

neuroscience↗

bioRxiv2025

Sex differences define the molecular and cellular phenotypes of pain resolution in dorsal root ganglia

The dorsal root ganglion (DRG), a key site for the initiation and maintenance of neuropathic pain, was examined for sex-dependent phenotypes in sensory neurons, satellite glial cells (SGCs), and local macrophages following traumatic nerve injury and during natural pain resolution. Systematic analysis of 7,495 DRG immunofluorescence images and 62 transcriptomes revealed pronounced sex-specific, multicellular DRG phenotypes, especially during pain resolution. System parameters, including tissue size and neuron density also showed sex-dependent differences. Neuropathic pain resolved without tissue or sensory neuron loss. After injury, macrophages invaded the space between sensory neurons and satellite glial cells (SGCs); this was partially reversed during pain resolution, particularly in males. In females, immune-related gene expression and macrophage phenotypes persisted longer, while SGC activation and contact to sensory neurons was more persistent in males. During resolution, synaptic and excitability-related processes were pronounced in both sexes. However, while injury responses were largely shared between sexes, the resolution phase displayed distinctly sex-specific molecular and cellular signatures. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/691610v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@4063c7org.highwire.dtl.DTLVardef@156c0d2org.highwire.dtl.DTLVardef@8d4be4org.highwire.dtl.DTLVardef@7182bd_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefAnalysis of [~]7,500 bioimages and 62 transcriptomes reveals pronounced sex differences in rat dorsal root ganglia during pain resolution after peripheral nerve injury. HighlightsO_LIIn both female and male rats, peripheral nerve injury and subsequent pain resolution occur in the dorsal root ganglia (DRG) without neuronal or tissue loss. C_LIO_LISex influences DRG tissue size, neuron density, immune and glial phenotypes, and molecular-cellular responses to nerve injury and pain resolution. C_LIO_LIFollowing injury, macrophages infiltrate the space between sensory neurons and satellite glial cells (SGCs); this process reverses during pain resolution, particularly in males. C_LIO_LIIn females, immune phenotypes remain more stable throughout pain resolution, while SGC contact is reduced. C_LIO_LIPain resolution involves not only the reversal of injury-induced cell changes but also the activation of resolution-specific gene programs related to synaptic signaling, neuronal excitation, and cell-cell communication. C_LIO_LISex differences on the molecular-cellular level are less prevalent after nerve injury but become prominent during pain resolution. C_LI

neuroscience↗

bioRxiv2025

Resting calcium ion fluxes protect cells from fast mitochondrial fragmentation, cell stress responses, and immediate transcriptional reprogramming

Homeostatic calcium ion (Ca2+) fluxes between the endoplasmic reticulum, cytosol, and extracellular space occur not only in response to cell stimulation but also in unstimulated cells. Using murine astrocytes as a model, we asked whether there is a signaling function of these resting Ca2+-fluxes. The data showed that endoplasmic reticulum (ER) Ca{superscript 2} depletion, induced by sarcoplasmic/endoplasmic reticulum Ca{superscript 2}-ATPase (SERCA) inhibition, resulted to prolonged Ca{superscript 2} influx and mitochondrial fragmentation within 10 to 30 minutes. This mitochondrial fragmentation could be prevented in Ca2+- free medium or by inhibiting store-operated Ca2+ entry (SOCE). Similarly, attenuation of STIM proteins, which are vital ER Ca2+ sensors, protected mitochondrial morphology. On the molecular level, ER Ca2+ depletion, achieved either by removing extracellular Ca2+ or through acute SERCA inhibition, led to changes in gene expression of about 13% and 41% of the transcriptome within an hour, respectively. Transcriptome changes were associated with universal biological processes such as transcription, differentiation, or cell stress. Strong increase in expression was observed for the transcription factor ATF4, which is under control of the kinase PERK (EIF2AK3), a key protein involved in ER stress. Corroborating these findings, PERK was rapidly phosphorylated in Ca2+-free medium or after acute pharmacological inhibition of SOCE. In summary, resting, homeostatic Ca2+ fluxes prevent immediate- early cell stress and transcriptional reprogramming.

