Biology subjects

Halder, M.

Publications and source records attributed to Halder, M..

10 recordsLinked to original sources

bioRxiv2026

Compounds toxic to stationary-phase yeast reveal a role for lipid metabolism in quiescent cell survival

The mechanisms that enable quiescent cells to survive nutrient-limited conditions remain imcompletely understood. To investigate these mechanisms, we performed a large-scale chemical screen to identify compounds that reduce viability of stationary-phase fission yeast cells. We identified two structurally related compounds that impair quiescent cell survival. In stationary phase, these compounds inhibited cell cycle re-entry, altered lipid droplets (LDs), and affected nuclear and chromosomal size, all of which are associated with lipid metabolism. In proliferating cells, they induced cell cycle arrest accompanied by nucleolar accumulation of cyclin-dependent kinase (CDK), a hallmark of stationary-phase cells, and inhibited mitochondrial oxygen consumption. The lipid synthesis inhibitor cerulenin similarly inhibited cell cycle re-entry and induced cell cycle arrest with nucleolar CDK accumulation; however, it did not reduce viability in stationary-phase cells or reproduce the other cellular effects. These results indicate that the compounds may affect lipid metabolism potentially by impairing lipid mobilization. Furthermore, the compounds were also toxic to stationary-phase budding yeast, suggesting conservation of survival mechanisms in quiescent cells. Together, our findings suggest that lipid metabolism, possibly lipid mobilization, plays a critical role in quiescent cell survival.

Cell Biology↗

bioRxiv2026

Ion channel and receptor-mediated regulation of axonal conduction reliability in sympathetic preganglionic neurons.

Sympathetic preganglionic neurons (SPNs) provide the sole spinal output to the peripheral sympathetic nervous system. Although sympathetic control is traditionally attributed to synaptic integration within the spinal cord and ganglia, the reliability of spike propagation along SPN axons themselves has received little attention. Here, and in companion papers, we show that axonal conduction in adult mouse thoracic SPNs is highly modifiable and constitutes a critical site of sympathetic gain control. Using an ex vivo preparation preserving intact paravertebral and splanchnic pathways while blocking synaptic transmission, we recorded compound action potentials evoked across multiple ganglia. Slower-conducting, unmyelinated SPN axons, particularly those with branching axons traversing the interganglionic nerve (IGN), exhibited pronounced, temperature-dependent conduction failures. Elevation of temperature produced membrane hyperpolarization and loss of conduction, consistent with activation of temperature-sensitive K2P leak channels, as supported by pharmacological evidence. Pharmacological activation of TREK-family channels with riluzole or arachidonic acid preferentially suppressed conduction in these axons. In contrast, blockade of voltage-gated K+ channels with 4-aminopyridine (4-AP) robustly facilitated conduction, recruited previously silent axons, and restored propagation under conditions of temperature-induced failure. Surprisingly, tetraethylammonium (TEA) block of K+ channels were without effect or depressant. Transmitter systems further shaped axonal reliability: agonists and antagonists of GABAA receptors, as well as cholinergic manipulations, selectively depressed conduction in slow, branching axons. Together, these findings establish SPN axons, particularly slow-conducting branching fibers, as an active and dynamically regulated substrate for sympathetic output control, revealing a presynaptic mechanism with implications for autonomic physiology and disease. SIGNIFICANCESympathetic output is commonly viewed as being regulated primarily through synaptic integration within spinal and autonomic circuits, while axons are often treated as passive transmission elements. Emerging evidence suggests this assumption is incomplete, particularly in slowly conducting and highly branched sympathetic preganglionic neuron (SPN) axons that may operate near the limits of conduction reliability. This study identifies branch point conduction as a dynamic and pharmacologically modifiable control mechanism governing sympathetic signal transmission. By demonstrating selective vulnerability of distinct SPN populations and revealing strong modulation by potassium channel mechanisms, these findings establish axonal conduction security as an underappreciated site of autonomic gain control. These mechanisms may represent novel therapeutic targets for restoring autonomic function after spinal cord injury and related disorders.

neuroscience↗

bioRxiv2026

Probabilistic spike propagation shapes sympathetic output in mouse preganglionic neurons

Sympathetic preganglionic neurons (SPNs) provide the final pathway through which the central nervous system regulates autonomic function. SPN axons projecting to paravertebral sympathetic chain ganglia branch extensively and diverge across multiple segments, enabling amplification of central sympathetic commands through extensive postganglionic neuronal populations. Spike propagation along these projections has generally been assumed to occur reliably. However, most SPN axons are extremely small unmyelinated fibers, a structural feature predicted to reduce the safety factor for spike propagation. Using an isolated mouse thoracic sympathetic chain preparation, we combined anatomical tracing with multi-site compound action potential recordings to assess conduction across SPN axons. Neurobiotin labeling revealed widespread rostrocaudal divergence through interganglionic nerves, while axon measurements confirmed that most SPN axons are small unmyelinated fibers. Across preparations, supramaximal recruitment of SPNs revealed substantial intertrial variability in compound responses, indicating frequent conduction failures. Failures were most prominent in slow-conducting axons and occurred in both branching interganglionic pathways and the unbranching axons within the splanchnic nerve. During repetitive activation, frequency dependent depression was observed at 1, 5 and 10Hz, but only slow-conducting branching axons exhibited pronounced depression. Overall, these findings indicate that spike propagation in SPN axons may operate probabilistically rather than deterministically, with reliability strongly dependent on axonal subtype and recent activity history. We conclude that axonal conduction variability constitutes an intrinsic and dynamically regulated mechanism that shapes sympathetic output. By varying the recruitment of postganglionic populations, unreliable spike propagation in SPN axons introduces a previously unrecognized presynaptic gain-control mechanism, operating independently of central spike generation to modulate sympathetic output. SIGNIFICANCESympathetic preganglionic neurons provide the final pathway through which the central nervous system controls end-organs. These neurons project through the sympathetic chain where their axons branch extensively to recruit more numerous paravertebral postganglionic neurons. Spike propagation along these projections has generally been assumed to occur reliably. Here we show that this assumption is incorrect. Using anatomical tracing and electrophysiological recordings in mouse sympathetic chain preparations, we demonstrate that spike conduction in sympathetic preganglionic axons is frequently variable and prone to failure, particularly in the slowest-conducting unmyelinated fibers. Conduction variability was preferentially enhanced in branching axonal pathways during repetitive activation. These findings reveal that axonal conduction reliability represents an important presynaptic mechanism regulating the magnitude and variability of sympathetic output.

neuroscience↗

bioRxiv2026

Temperature and frequency dependence of conduction along sympathetic preganglionic axons

Sympathetic preganglionic neurons (SPNs) distribute signals widely across paravertebral ganglia, yet the reliability of spike propagation along their predominantly unmyelinated axons remains poorly defined. We examined temperature- and activity-dependent modulation of SPN axonal conduction using an ex vivo adult mouse thoracic sympathetic chain preparation. Population compound action potentials (CAPs) were evoked by supramaximal stimulation of T10 ventral roots and recorded from branching axons in interganglionic compared to unbranching axons in the splanchnic nerve. At physiological temperature (36{degrees}C), scaled CAP magnitude was reduced by [~]50% relative to 22{degrees}C, with preferential loss of slower-conducting axonal components. These reductions are consistent with substantial temperature-dependent decreases in effective axonal recruitment, likely reflecting conduction failure in a large fraction of SPNs. Losses were more pronounced in interganglionic pathways, suggesting increased vulnerability in branching projections. To assess activity-dependent effects, stimuli were delivered at 1, 5, and 20 Hz with focus on 5 and 20 Hz stimulus trains (20s duration). The overall time-course of train-evoked depression was similar across temperatures; however, the underlying axonal populations differed. At 22{degrees}C, slower-conducting axons exhibited marked frequency-dependent depression, whereas at 36{degrees}C the remaining faster-conducting axons displayed facilitation, particularly at 20 Hz. Slower-conducting responses also showed post-train potentiation at physiological temperature. These findings indicate that SPN axonal conduction is not uniformly reliable and is strongly modulated by temperature and activation history. Preferential vulnerability of slow-conducting, likely small-diameter and branching axons identifies axonal conduction as a physiologically regulated site of gain control in sympathetic output.

neuroscience↗

bioRxiv2025

Plasticity in thoracic paravertebral sympathetic postganglionic neurons after high spinal cord transection