physiology↗

bioRxiv2024

Re-analysis of CLAP data affirms PRC2 as an RNA binding protein

Using CLAP methodology, Guo et al. recently concluded that PRC2 is not an RNA binding protein (RBP). They suggest that prior findings were CLIP artifacts and argue against RNAs direct role in PRC2 regulation. Here, we re-analyze their raw datasets and reach contrary conclusions. Through an independent computational pipeline, we observe significant PRC2 enrichment throughout the transcriptome, including XIST. Applying the authors published computational pipeline also reaffirms PRC2 as an RBP. Detailed investigation of the authors pipeline reveals several unconventional practices. First, Guo et al. retained reads from foreign species and other unmappable reads to obtain a normalization factor. Second, they selectively removed read duplicates from the mappable fraction, while retaining them in the unmappable fraction. Finally, the authors applied an arbitrary cutoff for enrichment values in XIST. Their pipeline thereby inflated PRC2s background reads and suppressed mappable signals, creating the impression that PRC2 is not a robust RBP.

genomics↗

bioRxiv2024

Neuropathic pain and distinct CASPR2 autoantibody IgG subclasses drive neuronal hyperexcitability

Patients with autoantibodies (aAbs) against the contactin-associated protein-like 2 (CASPR2) suffer from a variety of clinical syndromes including neuropathic pain, in some patients even as the only symptom. CASPR2 is an adhesion protein of the neurexin IV family and part of the voltage-gated potassium channel complex (VGKC) in neurons of dorsal root ganglia (DRG). The subsequent pathological mechanisms following the binding of CASPR2 aAbs and their association with pain are only partially understood. CASPR2 aAbs are mainly of the IgG4 subclass. Previous studies have neglected subclass-dependent effects. Here we investigated 49 subclassified patient serum samples positive for CASPR2 aAbs. To unravel underlying molecular mechanisms, we used a combination of super-resolution lattice structural illumination microscopy (SIM2) and functional readouts by calcium imaging and electrophysiological recordings. CASPR2-positive patient sera subclassified in IgG4 together with at least one other IgG subclass (IgGX) and patients with only IgG4 were further subdivided into the pain and no pain group. Patient subclassification shed further light on the pathological mechanisms of CASPR2 aAbs. A decrease of CASPR2 expression after long-term exposure to CASPR2 aAbs was only observed for the patient group without pain. Upon withdrawal of the CASPR2 aAbs, CASPR2 expression returned to normal level. Structural alterations were obtained by increased distances between CASPR2 and associated potassium channels along DRG axons using high-resolution lattice SIM2 microscopy but only following binding of CASPR2 aAbs from patients with pain. Similarly, CASPR2 aAbs of patients with pain significantly increased overall neuronal excitability of cultured DRG neurons as measured by calcium imaging. Patch-clamp recordings revealed significantly decreased current amplitudes of voltage-gated potassium (Kv) channels after incubation with all four CASPR2 aAbs subclassifications with the most prominent effect of serum samples harboring IgG4 aAbs. Notably, a patient serum sample lacking IgG4 did not alter Kv channel function. Withdrawal of aAbs rescued Kv channel function to normal levels suggesting that the affected potassium channel function is rather due to a functional block of the VGKC rather than altered structural integrity of the VGKC. Taken together, we found IgG4 aAbs to be a major modifier of potassium channel function. The increase in DRG excitability is primarily due to impaired Kv channel conductance as a consequence of CASPR2 aAbs binding but additional and so far unidentified signal pathways contribute to this process in patients with neuropathic pain.

neuroscience↗

bioRxiv2024

Satellite glial cells from adult DRG dedifferentiate in vitro and can be reprogrammed into nociceptor-like neurons

In dorsal root ganglia (DRG), neuronal loss has been reported in patients with neuropathic pain, raising the question of whether the DRG, as part of the peripheral nervous system (PNS), harbor an endogenous cell source for neural repair. We found that adult mouse DRG harbor glial cells that dedifferentiate in vitro into Sox2/Sox10-positive glial progenitor-like cells. Coexpression of the developmental transcription factors Neurog1 and Neurog2 was sufficient to induce both neuronal and glial phenotypes. Nerve growth factor supported the maturation of a subset of neurons into nociceptor-like cells expressing functional TrpA1, TrpV1, and TTX-resistant NaV channels. We report the limitation that we miss factors allowing consistent maturation to the sensory neuron profile. In summary, in the PNS, adult DRG-derived glial cells can acquire neural progenitor-like properties, show bipotent reprogramming competence, and may serve as an intrinsic cell source for sensory circuit regeneration.

neuroscience↗

bioRxiv2023

Human dorsal root ganglia after plexus injury: either preservation or loss of the multicellular unit

ObjectivePlexus injury results in lifelong suffering of flaccid paralysis, sensory loss, and intractable pain. For this clinical problem, regenerative medicine concepts, such as cell replacement for restoring dorsal root ganglion (DRG) function, set high expectations. However, it is completely unclear which DRG cell types are affected by plexus injury. MethodsWe investigated the cellular composition of human DRG in a clinically characterized cohort of patients with plexus injury. Avulsed DRG of 13 patients were collected during reconstructive nerve surgery. Then, we analyzed the cellular composition of the DRG with a human-adapted objective deep learning-based analysis of large-scale microscopy images. ResultsSurprisingly, in about half of the patients, the injury-affected DRG no longer contained DRG cells. The complete entity of neurons, satellite glial cells, and microglia was lost and replaced by mesodermal/connective tissue. In the other half of patients, the cellular entity of the DRG was well preserved. We found no loss of neurons, no gliosis, and macrophages close to single sensory neuron/satellite glial cell entities. Patients with neuronal preservation had less pain than patients with neuronal loss. InterpretationThe findings classify plexus injury patients in two categories: type I (neuronal preservation) and type II (neuronal loss). We call for early, post-accidental interventions to protect the entire DRG and improved MRI diagnostics to detect neuronal loss. Regenerative medicine to restore DRG function will need at least two translational directions: reafferentation of existing DRG units for type I injuries; or replacement of the entire DRG structure for type II patients.

neuroscience↗

bioRxiv2022

Modelling non-local neural information processing in the brain

The representation of the surrounding world emerges through integration of sensory information and actions. We present a novel neural model which implements non-local, parallel information processing on a neocolumnar architecture with lateral interconnections. Information is integrated into a holographic wave interference pattern. We compare the simulated in silico pattern with observed in vivo invasive and non-invasive electrophysiological data in human and non-human primates. Our model replicates the modulation of neural high-frequency activity during visual perception showing that phase-locked low and high-frequency oscillations self-organize efficiently and carry high information content. The simulation further models how criticality (high content) of information processing emerges given a sufficiently high number of correlated neurons. Non-local information processing, forming one holographic wave pattern, suggests a platform for emergence of conscious perception. One sentence summarySimulated non-local information processing on a neocolumnar architecture models well multiple electrophysiological observations of brain activity, including high-frequency activity during visual perception in primates.

neuroscience↗

bioRxiv2020

Constitutively active TrkB kinase signalling reduces actin filopodia dynamics and cell migration