Various pre-sympathetic descending brain circuits recruit spinal cord preganglionic neurons to encode central sympathetic drive via their synaptic actions onto sympathetic postganglionic neurons (SPNs) - the final sympathetic output neurons. Thoracic paravertebral ganglia SPNs (tSPNs) provide distributed control over body tissue systems via functional subpopulations. High thoracic spinal cord injuries (SCIs) compromise descending excitatory drive to SPNs, causing dysautonomias including hypotension. In adult mice, we tested whether the SCI-induced chronic reduction in tSPN activity leads to homeostatic increases in their excitability. tSPN excitability spanned a >10 fold range in both sham and SCI populations, governed by a strong linear (ohmic) relationship between cell resistance and threshold depolarizing current (rheobase), with a clear trend towards increased excitability after SCI. Dendritic length was reduced, as was measured cell capacitance in Neuropeptide Y expressing (NPY+) tSPNs (putative vasoconstrictors), which represent >40% of tSPNs. NPY+ tSPNs also had changes in active membrane properties including an increased repetitive firing output gain ({uparrow}f-I slope), which modelling attributed to reduced delayed rectifier currents (IK). After SCI, spontaneous quantal excitatory synaptic frequency increased overall (226%) and in the NPY+ tSPN subpopulation (300%); their temporal summation recruited spiking in 10.5% of sham and 22.2% of SCI recordings. Computational modeling showed that spontaneous synaptic activity was particularly effective at recruiting spiking after SCI. Overall, tSPNs, including in vasoconstrictors, appear to undergo CNS-independent compensatory increases in excitability after SCI. The alterations further contribute to observed central and peripheral changes that limit hypoactivity and hypotension but exaggerate reflex responses. Significance StatementRecruited by preganglionic neurons located in thoracolumbar spinal cord, sympathetic postganglionic neurons (SPNs) represent the final step in sympathetic neural homeostatic control of target organs. The dramatic reductions or complete loss of brain pre-sympathetic drive in higher level spinal cord injuries (SCIs) contribute to emergent dysautonomias. Given the crucial role of SPNs in maintaining organismal homeostasis, we undertook comprehensive studies to test whether thoracic SPNs undergo homeostatic compensatory increases in their cellular excitability weeks after a high thoracic SCI. We observed changes consistent with increased cellular and synaptic excitability including in SPN vasoconstrictors, whose increased output gain, could mitigate hypotension but also strengthen hypertensive responses generated by afferent-driven exaggerated preganglionic drive (e.g. autonomic dysreflexia).

neuroscience↗

bioRxiv2024

Shift in cellular crosstalk reveals the immunosuppressive environment in cholangiocarcinoma patients.

Background and aimsCholangiocarcinoma (CCA) is a deadly disease, and this cancer entity is characterized by an abundant stroma. The tumor microenvironment (TME) plays an important role in aggressive behavior and poor response to therapeutics; however, underlying pathways are unknown. MethodsTo fill this gap, we used multiplexed immunohistochemistry, high-dimensional phenotyping, and transcriptomics to analyze human CCA samples and identify cell cluster crosstalk in patients with a poor prognosis. ResultsOur findings confirmed the presence of Tregs and the lack of effector memory cells in the tumor. New findings are the spatiality of the effector memory cells being more present in the peripheral tissue, for some reason these immune cells fail to reach the tumor niche. We revealed cancer crosstalk with macrophages and stromal cells and identified responsible genes in the poor prognosis group. Amongst the responsible ligand pairs are GAS6-AXL belonging to the TAM family. We then identified VCAN-TLR2 to be present and influencing the ECM in a way to supports immune exhaustion. Last, EGFR-TGF-{beta} is expressed in macrophages and this finding is important in Tregs induction and blocking cytotoxic T cell function. ConclusionsThe multiple mechanisms leading to the exclusion of relevant immune cells needed for an anti-cancer response and mechanisms leading to active immune suppression are part of complex cell-cell crosstalk. This study provides a deeper insight into the immune exhausted phenotype in CCA.

cancer biology↗

bioRxiv2023

Encompassing view of spatial and single-cell RNA-seq renews the role of the microvasculature in human atherosclerosis