Trk receptors and gene fusions of NTRK are targets in precision oncology. Classical Trk signalling concepts fail to explain ligand-independent signalling of intracellular TrkB or NTRK fusion proteins. Here, we show that abundance of the intracellular domain of TrkB is sufficient for ligand-independent autophosphorylation. This constitutive TrkB signalling reduced actin filopodia dynamics, could phosphorylate FAK, and changed cell morphology. Mutating Y705 in the kinase domain of TrkB alone specifically blocked these pathways. Engineered intracellular kinase domain proteins and a cancer-related intracellular NTRK2-fusion protein (SQSTM1-NTRK2) also underwent constitutive activation. In migrating glioblastoma-like U87MG cells, self-active TrkB kinase reduced cell migration. Moreover, we found evidences for constitutively active, intracellular TrkB in tissue of human grade IV glioblastoma. Structural modelling of the kinase domain let us postulate that release from cis-autoinhibition by abundance is sufficient for TrkB/FAK/Actin signalling via Y705. These constitutive signalling pathways could be fully blocked within minutes by clinically approved, anti-tumorigenic Trk inhibitors. In conclusion, our data provide an explanation and biological function for TrkB kinase domain signalling in the absence of a ligand.

neuroscience↗

bioRxiv2019

Quantifying and modelling non-local information processing of associative brain regions

Short abstractBrain world representation emerges not by philosophy but from integrating simple followed by more complex actions (due to drives, instincts) with sensory feedback and inputs such as rewards. Our simulation provides this world representation holistically by identical information encoded as holographic wave patterns for all associative cortex regions. Observed circular activation in cell culture experiments provides building blocks from which such an integrative circuit can evolve just by excitation and inhibition transfer to neighbouring neurons. Large-scale grid-computing of the simulation brought no new emergent phenomena but rather linear gains and losses regarding performance. The circuit integrates perceptions and actions. The resulting simulation compares well with data from electrophysiology, visual perception tasks, and oscillations in cortical areas. Non-local, wave-like information processing in the cortex agrees well with EEG observations such as cortical alpha, beta, and gamma oscillations. Non-local information processing has powerful emergent properties, including key features of conscious information processing.

neuroscience↗

bioRxiv2019

Essential role of the mouse synapse associated protein Syap1 in circuits for spontaneous motor activity and rotarod balance

Synapse-associated protein 1 (Syap1) is the mammalian homologue of synapse-associated protein of 47 kDa (Sap47) in Drosophila. Genetic deletion of Sap47 leads to deficiencies in short-term plasticity and associative memory processing in flies. In mice, Syap1 is prominently expressed in the nervous system, but its function is still unclear. We have generated Syap1 knockout mice and tested motor behaviour and memory. These mice are viable and fertile but display distinct deficiencies in motor behaviour. Locomotor activity specifically appears to be reduced in early phases when voluntary movement is initiated. On the rotarod, a more demanding motor test involving control by sensory feedback, Syap1-deficient mice dramatically fail to adapt to accelerated speed or to a change in rotation direction. Syap1 is highly expressed in cerebellar Purkinje cells and cerebellar nuclei. Thus, this distinct motor phenotype could be due to a so far unknown function of Syap1 in cerebellar sensorimotor control. The observed motor defects are highly specific since other tests in the modified SHIRPA test, as well as cognitive tasks like novel object recognition, Pavlovian fear conditioning, and anxiety-like behaviour in open field, dark-light transition, and elevated plus maze, do not appear to be strongly affected in Syap1 knockout mice.

animal behavior and cognition↗

bioRxiv2018

DeepFLaSh, a deep learning pipeline for segmentation of fluorescent labels in microscopy images

Fluorescent labeling of biomolecules is widely used for bioimage analyses throughout the life sciences. Recent advances in deep learning (DL) have opened new possibilities to scale the image analysis processes through automation. However, the annotation of fluorescent features with a low signal-to-noise ratio is frequently based on subjective criteria. Training on subjective annotations may ultimately lead to biased DL models yielding irreproducible results. An end-to-end analysis process that integrates data annotation, ground truth estimation, and model training can mitigate this risk. To highlight the importance of this integrated process, we compare different DL-based analysis approaches. Based on data from different laboratories, we show that ground truth estimation from multiple human annotators is indispensable to establish objectivity in fluorescent feature annotations. We demonstrate that ensembles of multiple models trained on the estimated ground truth establish reliability and validity. Our research provides guidelines for reproducible and transparent bioimage analyses using DL methods.

neuroscience↗