Atherosclerosis is a pervasive contributor to cardiovascular diseases including ischemic heart disease and stroke. Despite the advance and success of effective lipid lowering-therapies and hypertensive agents, the residual risk of an atherosclerotic event remains high and improving disease understanding and development of novel therapeutic strategies has proven to be challenging. This is largely due to the complexity of atherosclerosis with a spatial interplay of multiple cell types within the vascular wall. Here, we generated an integrative high-resolution map of human atherosclerotic plaques by combining single-cell RNA-seq from multiple studies and novel spatial transcriptomics data from 12 human specimens to gain insights into disease mechanisms. Comparative analyses revealed cell-type and atherosclerosis-specific expression changes and associated alterations in cell-cell communication. We highlight the possible recruitment of lymphocytes via different endothelial cells of the vasa vasorum, the migration of vascular smooth muscle cells towards the lumen to become fibromyocytes, and cell-cell communication in the plaque, indicating an intricate cellular interplay within the adventitia and the subendothelial space in human atherosclerosis.

bioinformatics↗

bioRxiv2022

Cyclin B3 implements timely vertebrate oocyte arrest for fertilization

To ensure successful offspring ploidy, vertebrate oocytes must halt the cell cycle in meiosis II until sperm entry. Emi2 is essential to keep oocytes arrested until fertilization. Yet, how this arrest is implemented exclusively in meiosis II and not prematurely in meiosis I remained enigmatic. Using mouse and frog oocytes, we show here that cyclin B3, an understudied B- type cyclin, is essential to keep Emi2 levels low in meiosis I. Direct phosphorylation of Emi2 at an evolutionarily highly conserved site by Cdk1/cyclin B3 targets Emi2 for degradation. In contrast, Cdk1/cyclin B1 is inefficient in Emi2 phosphorylation providing a molecular explanation for the requirement of different B-type cyclins for oocyte maturation. Cyclin B3 degradation at exit from meiosis I enables Emi2 accumulation and thus, timely arrest in meiosis II. Our findings illuminate the evolutionarily conserved mechanisms controlling oocyte arrest for fertilization at the correct cell cycle stage, essential for embryo viability.

cell biology↗

bioRxiv2020

Spatial multi-omic map of human myocardial infarction

Myocardial infarction is a leading cause of mortality. While advances in the acute treatment have been made, the late-stage mortality is still high, driven by an incomplete understanding of cardiac remodeling processes1,2. Here we used single-cell gene expression, chromatin accessibility and spatial transcriptomic profiling of different physiological zones and timepoints of human myocardial infarction and human control myocardium to generate an integrative high-resolution map of cardiac remodeling. This approach allowed us to increase spatial resolution of cell-type composition and provide spatially resolved insights into the cardiac transcriptome and epigenome with identification of distinct cellular zones of injury, repair and remodeling. We here identified and validated mechanisms of fibroblast to myofibroblast differentiation that drive cardiac fibrosis. Our study provides an integrative molecular map of human myocardial infarction and represents a reference to advance mechanistic and therapeutic studies of cardiac disease.

systems biology↗

bioRxiv2020

Deep learning-based molecular morphometrics for kidney biopsies

Morphologic examination of tissue biopsies is essential for histopathological diagnosis. However, accurate and scalable cellular quantification in human samples remains challenging. Here, we present a deep learning-based approach for antigen-specific cellular morphometrics in human kidney biopsies, which combines indirect immunofluorescence imaging with U-Net-based architectures for image-to-image translation and dual segmentation tasks, achieving human-level accuracy. In the kidney, podocyte loss represents a hallmark of glomerular injury and can be estimated in diagnostic biopsies. Thus, we profiled over 27,000 podocytes from 110 human samples, including patients with anti-neutrophil cytoplasmic antibody-associated glomerulonephritis (ANCA-GN), an immune-mediated disease with aggressive glomerular damage and irreversible loss of kidney function. Previously unknown morphometric signatures of podocyte depletion were identified in patients with ANCA-GN, which allowed patient classification and showed potential for risk stratification in combination with routine clinical tools. Together, our approach enables robust and scalable molecular morphometric analysis of human tissues, yielding deeper biological insights into the human kidney pathophysiology. SummaryDeep learning enables robust and scalable molecular morphometric analysis of human tissues, yielding deeper biological insights into the human kidney pathophysiology.

pathology↗